Contacts of the helix formed by residues 425 - 435 (chain A) in PDB entry 2G4C
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 LEU 425 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ARG* 4.9 15.5 - - - +
423A SER 3.6 1.4 + - - -
424A SER* 1.3 81.5 + - - +
426A GLU* 1.3 73.1 + - + +
427A GLN 3.2 0.7 - - - -
428A LEU* 3.5 16.4 - - + -
429A TYR* 2.8 65.9 + - + +
442A LEU* 4.0 26.7 - - + -
463A LYS* 5.4 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 426 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A SER* 2.8 16.8 + - - +
425A LEU* 1.3 87.1 + - + +
427A GLN* 1.3 59.3 + - + +
428A LEU 3.0 4.5 - - - -
429A TYR* 4.3 5.2 - - - +
430A SER* 3.0 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 427 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A MET* 5.7 3.0 - - - -
423A SER* 3.1 27.1 + - - +
424A SER* 3.3 19.8 + - - +
425A LEU 3.2 0.2 - - - -
426A GLU* 1.3 80.7 - - + +
428A LEU* 1.3 56.5 + - - +
430A SER* 5.3 1.1 - - - -
431A LYS* 2.8 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 428 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ASP* 3.2 27.8 - - + +
422A GLN* 3.9 9.4 - - - +
423A SER* 3.6 25.6 - - - +
425A LEU* 3.5 24.4 - - + +
426A GLU 3.0 0.4 - - - -
427A GLN* 1.3 81.9 - - - +
429A TYR* 1.3 66.4 + - + +
430A SER 3.8 0.2 - - - -
431A LYS* 4.2 10.1 - - + +
432A TYR* 3.1 63.0 - - + +
442A LEU* 6.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 429 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU* 2.8 50.4 + - + +
426A GLU* 3.5 4.7 + - - +
428A LEU* 1.3 88.1 - - + +
430A SER* 1.3 66.7 + - - +
431A LYS 3.1 1.1 - - - -
432A TYR* 3.3 4.8 + - - +
433A ASP* 2.9 25.8 + - - +
440A THR* 3.6 39.0 + - + -
442A LEU* 4.2 14.5 - - + +
454A HIS* 5.1 7.6 + - - -
456A ARG* 3.2 50.8 + - + +
463A LYS* 4.4 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ARG* 5.2 5.0 - - - +
370A LYS* 4.4 21.5 + - - +
426A GLU 3.0 18.9 + - - -
427A GLN* 5.3 1.3 - - - -
429A TYR* 1.3 78.4 - - - +
431A LYS* 1.3 60.0 + - - +
433A ASP* 2.9 31.8 - - - +
434A GLU* 3.3 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 3.8 36.8 - - - +
423A SER* 6.1 2.0 - - - -
427A GLN* 2.8 35.2 + - - +
428A LEU* 4.1 10.2 - - + +
429A TYR 4.1 0.4 - - - +
430A SER* 1.3 74.1 - - - +
432A TYR* 1.3 78.8 + - + +
433A ASP 2.9 4.0 - - - -
434A GLU* 2.7 41.8 + - - +
435A MET* 3.1 13.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ALA* 3.2 26.4 - - + +
386A ASP* 3.1 20.0 + - - -
414A TRP* 3.7 24.7 + + - -
416A GLY* 4.3 1.4 - - - -
428A LEU* 3.1 40.6 + - + +
429A TYR* 3.3 8.1 + + - +
431A LYS* 1.3 96.6 - - + +
433A ASP* 1.3 59.4 + - - +
435A MET* 3.3 14.2 + - - -
436A SER 3.0 3.5 + - - -
437A ILE* 2.9 47.7 + - + +
440A THR* 3.4 36.8 - - + +
456A ARG* 6.1 0.4 - - - +
458A ARG* 5.6 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A ARG* 2.9 32.4 + - - +
370A LYS 5.9 0.2 - - - +
371A VAL* 3.0 33.4 - - + +
372A LEU 2.7 28.1 + - - +
429A TYR 2.9 19.9 + - - +
430A SER* 2.9 21.1 + - - +
431A LYS 2.9 0.4 - - - -
432A TYR* 1.3 76.8 - - - +
434A GLU* 1.3 55.7 + - - +
436A SER* 3.2 7.8 + - - -
456A ARG* 3.3 17.4 + - - -
458A ARG* 3.5 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ILE* 3.5 30.4 - - + +
75A ARG* 5.3 4.9 - - - +
76A ARG* 2.8 38.8 + - + +
78A PHE* 3.6 3.5 - - - -
370A LYS* 3.3 44.3 - - + +
371A VAL* 4.5 0.2 - - - +
372A LEU* 2.9 31.1 - - - +
430A SER* 3.8 6.5 - - - +
431A LYS* 2.7 15.6 + - - +
433A ASP* 1.3 73.2 - - - +
435A MET* 1.3 52.0 - - - +
436A SER 2.6 15.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ARG* 3.9 32.3 - - + +
78A PHE* 3.8 11.3 - - - -
102A LEU* 4.4 12.5 - - + +
380A PRO* 3.7 18.0 - - - +
381A ILE* 4.1 18.7 - - + +
414A TRP* 3.6 41.3 - - + -
431A LYS* 3.1 14.4 + - + +
432A TYR* 3.3 32.7 + - - +
434A GLU* 1.3 76.7 - - - +
436A SER* 1.3 68.3 + - - +
437A ILE* 3.2 12.3 + - + +
199C LEU* 4.8 10.1 - - + -
----------------------------------------------------------
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