Contacts of the helix formed by residues 65 - 76 (chain A) in PDB entry 10GS
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 SER 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ARG* 3.3 45.6 + - - -
17A LEU* 4.6 3.1 - - - +
53A PRO* 4.2 5.9 - - - +
64A GLN* 1.3 69.9 - - - +
66A ASN* 1.3 62.5 + - - +
68A ILE* 3.2 17.2 + - - +
69A LEU* 2.9 32.2 + - - +
210A VWW 2.7 32.9 + - - -
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Residues in contact with ASN 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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13A ARG* 4.2 1.0 - - - +
64A GLN* 3.3 0.8 + - - -
65A SER* 1.3 85.7 + - - +
67A THR* 1.3 60.6 + - - +
69A LEU* 3.6 9.7 - - - +
70A ARG* 2.9 48.1 + - - +
93A ASN* 2.9 25.5 + - - +
97A GLU* 2.9 38.3 + - - +
154A ASN* 3.7 13.9 + - - -
210A VWW 4.5 2.6 + - - -
94B ASP* 3.7 14.7 + - - +
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Residues in contact with THR 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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62A LEU* 4.1 14.4 - - + -
63A TYR 3.4 13.0 - - - +
64A GLN* 3.0 11.3 + - - +
66A ASN* 1.3 75.4 - - - +
68A ILE* 1.3 58.6 + - - +
70A ARG* 3.3 2.4 + - - +
71A HIS* 2.8 28.6 + - - +
74A ARG* 4.9 0.7 + - - -
87B ALA* 3.2 30.5 - - - +
90B ASP* 3.2 12.3 - - + -
91B MET* 3.1 25.5 + - + +
94B ASP* 2.8 22.5 + - - -
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Residues in contact with ILE 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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17A LEU* 4.0 19.3 - - + -
53A PRO* 4.0 23.1 - - + +
55A PHE* 3.7 52.0 - - + +
62A LEU* 4.3 13.2 - - + -
63A TYR 4.4 5.6 - - - +
64A GLN 3.1 18.5 + - - +
65A SER* 3.3 16.2 - - - +
67A THR* 1.3 75.9 - - - +
69A LEU* 1.3 62.6 + - - +
71A HIS* 3.2 7.5 + - - +
72A LEU* 3.0 36.3 + - + +
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Residues in contact with LEU 69 (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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16A ALA* 4.3 8.5 - - + -
17A LEU* 3.9 34.1 - - + +
20A LEU* 4.0 19.3 - - + -
65A SER* 2.9 18.0 + - - +
66A ASN* 3.6 18.6 - - - +
68A ILE* 1.3 76.8 - - - +
70A ARG* 1.3 56.9 + - - +
72A LEU* 3.3 4.5 + - - +
73A GLY* 2.8 26.5 + - - -
93A ASN* 4.3 4.0 - - - +
150A PHE* 3.8 26.9 - - + +
153A TYR* 5.5 0.4 - - + -
154A ASN* 3.7 37.0 - - + +
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Residues in contact with ARG 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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66A ASN* 2.9 41.9 + - - +
67A THR 3.8 2.2 - - - +
69A LEU* 1.3 74.9 - - - +
71A HIS* 1.3 57.6 + - - +
73A GLY 3.8 0.5 - - - -
74A ARG* 2.9 33.8 + - - +
79A TYR* 3.2 26.0 + - + +
90A ASP* 2.8 39.2 + - - +
93A ASN* 4.0 14.5 - - - +
94A ASP* 3.1 26.3 + - - -
150A PHE* 3.6 13.9 - - + -
70B ARG* 3.6 40.0 - - - +
79B TYR* 4.5 0.2 - - - -
90B ASP* 3.7 23.6 - - - +
94B ASP* 4.6 1.6 + - - -
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Residues in contact with HIS 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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55A PHE* 4.4 7.0 - + - -
57A ASP* 2.9 30.2 + - + +
60A LEU* 3.9 17.4 - - + +
62A LEU* 3.8 25.1 - - + -
67A THR 2.8 18.2 + - - +
68A ILE 3.5 4.0 - - - +
70A ARG* 1.3 78.0 - - - +
72A LEU* 1.3 73.2 + - + +
74A ARG* 3.3 13.0 + - - +
75A THR* 2.9 54.3 + - + +
83B GLN* 4.5 10.3 + - + +
84B GLN* 5.5 0.4 - - - -
87B ALA* 3.8 17.5 - - + +
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Residues in contact with LEU 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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3A TYR* 4.2 17.3 - - + +
17A LEU* 4.6 11.7 - - + -
20A LEU* 4.2 22.0 - - + -
21A LEU* 4.3 24.9 - - + -
55A PHE* 3.9 23.6 - - + -
68A ILE* 3.0 34.8 + - + +
69A LEU* 3.7 4.7 - - - +
71A HIS* 1.3 91.5 - - + +
73A GLY* 1.3 60.7 + - - +
75A THR* 3.6 6.5 - - - +
76A LEU* 2.8 41.1 + - + +
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Residues in contact with GLY 73 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A LEU* 5.1 0.2 - - - +
69A LEU 2.8 17.1 + - - -
70A ARG 3.4 1.8 + - - -
72A LEU* 1.3 76.5 - - - +
74A ARG* 1.3 56.1 + - - +
77A GLY* 3.1 7.8 + - - -
78A LEU* 2.7 50.8 + - - -
79A TYR* 3.6 9.8 + - - +
150A PHE* 4.1 9.6 - - - +
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Residues in contact with ARG 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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67A THR 4.9 0.2 + - - -
70A ARG* 2.9 14.9 + - - +
71A HIS* 3.6 24.2 + - - +
72A LEU 3.2 0.2 - - - -
73A GLY* 1.3 80.2 - - - +
75A THR* 1.3 63.0 + - + +
77A GLY* 3.7 6.8 + - - -
79A TYR* 3.8 30.4 - - + -
74B ARG* 5.7 0.4 - - - +
79B TYR* 3.8 20.4 + - - -
83B GLN* 3.4 31.4 + - + +
86B ALA* 3.7 20.5 - - - +
87B ALA* 3.7 23.0 - - - +
90B ASP* 3.1 28.1 + - - -
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Residues in contact with THR 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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3A TYR* 4.7 3.4 + - - -
57A ASP* 5.0 3.9 + - - +
71A HIS* 2.9 44.2 + - + +
72A LEU* 3.4 14.0 + - - +
74A ARG* 1.3 77.0 - - + +
76A LEU* 1.3 75.4 + - - +
77A GLY 3.4 0.4 + - - -
83B GLN* 3.3 32.8 - - + +
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Residues in contact with LEU 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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3A TYR* 3.8 20.4 - - - +
20A LEU* 4.0 23.8 - - + -
21A LEU* 4.9 1.8 - - + -
24A GLN* 4.5 11.7 - - + +
26A GLN* 4.2 32.8 - - + +
72A LEU* 2.8 31.9 + - + +
75A THR* 1.3 86.2 - - - +
77A GLY* 1.3 62.7 + - - +
78A LEU* 4.1 15.8 - - + +
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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
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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