Contacts of the helix formed by residues 59 - 77 (chain A) in PDB entry 3G2S
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 GLN 59 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO* 3.7 13.1 - - + +
57A SER* 3.0 13.6 + - - +
58A PRO* 1.3 76.5 - - + +
60A GLU* 1.3 66.4 + - - +
61A TRP* 3.3 2.7 - - + +
62A GLU* 3.0 28.1 + - + +
63A ALA 3.2 9.5 + - - -
11B GLU* 3.8 22.5 - - + +
14B ILE* 4.2 3.2 - - - +
15B ASN* 3.0 42.4 + - - -
50B LEU* 3.8 27.8 - - + +
53B HIS* 5.9 1.0 + - - -
54B LYS* 4.1 12.5 - - - +
148B HEZ 4.4 2.8 - - - +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER 5.1 0.7 - - - -
58A PRO 3.4 6.8 + - - +
59A GLN* 1.3 71.8 - - - +
61A TRP* 1.3 58.6 + - - +
63A ALA* 3.2 5.1 + - - +
64A ILE* 2.9 39.4 + - + +
108A SER* 2.6 38.2 + - - +
110A LYS* 3.8 28.6 + - - +
111A VAL* 4.1 6.5 - - + -
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Residues in contact with TRP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 3.3 27.3 + - + -
22A ASN 2.8 25.7 + - - -
23A LYS 4.7 1.8 - - - -
24A GLU* 4.0 17.9 - - - -
25A LEU* 3.8 27.8 - - + -
59A GLN* 3.2 1.6 + - + -
60A GLU* 1.3 81.9 + - - +
62A GLU* 1.3 61.3 + - - +
64A ILE* 4.1 22.9 - - + -
65A GLN* 3.0 67.1 + - + +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A THR* 3.6 25.8 - - - +
20A PRO* 4.2 20.6 - - + +
54A LYS* 3.7 37.6 + - + +
57A SER* 2.5 30.8 + - - +
59A GLN* 3.0 28.3 + - + +
61A TRP* 1.3 79.6 - - - +
63A ALA* 1.3 57.2 + - - +
65A GLN* 3.5 2.8 + - - +
66A ALA* 3.0 27.0 + - - +
53B HIS* 4.0 8.9 + - - -
54B LYS* 4.8 9.9 + - - -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LYS 3.6 13.4 + - - +
55A ILE* 3.5 24.0 - - - +
57A SER 4.0 14.4 - - - +
59A GLN 3.2 2.1 + - - +
60A GLU* 3.2 7.9 + - - +
62A GLU* 1.3 76.6 - - - +
64A ILE* 1.3 62.3 + - - +
66A ALA* 3.3 3.8 + - - +
67A LEU* 2.9 34.3 + - - +
111A VAL* 3.9 19.7 - - + -
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Residues in contact with ILE 64 (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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25A LEU* 5.8 0.7 - - + -
60A GLU* 2.9 29.1 + - + +
61A TRP* 4.1 25.4 - - + +
63A ALA* 1.3 71.4 - - - +
65A GLN* 1.3 65.8 + - - +
67A LEU* 3.3 11.9 + - + +
68A THR* 3.0 32.2 + - - +
110A LYS* 3.6 34.8 - - + +
111A VAL* 3.8 25.8 - - + -
114A LYS* 4.6 9.8 - - + -
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Residues in contact with GLN 65 (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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17A ALA 3.5 18.7 - - - +
18A THR* 3.4 13.9 + - - -
19A ASN 2.9 23.2 + - - -
22A ASN* 2.9 30.8 + - - +
24A GLU 4.4 2.3 - - - +
25A LEU* 4.0 12.3 - - + -
26A ASP 4.8 0.2 + - - -
30A ILE* 5.3 1.1 - - + +
61A TRP* 3.0 65.1 + - + +
62A GLU 3.8 3.1 - - - +
64A ILE* 1.3 74.8 - - - +
66A ALA* 1.3 59.3 + - - +
68A THR* 3.0 10.1 + - - -
69A VAL* 2.9 30.1 + - - +
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Residues in contact with ALA 66 (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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18A THR* 3.7 12.2 - - + +
51A LEU* 3.5 11.3 - - + +
54A LYS* 3.5 30.5 - - + -
55A ILE* 3.7 16.6 - - + -
62A GLU 3.0 17.6 + - - +
63A ALA 3.5 5.6 - - - +
64A ILE 3.3 0.2 - - - -
65A GLN* 1.3 76.1 - - - +
67A LEU* 1.3 57.5 + - - +
69A VAL* 3.1 7.4 + - - +
70A LEU* 3.0 24.1 + - - +
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Residues in contact with LEU 67 (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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55A ILE* 3.8 26.5 - - + -
63A ALA 2.9 19.7 + - - +
64A ILE* 3.7 10.1 - - + +
65A GLN 3.2 0.2 - - - -
66A ALA* 1.3 75.5 - - - +
68A THR* 1.3 58.1 + - - +
70A LEU* 3.3 10.5 + - + +
71A GLU* 2.9 29.5 + - - +
94A LEU* 4.7 1.3 - - + -
111A VAL* 3.9 34.8 - - + +
114A LYS* 3.7 32.5 - - + -
115A ILE* 3.8 20.9 - - + -
118A LEU* 3.8 19.7 - - + +
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Residues in contact with THR 68 (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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25A LEU* 4.1 28.5 - - + +
27A TRP* 3.7 28.0 - - + -
30A ILE* 4.3 6.3 - - + -
64A ILE* 3.0 19.0 + - - +
65A GLN 3.3 9.2 - - - -
67A LEU* 1.3 74.0 - - - +
69A VAL* 1.3 62.7 + - - +
71A GLU* 3.4 16.9 + - - +
72A THR* 2.8 30.5 + - - +
114A LYS* 4.9 5.8 + - - +
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 5.5 1.6 - - + -
17A ALA* 4.1 17.5 - - + +
18A THR* 4.3 10.3 - - + -
30A ILE* 3.9 30.5 - - + -
33A PHE* 3.5 35.7 - - + -
34A CYS* 4.6 2.9 - - - -
51A LEU* 3.8 14.6 - - + -
65A GLN 2.9 19.3 + - - +
66A ALA 3.5 7.2 - - - +
68A THR* 1.3 76.4 - - - +
70A LEU* 1.3 57.7 + - - +
72A THR* 3.2 1.6 + - - -
73A CYS* 2.8 35.2 + - - +
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Residues in contact with LEU 70 (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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51A LEU* 4.2 13.6 - - + +
55A ILE* 4.0 13.9 - - + -
66A ALA 3.0 12.3 + - - +
67A LEU* 3.3 19.3 + - + +
69A VAL* 1.3 76.3 - - - +
71A GLU* 1.3 63.7 + - - +
73A CYS* 3.4 1.8 + - - +
74A MET* 3.0 30.5 + - + +
81A PHE* 4.1 8.3 - - + -
85A VAL* 3.9 22.7 - - + -
90A PHE* 3.8 35.4 - - + -
94A LEU* 4.6 6.1 - - + -
118A LEU* 4.4 3.1 - - + -
122A TRP* 3.6 28.5 - - + -
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Residues in contact with GLU 71 (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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67A LEU 2.9 16.1 + - - +
68A THR* 3.6 14.5 + - - +
70A LEU* 1.3 76.8 - - - +
72A THR* 1.3 63.9 + - - +
74A MET* 3.4 7.7 + - - +
75A LYS* 3.4 40.9 + - + +
114A LYS* 2.7 32.6 + - - -
118A LEU* 3.7 25.6 - - + +
122A TRP* 4.8 3.0 + - - +
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Residues in contact with THR 72 (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 TRP* 3.4 25.2 - - + -
30A ILE* 3.9 15.4 - - + +
31A ASN* 3.9 22.0 - - - +
34A CYS* 4.0 8.3 - - + -
68A THR* 2.8 22.8 + - - +
69A VAL 3.6 3.1 - - - -
71A GLU* 1.3 75.4 - - - +
73A CYS* 1.3 62.0 + - - +
75A LYS* 3.1 19.7 + - - +
76A SER* 3.0 30.4 + - - +
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Residues in contact with CYS 73 (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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33A PHE* 3.8 19.7 - - - -
34A CYS* 2.0 53.8 - - - -
37A LEU* 3.9 5.8 - - - -
51A LEU* 5.4 0.2 - - - -
69A VAL* 2.8 18.7 + - - +
70A LEU* 3.9 0.4 - - - +
72A THR* 1.3 75.0 - - - +
74A MET* 1.3 60.9 + - - +
76A SER* 3.7 3.1 - - - -
77A CYS* 2.8 39.3 + - - +
81A PHE* 3.4 25.2 - - + -
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Residues in contact with MET 74 (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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70A LEU* 3.0 22.2 + - + +
71A GLU 3.7 5.8 - - - +
72A THR 3.2 0.2 - - - -
73A CYS* 1.3 78.8 - - - +
75A LYS* 1.3 59.9 + - + +
77A CYS 4.1 0.2 - - - +
81A PHE* 3.9 8.7 - - + -
82A HIS* 2.8 47.2 + - + +
85A VAL* 3.8 34.5 - - + -
122A TRP* 3.6 46.2 - - + +
126A LEU* 3.7 31.3 - - + +
129A GLU* 5.9 0.9 - - + -
132A ILE* 4.5 6.7 - - + -
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Residues in contact with LYS 75 (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 TRP* 6.3 0.6 - - - -
71A GLU* 3.4 35.6 + - + +
72A THR* 3.1 18.2 + - - +
74A MET* 1.3 79.8 - - + +
76A SER* 1.3 59.8 + - - +
77A CYS 3.5 3.2 - - - +
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Residues in contact with SER 76 (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 CYS* 3.3 27.2 - - - +
35A GLU* 6.3 2.9 - - - -
72A THR* 3.0 21.1 + - - -
73A CYS* 3.7 0.3 - - - -
75A LYS* 1.3 76.0 - - - +
77A CYS* 1.3 65.3 + - - +
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Residues in contact with CYS 77 (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 CYS* 3.4 34.1 - - - -
37A LEU* 4.1 13.0 - - - -
38A ASN* 4.2 9.6 - - - +
73A CYS* 2.8 28.0 + - - +
74A MET 4.1 1.9 - - - +
75A LYS 4.2 2.6 - - - +
76A SER* 1.3 91.5 + - - +
78A GLY* 1.3 60.1 + - - +
81A PHE* 3.8 20.6 - - + -
82A HIS* 3.5 15.5 + - - -
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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
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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