Contacts of the helix formed by residues 35 - 52 (chain A) in PDB entry 1GQA
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 35 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.5 11.5 - - + +
32A MET* 6.0 0.9 - - + -
33A PRO* 3.4 5.3 + - + +
34A TYR* 1.3 78.7 - - - +
36A ALA* 1.3 58.3 + - - +
37A ALA* 3.2 19.1 + - - +
38A ALA* 3.3 24.2 + - + +
39A ALA* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TYR* 3.5 35.1 - - + +
35A ASP* 1.3 73.2 + - - +
37A ALA* 1.3 58.0 + - - +
39A ALA* 3.5 4.2 + - - +
40A LYS* 3.0 40.1 + - - +
101A ALA 4.2 0.2 - - - -
102A GLY* 4.0 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ASP* 3.2 9.3 + - - +
36A ALA* 1.3 74.5 - - - +
38A ALA* 1.3 67.5 + - - +
40A LYS* 3.3 8.9 + - - +
41A ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 4.0 10.5 - - + -
32A MET* 5.5 3.6 - - + -
35A ASP* 3.3 30.0 + - + +
37A ALA* 1.3 77.5 - - - +
39A ALA* 1.3 62.9 + - - +
41A ALA* 3.3 6.5 + - - +
42A HIS* 3.1 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.4 25.0 - - + +
27A MET* 4.2 13.6 - - - +
34A TYR* 4.6 3.4 - - + -
35A ASP 2.8 19.1 + - - +
36A ALA* 3.6 5.8 - - - +
37A ALA 3.2 0.2 - - - -
38A ALA* 1.3 75.9 - - - +
40A LYS* 1.3 62.5 + - - +
43A ALA* 3.0 24.4 + - - +
101A ALA* 3.8 24.2 - - + +
108A LEU* 4.8 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 3.0 31.2 + - - +
37A ALA* 3.9 6.5 - - - +
38A ALA 3.3 0.2 - - - -
39A ALA* 1.3 74.3 - - - +
41A ALA* 1.3 61.3 + - - +
43A ALA* 3.5 2.5 - - - +
44A SER* 2.8 33.6 + - - -
98A GLU* 4.9 5.4 - - - +
101A ALA* 3.9 19.1 - - + -
102A GLY* 3.2 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 5.0 0.2 - - - -
37A ALA 3.0 16.4 + - - +
38A ALA* 3.5 7.9 - - - +
40A LYS* 1.3 78.9 - - - +
42A HIS* 1.3 66.1 + - + +
44A SER* 3.3 7.0 + - - -
45A ASP* 3.1 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 5.2 1.6 - - + -
20A GLU* 2.8 46.3 + - - +
23A PRO* 3.6 36.6 - - + +
24A LEU* 4.2 10.8 - - + -
27A MET* 5.4 1.3 - - + -
32A MET* 5.8 2.2 - - - +
38A ALA* 3.1 35.5 + - + +
39A ALA* 4.0 4.5 - - - +
41A ALA* 1.3 78.6 - - + +
43A ALA* 1.3 64.1 + - - +
45A ASP* 3.2 3.6 + - - +
46A LEU* 3.0 23.2 + - - +
56D ASP* 3.0 29.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 4.0 11.3 - - + +
39A ALA 3.0 19.5 + - - +
40A LYS* 3.5 8.3 - - - +
42A HIS* 1.3 76.5 - - - +
44A SER* 1.3 63.2 + - - +
46A LEU* 3.2 7.3 + - - +
47A VAL* 3.0 25.1 + - - +
94A VAL* 4.9 0.9 - - - +
97A LEU* 4.3 15.2 - - + +
98A GLU* 4.2 18.8 - - + -
101A ALA* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LYS 2.8 20.2 + - - -
41A ALA* 3.8 6.5 + - - -
43A ALA* 1.3 73.7 - - - +
45A ASP* 1.3 64.9 + - - +
47A VAL* 3.1 5.5 + - - +
48A THR* 3.1 24.4 + - - -
98A GLU* 3.3 25.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 3.0 33.4 - - + +
41A ALA 3.1 12.7 + - - +
42A HIS 3.4 9.0 - - - +
44A SER* 1.3 77.7 + - - +
46A LEU* 1.3 62.1 + - - +
48A THR* 3.3 9.2 + - - -
49A LEU* 3.1 26.4 + - - +
52D TYR* 3.3 15.2 - - - -
53D ASP* 3.0 47.8 + - - +
56D ASP* 4.5 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 4.2 36.1 - - + +
20A GLU* 4.3 8.4 - - + +
21A PHE* 4.2 24.0 - - + +
24A LEU* 4.0 14.8 - - + -
42A HIS 3.0 9.9 + - - +
43A ALA* 3.3 9.6 - - - +
45A ASP* 1.3 73.4 - - - +
47A VAL* 1.3 65.5 + - - +
49A LEU* 3.3 12.7 + - + +
50A THR* 3.1 26.5 + - - +
90A PHE* 4.8 8.1 - - + -
94A VAL* 3.9 18.8 - - + -
97A LEU* 3.9 25.1 - - + -
115A VAL* 5.5 1.1 - - + -
131A HEC 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA 3.0 16.8 + - - +
44A SER* 3.1 10.1 + - - +
46A LEU* 1.3 77.0 - - - +
48A THR* 1.3 62.9 + - - +
50A THR* 2.8 24.7 + - - +
51A LYS* 3.1 42.2 + - - +
94A VAL* 3.8 25.4 - - + +
95A ALA* 4.6 6.3 - - - -
98A GLU* 3.9 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 3.1 12.2 + - - -
45A ASP* 3.3 13.4 + - - -
47A VAL* 1.3 76.4 - - - +
49A LEU* 1.3 64.9 + - + +
51A LYS* 2.9 21.4 + - + +
52A TYR* 3.2 9.0 + - - +
48D THR* 3.9 31.1 - - + +
51D LYS* 4.4 10.7 + - + +
52D TYR* 4.0 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.1 30.2 + - + +
16A LEU* 3.9 26.9 - - + +
17A VAL* 3.8 37.7 - - + +
20A GLU* 4.6 2.5 - - + -
45A ASP 3.1 11.6 + - - +
46A LEU* 3.5 17.9 - - + +
47A VAL 3.3 0.2 - - - -
48A THR* 1.3 79.5 - - + +
50A THR* 1.3 61.6 + - + +
51A LYS 3.4 0.3 + - - -
52A TYR* 3.4 20.9 + - + +
90A PHE* 6.5 0.2 - - + -
16D LEU* 6.1 0.4 - - + -
49D LEU* 5.8 7.2 - - + -
52D TYR* 3.5 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 4.2 5.4 - - - -
46A LEU 3.1 12.2 + - - +
47A VAL* 2.8 24.5 + - - +
49A LEU* 1.3 75.6 - - + +
51A LYS* 1.3 63.6 + - - +
52A TYR 3.3 6.1 + - - +
90A PHE* 3.6 34.5 - - + -
91A PHE* 3.7 37.5 + - - -
94A VAL* 3.9 21.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.2 37.7 - - - +
48A THR* 2.9 11.9 + - - +
50A THR* 1.3 79.6 - - - +
52A TYR* 1.3 63.2 + - - +
53A ASP* 3.3 4.7 + - - +
91A PHE* 5.0 18.4 - - + -
45D ASP* 5.1 0.2 - - - +
48D THR* 4.5 12.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A TYR* 3.8 19.8 + + + -
48A THR 3.2 8.1 + - - +
49A LEU* 3.4 18.7 - - + +
50A THR 3.3 7.7 - - - +
51A LYS* 1.3 76.2 - - - +
53A ASP* 1.3 74.1 + - - +
54A PRO* 3.2 25.8 - - + +
56A ASP* 5.3 0.7 - - - +
57A LEU* 4.2 12.4 - - + +
16D LEU* 3.7 30.1 - - + +
19D LEU* 4.7 2.3 - - - +
20D GLU* 3.1 23.8 + - - +
45D ASP* 3.4 36.3 - - + -
48D THR* 4.0 12.9 - - + +
49D LEU* 4.0 32.8 - - + -
----------------------------------------------------------
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