Contacts of the helix formed by residues 365 - 379 (chain I) in PDB entry 3V3K
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 ASP 365 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364I GLU* 1.3 73.7 - - - +
366I LEU* 1.3 59.5 + - - +
367I GLN* 3.5 25.6 + - - +
368I SER* 2.7 26.4 + - - -
369I LEU* 2.9 32.0 + - - +
397I LYS* 4.2 29.4 + - + +
398I LEU 3.4 17.2 + - - +
399I PHE* 3.5 27.5 - - + +
400I PHE* 5.5 0.2 - - - -
371K LEU* 5.5 1.7 - - - +
397K LYS* 5.0 0.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
279I LEU* 3.6 21.3 - - + -
281I PHE* 4.1 18.6 - - + -
328I PHE* 3.7 31.2 - - + -
357I PHE* 4.2 9.2 - - + -
365I ASP* 1.3 72.1 - - - +
367I GLN* 1.3 62.1 + - + +
369I LEU* 3.4 4.5 + - - +
370I LEU* 3.1 26.4 + - + +
394I LEU* 4.6 3.4 - - + -
398I LEU* 2.9 50.5 + - + +
400I PHE* 3.8 26.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 367 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328I PHE* 4.2 8.0 - - + -
365I ASP* 3.3 13.4 + - - +
366I LEU* 1.3 74.7 - - - +
368I SER* 1.3 65.0 + - - +
370I LEU* 3.5 3.5 + - - +
371I LEU* 3.1 32.4 + - + +
389I CYS* 3.4 27.8 - - - -
392I ASN* 2.7 39.3 + - - +
394I LEU* 5.6 2.7 - - + -
367K GLN* 4.0 24.7 - - + +
371K LEU* 5.4 7.2 - - + -
389K CYS* 5.9 0.9 - - - +
392K ASN* 3.7 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 368 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364I GLU* 3.8 25.7 - - - +
365I ASP* 2.7 30.6 + - - -
367I GLN* 1.3 78.5 - - - +
369I LEU* 1.3 62.6 + - - +
371I LEU* 3.6 12.7 - - - +
372I ARG* 3.6 21.8 + - - +
397K LYS* 3.1 32.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
356I ILE* 3.7 23.8 - - + +
357I PHE* 3.7 37.9 - - + -
360I TRP* 3.7 38.6 - - + +
361I ALA* 3.9 15.0 - - - +
364I GLU* 4.2 10.8 - - + +
365I ASP 2.9 23.7 + - - +
366I LEU* 3.6 9.2 - - - +
367I GLN 3.3 0.2 - - - -
368I SER* 1.3 76.7 - - - +
370I LEU* 1.3 58.3 + - - +
372I ARG* 3.3 7.8 + - - +
373I VAL* 3.1 28.5 + - - +
400I PHE* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 370 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281I PHE* 4.5 7.2 - - + -
328I PHE* 3.4 36.6 - - + -
330I SER* 3.2 28.7 - - - +
349I TYR* 4.3 9.2 - - + +
353I LEU* 4.4 12.6 - - + -
357I PHE* 4.6 6.1 - - + -
366I LEU* 3.1 18.1 + - + +
367I GLN* 4.2 4.5 - - - +
368I SER 3.5 0.2 - - - -
369I LEU* 1.3 76.1 - - - +
371I LEU* 1.3 56.1 + - - +
373I VAL* 3.6 20.1 - - + +
374I ALA* 2.8 35.0 + - - +
387I PRO* 5.8 0.3 - - - +
388I GLY* 4.8 3.3 - - - +
389I CYS* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 371 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367I GLN* 3.1 24.3 + - - +
368I SER* 3.6 15.7 - - - +
369I LEU 3.3 0.4 - - - -
370I LEU* 1.3 76.3 - - - +
372I ARG* 1.3 57.4 + - + +
374I ALA* 3.5 2.1 + - - +
375I ASN* 3.0 22.0 + - - +
367K GLN* 3.2 33.4 - - + +
392K ASN* 4.5 4.7 - - - +
394K LEU* 3.3 28.9 - - + +
395K ARG 3.0 18.5 - - - +
396K LYS* 3.6 19.1 - - - +
397K LYS* 3.6 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 372 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I ILE* 3.3 19.2 - - + +
360I TRP* 3.5 51.9 - - - +
364I GLU* 2.8 43.2 + - - -
368I SER 3.6 7.9 + - - +
369I LEU* 3.3 8.1 + - - +
371I LEU* 1.3 75.4 - - + +
373I VAL* 1.3 55.3 + - - +
375I ASN* 3.2 7.2 + - - +
376I ALA* 2.8 36.7 + - - +
151K LEU* 3.3 49.6 - - + +
395K ARG 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 373 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349I TYR* 3.9 40.4 - - + +
352I THR* 3.8 11.6 - - + +
353I LEU* 3.9 20.0 - - + +
356I ILE* 3.4 22.2 - - + -
357I PHE* 5.2 1.6 - - + -
369I LEU 3.1 17.1 + - - +
370I LEU* 3.4 22.2 + - + +
372I ARG* 1.3 75.2 - - - +
374I ALA* 1.3 61.3 + - - +
377I VAL* 3.1 34.5 + - + +
387I PRO* 4.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 374 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370I LEU 2.8 21.3 + - - +
371I LEU 3.7 4.9 - - - +
373I VAL* 1.3 74.7 - - - +
375I ASN* 1.3 55.8 + - - +
378I SER* 3.1 30.1 + - - -
386I MET* 4.2 5.8 - - + +
387I PRO* 3.4 40.2 - - + +
388I GLY* 5.3 1.6 - - - -
394K LEU 3.8 18.6 - - - +
395K ARG* 4.2 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 375 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371I LEU 3.0 18.5 + - - +
372I ARG* 3.7 7.0 - - - +
374I ALA* 1.3 74.4 - - - +
376I ALA* 1.3 62.0 + - - +
378I SER* 2.6 21.5 + - - -
379I VAL* 3.6 15.0 - - - +
150K ASP* 4.1 26.1 + - - -
151K LEU* 6.2 0.8 - - - +
395K ARG* 3.5 43.4 + - - +
396K LYS* 4.4 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 376 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352I THR* 3.3 30.3 - - + +
356I ILE* 4.3 3.6 - - + -
372I ARG 2.8 15.9 + - - +
375I ASN* 1.3 73.6 - - - +
377I VAL* 1.3 61.0 + - - +
379I VAL* 3.1 27.6 - - - +
380I LYS* 3.7 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 377 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348I TRP* 3.7 23.7 - - + +
349I TYR* 4.3 4.9 - - - +
352I THR* 3.6 22.9 - - - +
373I VAL* 3.1 20.0 + - + +
376I ALA* 1.3 74.7 - - - +
378I SER* 1.3 64.9 + - - +
380I LYS* 3.3 22.9 + - + +
385I GLN* 3.5 44.8 + - + +
387I PRO* 3.6 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 378 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374I ALA 3.1 15.6 + - - -
375I ASN* 2.6 23.7 + - - -
377I VAL* 1.3 77.0 - - - +
379I VAL* 1.3 59.6 + - - +
380I LYS 3.4 0.2 - - - -
384I LYS* 3.1 24.9 + - - -
385I GLN 3.6 10.3 + - - -
386I MET* 4.2 4.3 - - - -
320K SER 3.6 2.3 - - - +
321K LEU* 4.2 3.4 - - - +
322K PRO* 3.5 23.3 - - - +
395K ARG* 3.2 30.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 379 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375I ASN* 3.6 17.7 - - - +
376I ALA* 3.1 20.9 - - - +
378I SER* 1.3 79.2 - - - +
380I LYS* 1.3 67.3 + - + +
381I GLY 3.7 2.1 + - - +
384I LYS* 3.2 11.1 + - - +
320K SER 4.3 5.9 + - - +
321K LEU* 5.1 8.1 - - + -
----------------------------------------------------------
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