Contacts of the helix formed by residues 31 - 54 (chain A) in PDB entry 1GN2
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 2.8 33.0 + - + +
29A HIS 3.3 0.2 - - - -
30A SER* 1.3 92.0 + - - +
32A HIS* 1.3 64.0 + - - +
34A ALA* 3.9 1.7 - - - +
35A THR* 2.8 30.9 + - - -
172B ASN* 3.6 45.1 - - + +
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Residues in contact with HIS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU 3.1 18.2 + - - -
28A HIS* 3.3 25.1 - - + +
31A LYS* 1.3 76.8 - - - +
33A HIS* 1.3 67.4 + - - +
35A THR* 3.1 16.4 + - - -
36A TYR* 3.2 25.6 + - + -
164A HIS* 3.7 35.9 + + + +
163B GLU* 4.1 5.8 + - - -
167B TYR* 2.6 41.0 + + - -
172B ASN* 3.8 22.2 - - + +
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Residues in contact with HIS 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.8 9.4 - - + +
7A PRO* 3.8 12.6 - - + +
28A HIS 2.9 16.2 + - - +
29A HIS* 3.3 15.3 - - - +
32A HIS* 1.3 73.2 - - - +
34A ALA* 1.3 63.0 + - - +
36A TYR* 3.1 18.2 + - + +
37A VAL* 3.1 19.7 + - + +
73A HIS* 3.1 33.5 + - - -
76A HIS* 3.0 30.9 - - + +
77A THR* 3.4 19.1 - - - -
80A TRP* 2.9 26.4 + + - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.8 26.0 - - + -
29A HIS 3.3 3.8 + - - -
30A SER 3.5 24.2 - - - +
31A LYS 3.9 2.2 - - - +
32A HIS 3.2 1.0 - - - -
33A HIS* 1.3 77.6 - - - +
35A THR* 1.3 56.8 + - - +
37A VAL* 3.4 7.2 + - - +
38A LYS* 3.0 27.9 + - - +
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Residues in contact with THR 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LYS 2.8 17.4 + - - -
32A HIS* 3.1 11.8 + - - -
33A HIS 3.1 0.2 - - - -
34A ALA* 1.3 77.7 - - - +
36A TYR* 1.3 64.9 + - + +
38A LYS* 3.5 7.6 + - + +
39A GLY* 3.0 23.4 + - - -
69A ASN* 4.3 4.1 - - - +
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Residues in contact with TYR 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A HIS* 3.2 30.1 + - + -
33A HIS* 3.1 14.6 + - - +
35A THR* 1.3 78.6 - - + +
37A VAL* 1.3 57.0 + - - +
39A GLY 3.1 0.5 + - - -
40A ALA* 2.7 37.0 + - - +
68A PHE* 4.0 17.5 - + - -
69A ASN* 3.5 26.9 - - - +
72A GLY* 4.0 10.3 - - - -
73A HIS* 3.8 18.2 - - - +
76A HIS* 3.6 24.2 - + - -
145A HIS* 2.7 37.9 + + - -
162A TRP* 3.8 19.1 - - - -
164A HIS* 4.4 5.7 - + - -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.7 24.9 - - - +
5A THR* 4.1 0.2 - - - -
6A LEU* 3.9 25.6 - - + +
33A HIS* 3.1 18.0 + - + +
34A ALA* 3.6 9.4 - - - +
36A TYR* 1.3 79.6 - - - +
38A LYS* 1.3 66.4 + - - +
40A ALA* 3.3 6.3 + - - +
41A ASN* 3.1 26.8 + - - +
73A HIS* 3.5 38.1 - - + +
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Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA 3.0 16.8 + - - +
35A THR* 3.9 6.7 - - + +
36A TYR 3.2 0.2 - - - -
37A VAL* 1.3 79.8 - - + +
39A GLY* 1.3 59.3 + - - +
41A ASN* 3.2 7.9 + - + +
42A ASP* 2.9 60.5 + - - +
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Residues in contact with GLY 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR 3.0 15.9 + - - -
36A TYR 3.1 4.0 + - - -
38A LYS* 1.3 82.9 - - - +
40A ALA* 1.3 56.5 + - - +
42A ASP* 3.5 7.4 + - - +
43A ALA* 3.0 29.6 + - - +
65A ASN* 5.6 0.2 - - - +
69A ASN* 3.6 22.2 + - - -
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.8 24.7 - - + -
36A TYR 2.7 20.1 + - - +
37A VAL* 3.8 6.7 - - - +
38A LYS 3.2 0.2 - - - -
39A GLY* 1.3 70.1 - - - +
41A ASN* 1.3 67.1 + - - +
43A ALA* 3.3 5.4 + - - +
44A VAL* 3.1 27.2 + - - +
66A LEU* 4.7 1.9 - - + +
69A ASN* 3.4 19.2 - - - +
70A LEU* 4.1 14.4 - - + +
73A HIS* 5.0 2.2 - - + -
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Residues in contact with ASN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLU* 3.7 26.9 + - + +
4A TYR* 2.8 57.2 + - - +
37A VAL* 3.1 20.0 + - - +
38A LYS* 3.7 7.9 - - + +
40A ALA* 1.3 76.6 - - - +
42A ASP* 1.3 63.9 + - - +
44A VAL* 3.1 9.4 + - - +
45A ALA* 3.0 21.9 + - - +
136C LYS* 4.8 1.4 + - - -
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Residues in contact with ASP 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LYS* 2.9 60.2 + - - +
39A GLY* 3.8 7.8 - - - +
41A ASN* 1.3 73.4 - - - +
43A ALA* 1.3 58.3 + - - +
45A ALA* 3.1 7.6 + - - +
46A LYS* 2.9 34.4 + - + +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLY 3.0 18.6 + - - +
40A ALA 3.6 5.8 - - - +
42A ASP* 1.3 75.5 - - - +
44A VAL* 1.3 63.3 + - - +
46A LYS* 3.3 7.2 + - - +
47A LEU* 3.3 29.1 + - - +
62A ASN* 4.5 4.1 + - - +
65A ASN* 4.0 12.8 - - + +
66A LEU* 3.6 39.0 - - + +
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 4.0 20.2 - - + +
40A ALA 3.1 13.8 + - - +
41A ASN* 3.4 9.6 - - - +
43A ALA* 1.3 77.9 - - - +
45A ALA* 1.3 64.5 + - + +
47A LEU* 3.3 17.7 + - - +
48A GLU* 3.3 26.5 + - - +
51A ARG* 4.9 1.4 + - - -
66A LEU* 4.0 17.0 - - + -
136C LYS* 4.4 17.3 - - + +
138C LEU* 4.8 12.6 - - + -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN 3.0 13.5 + - - +
42A ASP* 3.5 9.6 - - - +
44A VAL* 1.3 79.1 - - + +
46A LYS* 1.3 64.0 + - + +
48A GLU* 2.9 27.4 + - - +
49A GLU* 2.9 15.2 + - - +
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Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP* 2.9 19.5 + - + +
43A ALA* 3.3 6.5 + - - +
45A ALA* 1.3 75.8 - - + +
47A LEU* 1.3 52.3 - - - +
49A GLU* 3.5 34.1 + - - +
50A ALA* 2.8 34.0 + - - +
62A ASN* 3.6 28.8 - - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ALA 3.3 18.2 + - - +
44A VAL* 3.6 10.3 - - - +
45A ALA 3.0 0.4 - - - -
46A LYS* 1.3 75.9 - - - +
48A GLU* 1.3 55.9 + - - +
50A ALA* 3.1 7.6 + - + +
51A ARG* 2.7 53.4 + - - +
56A HIS* 4.9 2.2 - - + -
59A ILE* 4.3 15.5 - - + -
62A ASN* 3.8 40.6 - - + +
63A GLU* 4.7 2.9 - - - +
66A LEU* 4.1 22.2 - - + -
112C GLN* 4.1 24.0 - - - +
138C LEU* 6.2 1.8 - - + -
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 3.3 25.6 + - - +
45A ALA* 2.9 17.5 + - - +
47A LEU* 1.3 76.6 - - - +
49A GLU* 1.3 60.7 + - - +
51A ARG* 3.0 26.1 + - - +
52A ALA* 2.8 30.6 + - - +
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Residues in contact with GLU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA 2.9 10.8 + - - +
46A LYS* 3.8 37.4 + - - +
48A GLU* 1.3 82.3 - - - +
50A ALA* 1.3 59.6 + - - +
52A ALA* 3.5 5.3 + - - +
53A LYS* 3.1 59.5 + - + +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LYS 2.8 19.8 + - - +
47A LEU* 3.5 9.0 - - + +
48A GLU 3.1 0.2 - - - -
49A GLU* 1.3 78.2 - - - +
51A ARG* 1.3 61.9 + - - +
53A LYS* 3.9 2.4 - - - +
54A GLU* 3.1 3.3 + - - -
55A ASP* 3.1 45.9 + - - +
56A HIS* 3.9 18.3 - - + +
62A ASN* 4.3 11.7 - - - +
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL 4.9 0.8 + - - -
47A LEU* 2.7 30.5 + - - +
48A GLU* 3.4 39.3 + - - +
50A ALA* 1.3 76.6 - - - +
52A ALA* 1.3 64.8 + - - +
54A GLU* 3.4 10.2 + - - +
56A HIS* 4.0 16.4 - - + +
102C ALA 3.7 19.5 + - - -
103C PHE* 3.7 42.7 + - - +
108C LYS* 3.8 37.0 - - + +
112C GLN* 3.0 31.3 + - - +
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLU 2.8 14.8 + - - +
49A GLU* 3.8 7.2 - - - +
51A ARG* 1.3 78.3 - - - +
53A LYS* 1.3 65.8 + - + +
54A GLU* 3.1 8.7 + - - +
108C LYS* 4.2 14.7 + - - +
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 3.1 43.4 + - + +
50A ALA* 5.0 0.9 - - - +
52A ALA* 1.3 76.1 - - + +
54A GLU* 1.3 76.7 + - - +
55A ASP* 3.3 23.3 + - + +
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA 3.1 6.5 + - - -
51A ARG* 3.4 9.6 + - - +
52A ALA 3.1 13.2 - - - +
53A LYS* 1.3 84.4 - - - +
55A ASP* 1.3 58.1 + - - +
56A HIS* 4.1 6.9 + - - -
108C LYS* 5.2 9.2 - - + -
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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