Contacts of the helix formed by residues 366 - 384 (chain I) in PDB entry 1F1H
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 ASN 366 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I THR* 4.1 0.2 - - - +
23I ASP 3.3 15.6 + - - -
24I THR 2.8 25.4 + - - +
25I LYS 4.0 5.7 + - - +
26I GLY* 3.4 19.6 - - - -
104I PRO* 3.8 7.9 - - - +
311I LEU 4.0 4.9 + - - +
314I PRO* 4.8 1.6 - - - +
364I ALA 3.6 3.0 + - - -
365I ALA* 1.3 68.5 - - - +
367I PRO* 1.3 71.6 - - - +
368I TYR* 3.0 27.7 + - - +
369I LEU* 3.6 26.8 - - + +
370I CYS* 2.8 24.1 + - - +
442I TYR* 5.6 2.9 + - + +
446I ARG* 5.2 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 367 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I GLY 4.7 2.0 - - - +
232I ALA* 3.7 33.9 - - + +
235I ILE* 3.8 22.7 - - + -
236I GLN* 3.7 26.7 - - - +
239I LYS* 4.5 3.1 - - - +
268I MET* 5.2 3.4 - - + -
365I ALA 3.0 11.1 - - - +
366I ASN* 1.3 84.9 - - - +
368I TYR* 1.3 61.2 + - + +
370I CYS* 4.5 1.6 - - + -
371I PHE* 2.9 50.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 368 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I THR* 3.4 28.2 + - + -
88I ARG* 3.8 14.0 + - - -
104I PRO* 3.3 33.2 - - + +
105I ARG* 3.9 23.8 + - + -
108I ALA* 4.0 22.3 - - + +
229I THR* 4.0 5.6 - - + -
232I ALA* 3.3 26.5 + - + -
233I ASP* 2.6 35.7 + - - -
236I GLN* 4.1 11.0 - - + +
366I ASN* 3.0 14.6 + - - +
367I PRO* 1.3 78.0 - - + +
369I LEU* 1.3 58.5 + - - +
371I PHE* 3.9 1.5 - - - +
372I ALA* 2.9 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 369 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I THR* 3.8 24.9 - - + +
104I PRO* 3.8 28.3 - - + -
107I ILE* 3.8 24.0 - - + -
311I LEU* 3.5 20.6 - - + +
366I ASN* 3.3 19.5 + - + +
368I TYR* 1.3 80.3 - - - +
370I CYS* 1.3 57.7 + - - +
372I ALA* 3.9 4.6 - - - +
373I ALA* 3.0 30.8 + - - +
434I PHE* 4.2 13.3 - - + -
442I TYR* 3.8 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 370 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268I MET* 4.9 2.0 - - - -
270I CYS* 5.0 0.4 - - - -
308I ILE* 4.9 0.9 - - - +
311I LEU* 3.7 22.6 - - - +
312I ALA* 3.5 31.4 - - - -
361I PRO* 4.3 8.3 - - - -
365I ALA* 3.9 10.1 - - + -
366I ASN 2.8 23.1 + - - +
367I PRO* 4.0 2.7 - - + +
369I LEU* 1.3 73.8 - - - +
371I PHE* 1.3 71.9 + - + +
373I ALA* 3.3 3.5 + - - +
374I LEU* 3.0 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 371 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I PHE* 3.3 36.8 - + + -
128I PRO* 3.4 32.3 - - + -
228I MET* 3.6 36.5 - - + +
231I LYS* 4.1 6.1 - - + -
232I ALA* 3.8 28.9 - - + -
235I ILE* 4.2 3.1 - - + -
268I MET* 4.3 13.5 - - + -
270I CYS* 4.0 21.5 - - - -
367I PRO* 2.9 31.6 + - + +
368I TYR* 3.9 2.2 - - - +
370I CYS* 1.3 82.7 - - - +
372I ALA* 1.3 62.0 + - - +
374I LEU* 3.2 2.2 + - - -
375I LEU 3.1 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 372 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I ILE* 4.5 3.8 - - + -
108I ALA* 4.4 7.9 - - - -
111I ALA* 4.2 17.7 - - + -
228I MET* 3.7 16.5 - - + -
368I TYR 2.9 18.6 + - - +
369I LEU 3.9 3.4 - - - +
371I PHE* 1.3 76.1 - - - +
373I ALA* 1.3 58.6 + - - +
375I LEU* 3.1 4.6 + - - +
376I MET* 2.9 35.2 + - - +
434I PHE* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 373 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I ILE* 4.1 15.1 - - + +
311I LEU* 3.7 27.4 - - + -
369I LEU 3.0 19.9 + - - +
370I CYS 3.6 4.3 - - - +
371I PHE 3.3 0.2 - - - -
372I ALA* 1.3 75.8 - - - +
374I LEU* 1.3 62.5 + - - +
377I ALA* 3.2 24.4 + - - +
427I PHE* 3.7 5.0 - - - -
428I LEU* 3.9 20.0 - - + -
434I PHE* 4.6 2.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 374 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I PHE* 4.1 12.1 - - + -
270I CYS* 4.5 10.5 - - + -
272I MET* 3.9 24.5 - - + -
297I TYR* 3.8 5.7 + - - -
301I VAL* 4.2 22.4 - - + +
308I ILE* 3.5 31.9 - - + -
358I VAL* 4.5 11.4 - - + -
360I PHE* 4.7 1.6 - - + -
361I PRO* 4.5 11.7 - - + -
370I CYS* 3.0 38.6 + - - +
371I PHE 3.4 7.6 - - - +
373I ALA* 1.3 78.7 - - - +
375I LEU* 1.3 61.2 + - - +
377I ALA* 3.3 3.5 + - - +
378I GLY* 3.0 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 375 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I ALA* 3.7 32.8 - - + +
115I LEU* 4.4 5.8 - - + -
124I VAL* 3.7 40.2 - - + -
126I PHE* 4.6 0.9 - - + -
228I MET* 4.2 11.4 - - + -
274I LEU* 4.4 3.8 - - + -
297I TYR* 3.3 20.1 + - + +
371I PHE 3.1 8.9 + - - +
372I ALA 3.3 8.7 - - - +
374I LEU* 1.3 75.9 - - - +
376I MET* 1.3 55.6 + - - +
378I GLY* 2.8 4.7 + - - -
379I LEU* 2.8 59.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 376 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111I ALA* 4.1 15.9 - - + +
114I TYR* 4.1 21.1 - - + -
372I ALA 2.9 26.3 + - - +
375I LEU* 1.3 74.7 - - - +
377I ALA* 1.3 56.5 + - - +
379I LEU* 3.6 9.1 + - - +
380I ASP* 3.1 26.9 + - - +
427I PHE* 3.5 29.7 - - - +
428I LEU* 3.7 24.9 - - + +
430I ALA* 3.2 35.2 - - + +
433I VAL* 3.5 25.4 - - + -
434I PHE* 4.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 377 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300I GLY* 3.2 27.4 - - - +
301I VAL* 4.2 0.9 - - - -
304I HIS* 4.0 4.2 - - + -
308I ILE* 3.6 20.4 - - + -
373I ALA 3.2 19.0 + - - +
374I LEU 3.5 4.5 - - - +
375I LEU 3.1 0.4 - - - -
376I MET* 1.3 73.8 - - - +
378I GLY* 1.3 66.4 + - - +
380I ASP* 3.3 4.0 + - - +
381I GLY 3.1 16.1 + - - -
427I PHE* 3.5 22.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 378 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297I TYR* 3.5 52.5 - - - -
301I VAL* 4.5 0.8 - - - +
374I LEU 3.0 7.6 + - - -
375I LEU 2.8 6.9 + - - -
377I ALA* 1.3 78.6 - - - +
379I LEU* 1.3 54.6 + - - +
381I GLY* 3.0 15.4 + - - -
382I ILE* 3.0 13.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 379 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I TYR* 3.7 38.1 - - + -
115I LEU* 3.4 38.1 - - + -
118I THR* 5.0 2.9 - - - +
120I ILE* 4.2 17.7 - - + -
274I LEU* 4.3 14.6 - - + -
375I LEU* 2.8 39.0 + - + +
376I MET* 3.9 8.5 - - - +
378I GLY* 1.3 72.5 - - - +
380I ASP* 1.3 60.8 + - - +
381I GLY 3.0 2.2 - - - -
382I ILE* 3.2 6.0 + - + +
383I LYS* 2.8 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 380 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303I LYS* 4.4 5.2 + - - -
304I HIS* 2.9 29.0 + - - +
376I MET 3.1 19.6 + - - +
377I ALA 3.6 5.8 - - - +
378I GLY 3.3 0.2 - - - -
379I LEU* 1.3 76.9 - - - +
381I GLY* 1.3 60.7 + - - +
382I ILE 3.3 0.2 - - - -
383I LYS* 4.0 22.6 + - - +
384I ASN* 3.4 32.4 + - - +
386I ILE* 3.6 10.0 - - - +
427I PHE* 4.0 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 381 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I TYR* 3.1 27.3 - - - +
300I GLY* 3.7 5.8 - - - -
377I ALA 3.1 5.5 + - - -
378I GLY 3.0 6.0 + - - -
380I ASP* 1.3 79.3 - - - +
382I ILE* 1.3 56.8 + - - +
385I LYS 3.0 6.4 + - - -
386I ILE* 2.8 42.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 382 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I ILE* 3.5 37.9 - - + -
274I LEU* 4.1 8.3 - - + -
293I GLN* 3.5 50.3 - - + +
296I TYR* 3.7 11.7 - - + -
297I TYR* 4.0 17.3 - - + +
378I GLY 3.0 14.7 + - - +
379I LEU* 3.2 9.6 + - + +
381I GLY* 1.3 73.6 - - - +
383I LYS* 1.3 69.6 + - - +
384I ASN 3.0 3.0 + - - -
385I LYS* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 383 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I TYR* 3.3 28.5 + - + +
118I THR* 5.0 8.3 - - + -
120I ILE* 4.2 16.6 - - + -
379I LEU* 2.8 21.9 + - + +
380I ASP* 4.0 26.6 + - - +
382I ILE* 1.3 75.9 - - - +
384I ASN* 1.3 72.3 + - - +
385I LYS* 3.9 7.6 + - - +
430I ALA* 4.8 7.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 384 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303I LYS* 5.6 3.7 + - - +
380I ASP* 3.4 29.1 + - - +
382I ILE 3.0 1.0 - - - -
383I LYS* 1.3 103.8 + - - +
385I LYS* 1.3 72.1 + - - +
386I ILE* 2.9 16.6 + - + +
----------------------------------------------------------
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