Contacts of the helix formed by residues 31 - 53 (chain C) in PDB entry 1GN6
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 2.8 38.5 + - + +
30C SER* 1.3 93.2 + - - +
32C HIS* 1.3 67.9 + - + +
33C HIS 3.5 0.2 - - - -
34C ALA* 4.1 1.5 - - - +
35C THR* 3.0 27.2 + - - -
172D ASN* 3.8 34.8 - - + +
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Residues in contact with HIS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU 3.1 16.5 + - - -
28C HIS* 3.4 24.2 - - + +
31C LYS* 1.3 83.0 - - + +
33C HIS* 1.3 66.2 + - - +
35C THR* 3.1 19.3 + - - +
36C TYR* 3.4 25.4 + - + -
164C HIS* 3.6 39.6 + + + +
163D GLU* 3.9 6.0 + - - -
167D TYR* 2.8 35.2 + + - -
172D ASN* 3.9 16.3 - - + +
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Residues in contact with HIS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 3.7 9.1 - - + +
7C PRO* 3.6 19.1 - - + -
28C HIS* 2.9 15.9 + - - +
29C HIS* 3.6 13.7 - - - +
31C LYS 3.5 0.2 - - - -
32C HIS* 1.3 73.2 - - - +
34C ALA* 1.3 64.0 + - - +
36C TYR* 3.0 20.9 + - + +
37C VAL* 3.0 10.7 + - + +
73C HIS* 2.9 40.3 + - - -
76C HIS* 3.3 28.8 - + + +
77C THR* 3.6 19.3 - - - -
80C TRP* 3.0 23.9 + - - +
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Residues in contact with ALA 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LEU* 3.9 25.7 - - + +
29C HIS 3.5 4.2 + - - +
30C SER 3.7 22.0 - - - +
31C LYS* 4.1 2.0 - - - +
32C HIS 3.3 0.4 - - - -
33C HIS* 1.3 77.7 - - - +
35C THR* 1.3 59.1 + - - +
37C VAL* 3.1 8.2 + - - +
38C LYS* 2.9 28.4 + - - +
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Residues in contact with THR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LYS 3.0 12.8 + - - -
32C HIS* 3.1 12.5 + - - +
34C ALA* 1.3 80.2 - - - +
36C TYR* 1.3 68.7 + - + +
38C LYS* 3.1 7.1 + - - +
39C GLY* 2.8 26.7 + - - -
69C ASN* 4.3 3.0 - - - +
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Residues in contact with TYR 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C HIS* 3.4 29.0 + - + -
33C HIS* 3.0 9.1 + + - +
35C THR* 1.3 84.3 - - + +
37C VAL* 1.3 64.6 + - - +
40C ALA* 2.8 26.7 + - - +
68C PHE* 4.0 19.1 - + - -
69C ASN* 3.6 36.8 - - - +
72C GLY* 4.0 10.3 - - - -
73C HIS* 3.9 9.9 - - - +
76C HIS* 3.4 36.8 - + - -
145C HIS* 2.9 27.1 + - - -
162C TRP* 3.8 18.0 - - - -
164C HIS* 4.3 7.2 - + - -
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Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C TYR* 3.5 30.9 - - + +
5C THR* 4.0 7.0 - - - -
6C LEU* 4.0 21.1 - - + +
33C HIS* 3.0 22.0 + - + +
34C ALA* 3.1 9.2 + - - +
36C TYR* 1.3 78.2 - - - +
38C LYS* 1.3 65.3 + - - +
40C ALA* 3.2 5.6 + - - +
41C ASN* 3.1 25.2 + - - +
73C HIS* 3.6 33.7 - - + +
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Residues in contact with LYS 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C ALA 2.9 16.9 + - - +
35C THR* 3.8 5.6 - - - +
37C VAL* 1.3 79.8 - - - +
39C GLY* 1.3 56.0 + - - +
41C ASN* 3.2 5.8 + - - +
42C ASP* 2.9 60.9 + - - +
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Residues in contact with GLY 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C THR 2.8 17.2 + - - -
36C TYR 3.2 0.2 + - - -
38C LYS* 1.3 70.3 - - - +
40C ALA* 1.3 65.2 + - - +
42C ASP* 3.5 8.2 + - - +
43C ALA* 3.1 23.6 + - - +
65C ASN* 5.3 0.3 - - - +
69C ASN* 3.6 29.7 + - - -
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C TYR* 3.8 25.1 - - + -
36C TYR 2.8 17.2 + - - +
37C VAL* 3.6 5.6 - - - +
39C GLY* 1.3 76.6 - - - +
41C ASN* 1.3 65.1 + - - +
43C ALA* 3.3 5.2 + - - +
44C VAL* 3.2 29.3 + - - +
66C LEU* 4.8 3.0 - - + +
69C ASN* 3.5 20.4 - - + +
70C LEU* 4.3 10.3 - - + +
73C HIS* 5.0 1.8 - - + -
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Residues in contact with ASN 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 4.8 3.3 + - - -
3C GLU* 3.6 25.5 + - - +
4C TYR* 2.7 59.0 + - - +
37C VAL* 3.1 18.9 + - - +
38C LYS* 3.8 5.7 - - - +
40C ALA* 1.3 81.9 - - - +
42C ASP* 1.3 63.5 + - - +
44C VAL* 3.6 4.6 + - - +
45C ALA* 3.2 21.5 + - - +
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Residues in contact with ASP 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C LYS* 2.9 52.5 + - - +
39C GLY* 3.9 8.1 - - - +
40C ALA 3.2 0.2 - - - -
41C ASN* 1.3 80.6 - - - +
43C ALA* 1.3 57.6 + - - +
45C ALA* 3.1 7.7 + - - +
46C LYS* 2.9 34.0 + - + +
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Residues in contact with ALA 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C GLY 3.1 17.9 + - - +
40C ALA 3.3 4.5 + - - +
42C ASP* 1.3 73.7 - - - +
44C VAL* 1.3 65.9 + - - +
46C LYS* 3.4 7.1 + - - +
47C LEU* 3.0 30.6 + - - +
62C ASN* 4.4 5.3 - - - +
65C ASN* 4.0 11.4 - - + -
66C LEU* 3.6 39.3 - - + +
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Residues in contact with VAL 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LYS* 3.6 35.7 - - + +
138A LEU* 4.6 10.8 - - + -
4C TYR* 4.1 10.8 - - + -
40C ALA 3.2 16.6 + - - +
41C ASN* 4.0 5.6 - - - +
43C ALA* 1.3 76.2 - - - +
45C ALA* 1.3 64.5 + - - +
47C LEU* 3.3 8.3 + - - +
48C GLU* 3.1 38.4 + - + +
51C ARG* 5.0 1.2 + - - +
66C LEU* 4.1 17.7 - - + -
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Residues in contact with ALA 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C ASN 3.2 12.5 + - - +
42C ASP* 3.1 12.0 + - - +
44C VAL* 1.3 81.6 - - - +
46C LYS* 1.3 60.4 + - + +
48C GLU* 3.2 16.0 + - - +
49C GLU* 3.1 22.2 + - - +
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Residues in contact with LYS 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ASP* 2.9 23.0 + - + +
43C ALA* 3.8 6.5 - - - +
45C ALA* 1.3 69.8 - - - +
47C LEU* 1.3 60.7 + - - +
49C GLU* 3.2 31.4 + - - +
50C ALA* 3.0 27.4 + - - +
62C ASN* 4.0 26.6 - - - +
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLN* 3.3 31.0 - - - +
138A LEU* 5.9 2.9 - - + -
43C ALA 3.0 22.8 + - - +
44C VAL* 3.8 7.0 - - - +
45C ALA 3.3 0.2 - - - -
46C LYS* 1.3 73.2 - - - +
48C GLU* 1.3 65.7 + - - +
50C ALA* 3.4 3.6 + - + +
51C ARG* 3.2 41.0 + - - +
56C HIS* 5.1 4.9 - - + +
59C ILE* 4.3 12.3 - - + -
62C ASN* 3.8 36.8 - - + +
63C GLU* 4.4 3.6 - - - +
66C LEU* 4.0 28.9 - - + -
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Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 3.1 29.2 + - + +
45C ALA* 3.2 14.4 + - - +
47C LEU* 1.3 75.9 - - - +
49C GLU* 1.3 63.4 + - - +
51C ARG* 3.2 25.2 + - - +
52C ALA* 3.0 23.3 + - - +
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ALA 3.1 13.1 + - - +
46C LYS* 3.2 39.4 + - - +
47C LEU 3.3 0.2 - - - -
48C GLU* 1.3 78.2 - - - +
50C ALA* 1.3 61.7 + - - +
52C ALA* 3.1 5.9 + - - +
53C LYS* 2.9 58.8 + - + +
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Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LYS 3.0 15.9 + - - +
47C LEU* 3.9 7.0 - - + +
48C GLU 3.3 0.2 - - - -
49C GLU* 1.3 76.5 - - - +
51C ARG* 1.3 58.8 + - - +
53C LYS* 3.5 2.9 + - - +
54C GLU* 2.9 23.9 + - - -
55C ASP* 3.0 31.9 + - - +
56C HIS* 3.8 20.4 - - + +
62C ASN* 4.7 10.3 - - - +
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Residues in contact with ARG 51 (chain C).
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 3.2 19.0 + - - -
103A PHE* 3.4 51.1 + - - +
108A LYS* 3.0 37.5 + - + +
112A GLN* 2.8 41.4 + - - +
44C VAL* 5.0 1.0 + - - +
47C LEU* 3.2 35.3 + - - +
48C GLU* 3.7 30.9 - - - +
49C GLU 3.2 0.2 - - - -
50C ALA* 1.3 77.0 - - - +
52C ALA* 1.3 61.1 + - - +
54C GLU* 3.1 13.8 + - - +
56C HIS* 4.0 16.6 - - + +
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LYS* 4.4 10.5 + - - +
48C GLU 3.0 17.0 + - - +
49C GLU* 3.1 8.0 + - - +
51C ARG* 1.3 78.7 - - - +
53C LYS* 1.3 59.6 + - + +
54C GLU* 3.2 7.5 + - - +
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Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLU* 2.9 48.9 + - + +
50C ALA* 4.4 3.4 - - - +
52C ALA* 1.3 79.0 - - + +
54C GLU* 1.3 70.8 + - - +
55C ASP* 3.1 19.7 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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