Contacts of the helix formed by residues 351 - 372 (chain I) in PDB entry 5A31
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 351 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I PRO* 3.6 28.1 + - + +
144I THR 3.7 15.3 - - - -
145I LEU* 3.3 18.4 - - + +
146I PRO* 4.3 6.1 - - + +
264I TYR* 2.8 31.3 + - + +
268I SER* 4.2 5.2 - - - +
346I LYS 4.3 0.7 - - - -
347I LEU* 3.2 37.4 + - + +
350I SER* 1.3 97.2 - - - +
352I LEU* 1.3 62.5 + - - +
353I GLN 3.3 0.7 - - - -
354I SER* 3.0 4.6 + - - -
355I GLY* 2.8 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 352 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I ILE* 3.5 35.9 - - + +
268I SER* 4.2 9.7 - - - -
269I LEU* 3.6 28.9 - - + -
272I MET* 4.1 17.9 - - + -
347I LEU 3.5 2.4 + - - -
348I VAL* 3.5 20.4 - - + +
351I HIS* 1.3 77.9 - - - +
353I GLN* 1.3 57.9 + - - +
355I GLY* 3.9 0.8 - - - -
356I SER* 2.6 35.0 + - - -
396I PHE* 3.6 14.1 - - + -
400I ALA* 3.5 32.5 - - + -
522I LEU* 4.6 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348I VAL* 3.0 14.1 + - - +
349I ILE* 3.2 22.2 - - + +
351I HIS 3.3 0.2 - - - -
352I LEU* 1.3 75.4 - - - +
354I SER* 1.3 52.0 + - - +
356I SER* 3.3 3.2 + - - -
357I GLU* 2.8 60.8 + - + +
397I ILE* 3.9 10.6 + - + +
400I ALA* 3.7 28.5 - - - +
401I ASN* 4.1 4.7 + - - +
404I LEU* 3.4 26.0 - - - +
444O MET* 3.1 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 354 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142I LEU* 3.7 21.3 - - - +
143I PRO* 5.0 2.6 - - - +
264I TYR* 4.2 2.6 + - - -
349I ILE 3.9 2.6 + - - -
350I SER 3.4 20.1 + - - -
351I HIS* 3.0 10.2 + - - -
353I GLN* 1.3 76.6 - - - +
355I GLY* 1.3 62.1 + - - +
357I GLU* 3.9 4.9 - - - +
358I SER* 3.0 32.6 + - - -
403O LYS* 3.6 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 355 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142I LEU* 5.0 1.3 - - - -
261I LEU* 4.4 7.9 - - - +
264I TYR* 4.2 18.2 - - - -
265I ILE* 4.8 10.8 - - - -
351I HIS 2.8 13.5 + - - -
352I LEU* 3.9 1.6 - - - -
354I SER* 1.3 79.2 + - - +
356I SER* 1.3 56.8 + - - +
358I SER* 3.0 7.1 + - - -
359I LEU* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 356 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I ILE* 3.7 7.1 - - - +
352I LEU* 2.6 24.0 + - - +
353I GLN* 3.5 5.1 + - - -
355I GLY* 1.3 73.6 - - - +
357I GLU* 1.3 66.0 + - - +
359I LEU* 3.3 9.2 - - - +
360I LEU* 3.0 23.4 + - - +
393I VAL* 4.1 1.6 - - - +
396I PHE* 3.3 28.1 - - - -
397I ILE* 3.7 35.3 - - - +
400I ALA* 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 357 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353I GLN* 2.8 43.9 + - + +
354I SER* 3.9 3.1 - - - +
356I SER* 1.3 74.5 - - - +
358I SER* 1.3 63.0 + - - +
360I LEU* 3.2 5.4 + - - +
361I TYR* 3.1 15.9 + - - +
397I ILE* 4.6 4.5 - - + -
399O MET* 5.1 9.0 - - - +
403O LYS* 4.2 20.1 - - - +
425O LYS* 4.1 20.6 + - - -
429O TRP* 6.2 2.0 - - + -
437O MET* 3.4 22.3 - - + +
440O GLN* 4.4 21.3 - - - +
441O GLN* 4.2 14.7 + - - +
444O MET* 4.6 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 358 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I GLU* 4.8 8.3 - - - -
142I LEU* 5.1 6.4 - - - +
257I HIS* 6.0 0.7 - - - -
261I LEU* 3.5 22.6 - - - +
354I SER 3.0 14.8 + - - -
355I GLY* 3.0 10.9 + - - -
357I GLU* 1.3 73.7 - - - +
359I LEU* 1.3 69.0 + - - +
361I TYR* 2.9 22.2 + - - +
362I HIS* 3.0 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258I ILE* 4.1 22.0 - - + -
261I LEU* 3.5 25.6 - - + -
262I LEU* 3.9 24.2 - - + -
265I ILE* 4.1 21.5 - - + -
355I GLY 2.9 13.4 + - - +
356I SER* 3.3 5.6 - - - +
358I SER* 1.3 82.6 + - - +
360I LEU* 1.3 61.8 + - - +
362I HIS* 3.4 2.4 + - - +
363I LEU* 3.0 47.6 + - + +
393I VAL* 3.8 26.0 - - + -
529I MET* 4.2 1.8 - - - -
533I ILE* 4.7 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 360 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I SER 3.0 7.4 + - - +
357I GLU 3.3 10.3 - - - +
359I LEU* 1.3 77.0 - - - +
361I TYR* 1.3 61.8 + - - +
363I LEU* 3.2 3.2 + - + +
364I SER* 2.8 33.8 + - - +
390I ILE* 3.7 24.5 - - + +
393I VAL* 4.0 15.9 - - + -
394I GLY* 4.7 0.9 - - - -
397I ILE* 3.5 22.4 - - + -
514I PHE* 4.2 8.3 - - + -
436O THR* 3.5 28.5 - - + +
437O MET* 4.0 10.3 - - - -
440O GLN* 3.6 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 361 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I GLU* 3.4 31.7 + - - -
357I GLU 3.1 9.4 + - - +
358I SER* 2.9 18.7 + - - +
360I LEU* 1.3 76.9 - - - +
362I HIS* 1.3 65.7 + + + +
364I SER* 3.1 7.0 + - - -
365I GLU* 3.1 46.2 + - + +
395O ALA* 4.6 8.1 - - + +
396O ASN* 4.4 7.0 - - - -
429O TRP* 4.0 25.1 - + - -
434O ARG* 3.3 53.0 + - + -
437O MET* 3.8 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 362 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I GLU* 3.2 36.1 + - + -
135I SER* 5.5 2.0 - - - -
254I LYS* 3.9 22.1 + - + +
257I HIS* 3.1 47.7 + + - +
258I ILE* 3.9 20.1 - - + +
261I LEU* 4.1 4.7 - - + -
358I SER* 3.0 31.0 + - - -
359I LEU 3.9 5.8 - - - +
360I LEU 3.2 0.2 - - - -
361I TYR* 1.3 78.9 - - + +
363I LEU* 1.3 57.2 + - - +
365I GLU* 3.3 19.9 + - - +
366I LEU* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 363 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258I ILE* 3.8 36.1 - - + -
359I LEU* 3.0 23.9 + - + +
360I LEU* 3.8 4.5 - - - +
362I HIS* 1.3 72.8 - - - +
364I SER* 1.3 60.1 + - - +
366I LEU* 3.6 12.2 - - + +
367I LYS* 2.9 29.1 + - - +
386I ILE* 3.7 9.5 - - + +
389I ALA* 4.2 18.4 - - + +
390I ILE* 3.9 22.8 - - + +
393I VAL* 3.6 34.1 - - + -
533I ILE* 4.7 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 364 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360I LEU* 2.8 25.4 + - - +
361I TYR* 3.3 12.6 - - - -
363I LEU* 1.3 75.4 - - - +
365I GLU* 1.3 63.6 + - - +
367I LYS* 3.2 21.8 + - - +
368I GLY 3.4 4.0 + - - -
390I ILE* 4.4 10.9 - - - +
434O ARG* 5.9 3.6 - - - -
436O THR* 3.4 31.5 - - - +
437O MET* 4.7 4.7 + - - +
653O ALA* 3.8 10.3 - - - +
654O ASP* 4.5 11.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 365 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I GLU* 5.8 1.8 - - - +
135I SER* 5.4 7.8 - - - -
254I LYS* 4.0 23.1 - - - +
361I TYR* 3.1 48.4 + - + +
362I HIS* 3.3 30.3 + - - +
364I SER* 1.3 78.3 - - - +
366I LEU* 1.3 61.4 + - - +
368I GLY* 3.0 20.8 + - - -
369I MET* 3.5 4.6 + - - +
434O ARG* 4.1 13.7 + - - +
649O GLU* 3.9 16.2 - - - +
653O ALA* 4.8 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 366 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I MET* 4.8 1.1 - - + -
254I LYS* 4.6 16.4 - - + +
255I PHE* 3.9 36.1 - - + -
258I ILE* 4.0 14.8 - - + -
362I HIS 2.8 20.6 + - - +
363I LEU* 3.6 13.2 - - + +
365I GLU* 1.3 70.7 - - - +
367I LYS* 1.3 65.2 + - - +
369I MET* 3.0 33.3 + - - +
370I ALA* 3.1 11.8 + - - +
381I LEU* 4.1 19.7 - - + +
386I ILE* 3.6 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 367 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363I LEU 2.9 16.2 + - - +
364I SER* 3.2 14.3 + - - +
366I LEU* 1.3 72.4 - - - +
368I GLY* 1.3 55.8 + - - +
370I ALA* 3.8 5.1 - - + -
371I SER* 2.9 31.4 + - - +
383I ALA* 5.5 3.4 - - - +
386I ILE* 3.9 16.9 - - + +
387I GLU* 4.5 25.5 + - + +
390I ILE* 3.6 25.0 - - + +
512I LEU* 6.3 0.8 - - - +
436O THR* 3.5 24.0 + - - +
652O LEU 5.7 0.4 - - - +
653O ALA* 3.7 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364I SER 3.4 4.4 + - - -
365I GLU 3.0 11.6 + - - -
367I LYS* 1.3 81.0 - - - +
369I MET* 1.3 63.2 + - - +
371I SER* 3.2 14.7 + - - -
372I TRP* 3.3 8.0 + - - +
649O GLU* 3.6 25.9 - - - +
652O LEU* 4.3 3.6 - - - +
653O ALA* 3.7 16.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 369 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250I ARG* 3.6 29.8 - - + +
251I MET* 4.3 16.4 - - - +
254I LYS* 3.5 29.6 - - + +
365I GLU 3.5 2.6 + - - +
366I LEU* 3.0 31.0 + - - +
368I GLY* 1.3 72.8 - - - +
370I ALA* 1.3 63.0 + - - +
372I TRP* 3.0 15.6 + - - +
376I TYR* 3.1 51.6 - - + +
381I LEU* 4.3 5.4 - - + -
649O GLU* 3.1 33.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 370 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366I LEU 3.1 7.2 + - - +
367I LYS* 3.9 6.1 - - + +
369I MET* 1.3 74.3 - - - +
371I SER* 1.3 67.0 + - - +
372I TRP 3.2 0.5 + - - -
373I LYS* 4.0 12.5 + - - +
376I TYR* 4.8 2.3 - - - +
377I GLU 5.6 1.0 + - - -
381I LEU* 4.3 18.2 - - + +
382I ASP 4.1 0.9 - - - +
383I ALA* 3.8 35.0 + - - +
386I ILE* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 371 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367I LYS* 2.9 16.5 + - - +
368I GLY 3.2 11.7 - - - -
370I ALA* 1.3 76.4 - - - +
372I TRP* 1.3 52.4 + - - +
373I LYS* 2.8 21.3 + - - +
383I ALA* 4.8 6.5 - - - +
652O LEU* 3.7 29.8 + - - +
660O LYS* 4.8 0.2 - - - +
696O GLU* 3.6 14.6 - - - +
700O TYR* 3.2 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 372 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368I GLY 3.3 4.2 + - - +
369I MET* 3.0 16.3 + - - +
370I ALA 4.0 0.4 - - - -
371I SER* 1.3 73.7 - - - +
373I LYS* 1.3 65.3 + - - +
374I GLN* 3.4 24.7 - - + -
375I LYS* 3.3 37.4 + - + +
376I TYR* 3.2 25.9 + + + +
645O HIS* 4.0 24.2 + + - -
648O ILE* 3.3 31.6 - - + +
649O GLU* 5.0 9.4 - - + -
652O LEU* 3.8 17.3 - - + -
664O MET* 3.4 32.5 - - + -
667O VAL* 3.6 18.8 - - + -
671O GLN* 4.3 1.1 - - - -
693O ASN* 3.4 27.1 - - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il