Contacts of the helix formed by residues 31 - 53 (chain B) in PDB entry 1GN3
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 LYS 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 2.6 53.3 + - + +
30B SER* 1.3 91.2 + - - +
32B HIS* 1.3 70.5 + - + +
34B ALA* 3.2 3.3 - - - +
35B THR* 3.0 27.6 + - - -
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 3.1 32.4 + - + +
28B HIS* 3.5 24.0 - + + +
31B LYS* 1.3 83.8 - - + +
33B HIS* 1.3 66.4 + - - +
35B THR* 3.2 13.4 + - - -
36B TYR* 3.0 31.1 + - + -
164B HIS* 3.4 43.4 + + + +
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Residues in contact with HIS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.0 26.1 - - + +
7B PRO* 3.8 8.8 - - + +
28B HIS* 2.7 15.9 + - - +
29B HIS* 3.2 12.1 - - - +
32B HIS* 1.3 70.1 - - - +
34B ALA* 1.3 57.7 + - - +
35B THR 2.6 11.8 + - - -
36B TYR* 2.7 22.2 + - + -
37B VAL* 3.0 18.8 + - + -
73B HIS* 2.8 32.3 + - - -
76B HIS* 3.2 16.9 - - + +
77B THR* 3.3 36.6 - - - -
80B TRP* 2.9 25.1 + + + +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.3 19.2 - - + +
29B HIS 3.1 3.7 + - - +
30B SER* 2.9 33.0 - - - +
31B LYS 3.2 6.3 - - - +
33B HIS* 1.3 76.8 - - - +
35B THR* 1.3 62.6 + - - +
37B VAL* 3.3 6.8 + - - +
38B LYS* 3.3 18.0 + - - +
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Residues in contact with THR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LYS 3.0 13.6 + - - -
32B HIS* 3.4 11.6 - - - -
33B HIS 2.6 4.9 + - - -
34B ALA* 1.3 70.7 - - - +
36B TYR* 1.3 67.1 + - + +
37B VAL 3.0 1.8 - - - -
38B LYS* 2.7 26.1 + - + +
39B GLY* 2.9 12.1 + - - +
69B ASN* 5.0 5.6 - - - +
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B HIS* 3.0 34.7 + - + +
33B HIS* 2.7 13.5 + - - +
35B THR* 1.3 78.0 - - + +
37B VAL* 1.3 56.9 + - - +
40B ALA* 2.8 33.5 + - - +
68B PHE* 3.6 30.9 - + - -
69B ASN* 3.3 24.0 - - - +
72B GLY* 4.1 10.8 - - - -
73B HIS* 3.6 20.6 - - - +
76B HIS* 3.5 32.3 - + - -
145B GLN* 3.1 20.6 + - - -
162B TRP* 3.8 17.8 - - - -
164B HIS* 4.2 6.8 - + - -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 3.7 24.2 - - - +
5B THR* 3.8 1.3 - - - -
6B LEU* 3.6 28.5 - - + +
33B HIS* 3.0 20.9 + - + +
34B ALA 3.5 9.6 - - - +
35B THR 3.0 1.0 - - - -
36B TYR* 1.3 79.4 - - - +
38B LYS* 1.3 60.5 + - - +
40B ALA* 3.4 6.6 - - - +
41B ASN* 3.3 23.6 + - - +
73B HIS* 3.2 37.7 - - + +
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ALA 3.3 9.8 + - - +
35B THR* 2.7 17.1 + - + +
37B VAL* 1.3 71.8 - - + +
39B GLY* 1.3 69.2 + - - +
40B ALA 3.0 1.3 - - - -
41B ASN* 3.1 7.2 + - - +
42B ASP* 2.7 48.0 + - - +
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Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B THR* 2.9 12.8 + - - +
38B LYS* 1.3 78.8 - - - +
40B ALA* 1.3 57.3 - - - +
42B ASP* 2.7 27.4 + - - +
43B ALA* 2.8 18.1 + - - +
69B ASN* 3.7 25.6 - - - -
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B TYR* 3.8 24.9 - - + -
36B TYR 2.8 19.8 + - - +
37B VAL* 3.4 9.0 - - - +
39B GLY* 1.3 77.2 - - - +
41B ASN* 1.3 64.4 + - - +
42B ASP 3.1 0.2 + - - -
43B ALA* 3.4 4.3 + - - +
44B VAL* 3.2 23.1 + - - +
66B LEU* 4.6 3.0 - - - +
69B ASN* 3.2 20.1 - - + +
70B LEU* 4.3 10.8 - - + +
73B HIS* 4.7 2.9 - - + -
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Residues in contact with ASN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 5.2 2.1 + - - -
3B GLU* 3.2 28.7 + - - +
4B TYR* 2.7 55.2 + - - +
37B VAL* 3.3 14.5 + - - +
38B LYS* 3.1 9.4 + - - +
40B ALA* 1.3 81.3 - - - +
42B ASP* 1.3 69.8 + - - +
44B VAL* 3.6 6.7 + - - +
45B ALA* 3.3 17.2 + - - +
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Residues in contact with ASP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS* 2.7 52.7 + - - +
39B GLY* 2.7 18.5 + - - +
41B ASN* 1.3 72.9 - - - +
43B ALA* 1.3 54.9 + - - +
45B ALA* 2.7 38.3 + - - +
46B LYS* 3.0 13.1 + - + +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLY 2.8 17.3 + - - +
40B ALA 4.0 1.8 - - - +
42B ASP* 1.3 71.7 - - - +
44B VAL* 1.3 62.5 + - - +
46B LYS* 3.2 9.4 + - - +
47B LEU* 3.0 28.0 + - - +
62B ASN* 4.1 5.4 - - - +
65B ASN* 3.7 15.9 - - + +
66B LEU* 3.4 40.4 - - + +
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 4.0 26.9 - - + +
138A LEU* 4.4 9.2 - - + -
4B TYR* 3.9 20.9 - - + -
40B ALA 3.2 14.0 + - - +
41B ASN* 3.8 9.0 - - - +
42B ASP 2.9 0.6 + - - -
43B ALA* 1.3 80.4 - - - +
45B ALA* 1.3 55.1 - - - +
47B LEU* 3.1 24.1 - - - +
48B GLU* 3.1 23.9 + - - +
51B ARG* 5.1 1.2 + - - -
66B LEU* 3.4 26.9 - - + +
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ASN 3.3 10.5 - - - +
42B ASP* 2.7 20.4 + - - +
44B VAL* 1.3 75.0 - - - +
46B LYS* 1.3 63.0 + - + +
48B GLU* 3.0 31.8 - - - +
49B GLU* 3.1 10.0 + - - +
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Residues in contact with LYS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ASP* 3.0 20.6 + - + +
43B ALA* 3.2 9.6 + - - +
45B ALA* 1.3 78.4 - - + +
47B LEU* 1.3 54.9 + - - +
49B GLU* 3.0 32.5 + - + +
50B ALA* 2.7 34.7 + - - +
62B ASN* 4.1 20.4 - - - +
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLN* 3.6 24.7 - - - +
138A LEU* 6.0 3.1 - - + -
139A ILE 4.9 2.0 - - - +
43B ALA 3.0 15.0 + - - +
44B VAL* 3.1 13.9 - - - +
46B LYS* 1.3 76.1 - - - +
48B GLU* 1.3 57.8 + - - +
50B ALA* 3.1 5.7 + - + +
51B ARG* 2.9 48.7 + - - +
59B ILE* 4.6 6.5 - - + -
62B ASN* 3.2 42.8 - - + +
63B GLU* 4.7 5.8 - - - -
66B LEU* 4.1 26.0 - - + -
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B VAL* 3.1 18.4 + - - +
45B ALA* 3.0 26.3 - - - +
47B LEU* 1.3 76.9 - - - +
49B GLU* 1.3 54.9 - - - +
51B ARG* 3.6 21.8 + - - +
52B ALA* 3.0 26.1 + - - +
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ALA 3.1 8.3 + - - +
46B LYS* 3.0 37.4 + - + +
48B GLU* 1.3 79.1 - - - +
50B ALA* 1.3 65.1 + - - +
51B ARG 3.2 0.4 - - - -
52B ALA* 3.6 6.5 - - + +
53B LYS* 2.8 56.1 + - + +
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Residues in contact with ALA 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LYS 2.7 15.1 + - - +
47B LEU* 3.4 13.7 - - + +
49B GLU* 1.3 71.8 - - - +
51B ARG* 1.3 54.9 - - - +
53B LYS* 3.0 6.0 + - - +
54B GLU* 2.6 31.2 + - - -
55B ASP 3.0 21.9 + - - +
56B HIS* 3.3 27.6 - - + +
62B ASN* 4.3 12.3 - - - +
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Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ALA 3.4 18.2 + - - -
103A PHE* 3.6 37.0 + - - +
108A LYS* 3.2 39.7 - - + +
112A GLN* 2.5 40.2 + - - +
44B VAL 5.1 1.0 + - - -
47B LEU* 2.9 45.5 + - - +
48B GLU* 3.6 28.2 + - - +
50B ALA* 1.3 85.0 - - - +
52B ALA* 1.3 62.4 + - - +
54B GLU* 3.0 13.1 + - - +
56B HIS* 3.4 19.7 - - + +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LYS* 3.9 16.7 + - - +
48B GLU 3.0 20.1 + - - +
49B GLU* 3.1 10.2 + - + +
51B ARG* 1.3 78.3 - - - +
53B LYS* 1.3 62.4 + - + +
54B GLU* 3.3 3.7 + - - +
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Residues in contact with LYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 2.8 53.2 + - + +
50B ALA* 4.0 3.4 - - - +
52B ALA* 1.3 81.7 - - + +
54B GLU* 1.3 72.0 + - - +
55B ASP* 2.9 23.7 + - + +
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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) + - + + + + + -
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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