Contacts of the helix formed by residues 76 - 87 (chain B) in PDB entry 3GTU
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 76 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.5 43.0 - - - +
20B ILE* 4.4 7.7 - - - +
64B PRO* 3.6 15.5 - - - +
75B GLN* 1.3 70.9 + - - +
77B ASN* 1.3 65.3 + - - +
79B ILE* 3.1 16.3 + - - +
80B LEU* 3.0 36.4 + - - +
108B MET* 5.7 4.3 - - - -
111B ARG* 6.0 1.3 - - - -
162B LEU* 6.3 0.7 - - - -
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Residues in contact with ASN 77 (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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101A ASN* 3.3 26.4 + - - +
75B GLN 3.3 0.6 - - - -
76B SER* 1.3 82.6 - - - +
78B ALA* 1.3 57.2 + - - +
80B LEU* 4.0 15.9 - - - +
81B ARG* 3.0 38.5 + - - +
104B GLU* 3.6 41.1 + - - +
105B ASN* 5.6 2.4 + - - +
107B VAL* 6.0 0.2 - - - +
108B MET* 3.2 32.9 - - - +
111B ARG* 5.1 1.7 + - - -
158B PHE* 5.8 0.2 - - - -
162B LEU* 4.3 10.9 - - - +
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Residues in contact with ALA 78 (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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94A ILE* 6.0 1.1 - - + +
97A ASP* 3.6 33.3 - - + +
98A ILE* 3.7 13.0 - - + +
101A ASN* 4.1 2.6 - - - +
73B ILE* 3.7 11.8 - - + +
74B THR 3.3 14.8 - - - +
75B GLN* 2.8 13.3 + - + +
77B ASN* 1.3 77.6 - - - +
79B ILE* 1.3 58.0 + - - +
81B ARG* 4.0 0.9 - - - +
82B TYR* 3.0 28.9 + - - +
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Residues in contact with ILE 79 (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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8B LEU* 4.9 1.3 - - + -
20B ILE* 3.7 30.7 - - + -
64B PRO* 3.7 47.1 - - + +
65B TYR* 4.2 9.6 - - - +
66B LEU* 3.7 27.4 - - + -
73B ILE* 4.0 20.0 - - + -
74B THR 4.3 1.6 - - - -
75B GLN 3.4 15.9 - - - +
76B SER 3.1 4.9 + - - +
78B ALA* 1.3 75.0 - - - +
80B LEU* 1.3 65.1 + - - +
82B TYR* 3.2 5.2 + - - +
83B ILE* 3.1 25.7 + - + +
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Residues in contact with LEU 80 (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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16B LEU 5.9 0.9 - - - +
19B ALA* 3.8 36.8 - - + +
20B ILE* 3.9 15.0 - - + +
23B LEU* 3.7 21.3 - - + +
76B SER* 3.0 23.7 + - - +
77B ASN* 4.0 12.3 - - - +
79B ILE* 1.3 73.5 - - - +
81B ARG* 1.3 65.9 + - - +
83B ILE* 5.1 0.9 - - - -
84B ALA* 2.9 28.5 + - - +
158B PHE* 4.1 18.2 - - + +
161B PHE* 5.1 4.0 - - + -
162B LEU* 3.5 37.5 - - + -
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Residues in contact with ARG 81 (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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77A ARG* 3.8 26.9 - - - +
97A ASP* 3.4 34.5 + - - +
100A GLU* 4.7 1.2 + - - -
101A ASN* 5.8 1.1 - - - +
77B ASN* 3.0 25.7 + - - +
78B ALA 4.0 0.9 - - - +
80B LEU* 1.3 77.0 - - - +
82B TYR* 1.3 54.0 + - - +
84B ALA* 3.8 4.4 - - - +
85B ARG* 2.8 41.7 + - - +
90B CYS* 4.4 8.8 - - - +
100B VAL* 4.6 2.2 - - - +
101B ASP* 3.1 29.3 + - - +
104B GLU* 2.7 37.3 + - - +
158B PHE* 3.5 31.5 - - + -
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Residues in contact with TYR 82 (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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90A GLU* 3.5 21.3 - - - -
94A ILE* 3.6 29.8 - - + -
6B MET* 5.1 1.6 - - + -
66B LEU* 3.9 17.0 - - + -
68B ASP* 2.7 35.8 + - + -
71B ASN* 3.4 19.4 + - + +
73B ILE* 3.7 25.1 - - + -
78B ALA 3.0 20.1 + - - +
79B ILE* 3.2 5.6 + - - +
81B ARG* 1.3 77.3 - - - +
83B ILE* 1.3 67.6 + - + +
85B ARG* 3.2 22.1 + - - +
86B LYS* 3.2 45.8 + - + +
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Residues in contact with ILE 83 (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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6B MET* 4.8 5.2 - - + -
20B ILE* 4.1 9.0 - - + -
23B LEU* 4.1 22.9 - - + -
24B LEU* 3.6 34.3 - - + -
27B THR* 4.3 2.0 - - - +
29B THR* 4.2 11.0 - - + +
66B LEU* 3.8 26.2 - - + -
79B ILE* 3.1 24.0 + - + +
82B TYR* 1.3 77.2 - - + +
84B ALA* 1.3 64.3 + - - +
86B LYS* 3.1 16.7 + - + +
87B HIS* 3.0 39.2 - - + +
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Residues in contact with ALA 84 (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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23B LEU* 4.0 9.3 - - + +
80B LEU 2.9 20.4 + - - +
81B ARG 3.8 2.5 - - - +
83B ILE* 1.3 75.7 - - - +
85B ARG* 1.3 58.1 + - - +
87B HIS* 2.8 21.4 + - - +
89B MET* 2.9 47.2 + - + +
90B CYS* 4.3 0.9 - - - -
158B PHE* 3.7 22.0 - - + -
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Residues in contact with ARG 85 (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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90A GLU* 3.9 19.3 + - - +
93A GLN* 3.3 48.2 + - - +
94A ILE* 4.2 5.5 - - - +
97A ASP* 2.6 31.7 + - - -
78B ALA 4.9 0.2 + - - -
81B ARG* 2.8 21.7 + - - +
82B TYR* 3.2 46.4 + - - +
84B ALA* 1.3 71.3 - - - +
86B LYS* 1.3 63.1 + - + +
88B ASN* 3.1 13.7 + - - +
90B CYS* 4.1 16.6 - - + -
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Residues in contact with LYS 86 (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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90A GLU* 2.9 33.6 + - - +
6B MET* 5.3 9.0 - - + -
68B ASP* 4.2 8.6 + - - -
82B TYR* 3.2 49.9 + - + +
83B ILE* 3.1 14.1 + - + +
85B ARG* 1.3 77.3 - - + +
87B HIS* 1.3 72.2 + - + +
88B ASN 3.5 0.4 + - - -
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Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B THR* 3.6 43.9 + - + -
29B THR* 3.0 27.1 + - + +
83B ILE* 3.0 30.2 + - + +
84B ALA 2.8 6.4 + - - +
86B LYS* 1.3 89.8 + - + +
88B ASN* 1.3 70.2 + - - +
89B MET* 3.2 13.9 + - + +
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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