Contacts of the helix formed by residues 82 - 95 (chain A) in PDB entry 4K8T
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 ASP 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A ALA* 2.9 11.9 + - + +
81A ALA* 1.3 74.6 - - - +
83A GLN* 1.3 59.4 + - - +
85A GLY 2.9 14.9 + - - -
86A ASP* 2.9 34.7 + - - -
106A ALA* 4.2 7.0 - - + +
109A PRO* 3.5 8.8 - - - +
110A THR* 2.7 43.0 + - - -
83B GLN* 3.0 31.8 + - - +
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Residues in contact with GLN 83 (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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82A ASP* 1.3 72.9 - - - +
84A LEU* 1.3 61.8 + - + +
86A ASP* 3.2 12.1 + - - +
87A ILE* 2.9 34.2 + - + +
82B ASP* 3.0 29.3 + - - +
83B GLN* 3.1 19.2 + - + +
84B LEU* 2.9 46.4 + - + +
109B PRO* 4.0 5.9 - - - +
112B ARG* 3.8 21.2 - - - +
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Residues in contact with LEU 84 (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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12A VAL* 3.5 32.5 - - + +
14A ILE* 5.8 6.5 - - + -
53A GLU* 5.4 2.7 - - + -
83A GLN* 1.3 75.4 - - + +
85A GLY* 1.3 58.6 + - - +
87A ILE* 3.3 18.3 + - + +
88A PHE* 2.9 23.6 + - - +
110A THR* 3.9 19.7 - - + +
111A ALA 5.0 1.1 - - - +
112A ARG* 3.6 45.8 - - + +
403A DMS 6.2 0.4 - - + -
83B GLN* 3.0 29.6 + - + +
84B LEU* 6.3 0.2 - - + -
87B ILE* 4.4 20.9 - - + -
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Residues in contact with GLY 85 (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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79A VAL* 3.8 13.8 - - - +
80A ALA 3.6 9.2 - - - -
82A ASP* 2.9 15.6 + - - -
84A LEU* 1.3 78.0 - - - +
86A ASP* 1.3 58.2 + - - +
88A PHE* 3.3 2.1 + - - +
89A THR* 2.8 35.4 + - - -
110A THR* 3.2 18.0 + - - -
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Residues in contact with ASP 86 (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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80A ALA 5.2 0.9 - - - +
81A ALA* 5.2 3.3 - - - -
82A ASP 2.9 25.5 + - - +
83A GLN* 3.2 14.4 + - + +
85A GLY* 1.3 73.2 - - - +
87A ILE* 1.3 60.8 + - - +
89A THR* 3.8 7.4 + - - -
90A HIS* 2.9 30.0 + - - +
45B TYR* 4.1 9.3 + - + -
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Residues in contact with ILE 87 (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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12A VAL* 4.7 10.5 - - + -
53A GLU* 5.9 1.6 - - + -
55A SER* 3.8 4.9 - - - +
83A GLN* 2.9 21.5 + - + +
84A LEU* 3.5 25.1 - - + +
86A ASP* 1.3 73.7 - - + +
88A PHE* 1.3 66.5 + - - +
90A HIS* 3.3 1.0 + - - +
91A ASP* 3.0 46.3 + - - +
14B ILE* 6.2 3.1 - - + -
45B TYR* 3.6 17.3 - - + +
53B GLU* 3.5 40.8 - - + +
84B LEU* 4.5 17.7 - - + -
87B ILE* 5.8 1.8 - - + -
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Residues in contact with PHE 88 (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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10A ALA* 3.7 9.9 - - + -
11A ILE 3.4 32.8 - - - -
12A VAL* 4.1 5.8 - - + -
55A SER* 3.4 18.2 + - - -
56A GLY 3.3 25.4 - - - -
75A TYR* 3.5 40.6 - + - -
79A VAL* 3.8 22.4 - - + -
84A LEU 2.9 15.6 + - - +
85A GLY 3.7 4.5 - - - +
87A ILE* 1.3 78.0 - - - +
89A THR* 1.3 66.1 + - - +
91A ASP* 3.4 1.0 + - - +
92A ILE* 3.2 33.5 + - + +
99A TYR* 4.1 10.3 - + - -
110A THR* 5.1 0.2 - - + -
313A ARG* 3.7 11.0 - - - -
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Residues in contact with THR 89 (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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79A VAL* 4.0 9.4 - - - +
85A GLY 2.8 24.1 + - - -
86A ASP* 3.8 7.7 + - - -
88A PHE* 1.3 76.1 - - - +
90A HIS* 1.3 62.0 + - - +
92A ILE* 3.8 0.5 - - - +
93A ARG* 3.2 53.4 + - - +
99A TYR* 3.5 28.5 - - + +
103A PRO* 6.1 0.3 - - - +
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Residues in contact with HIS 90 (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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86A ASP 2.9 14.6 + - - +
87A ILE 3.6 1.1 - - - +
89A THR* 1.3 78.5 - - - +
91A ASP* 1.3 79.7 + - - +
93A ARG* 3.9 2.5 - - - +
94A ALA* 2.8 32.4 + - + +
45B TYR* 2.9 71.8 + + + +
46B SER* 5.0 4.0 - - - -
48B MSE 2.9 21.6 + - + -
49B GLY 3.0 31.2 - - - -
51B ALA* 4.6 1.3 - - + -
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Residues in contact with ASP 91 (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 SER* 2.5 40.5 + - - +
87A ILE* 3.0 26.1 + - - +
90A HIS* 1.3 95.4 + - - +
92A ILE* 1.3 62.3 + - - +
95A GLN* 3.3 18.2 + - - +
313A ARG* 4.1 6.1 + - - +
45B TYR* 4.5 2.4 + - - -
50B PRO* 3.5 22.4 - - + +
51B ALA* 3.2 35.0 + - - +
53B GLU* 4.6 0.7 - - - +
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Residues in contact with ILE 92 (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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60A GLY* 4.0 25.4 - - - +
63A ALA* 4.8 0.4 - - + -
64A ALA* 5.1 1.1 - - + -
75A TYR* 3.6 38.6 - - + -
88A PHE* 3.2 26.4 + - + +
89A THR 3.8 0.7 - - - +
91A ASP* 1.3 76.9 - - - +
93A ARG* 1.3 67.9 + - - +
95A GLN* 3.3 10.7 + - - +
97A VAL* 3.3 44.6 + - + +
99A TYR* 3.5 33.0 - - + -
313A ARG* 3.9 14.5 - - - +
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Residues in contact with ARG 93 (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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89A THR* 3.2 36.7 + - - +
90A HIS* 4.1 2.5 - - - +
92A ILE* 1.3 77.2 - - - +
94A ALA* 1.3 57.4 + - - +
96A GLY* 2.8 22.7 + - - -
97A VAL 3.7 10.7 - - - +
99A TYR* 3.8 37.7 + - + +
100A GLN* 6.1 2.4 - - - +
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Residues in contact with ALA 94 (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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90A HIS* 2.8 34.4 + - + +
91A ASP 4.1 1.3 - - - +
92A ILE 3.4 0.2 - - - -
93A ARG* 1.3 71.0 - - - +
95A GLN* 1.3 58.3 + - - +
96A GLY* 3.2 1.0 + - - -
46B SER 5.7 2.5 - - - +
48B MSE 3.4 25.4 - - - +
49B GLY* 4.1 2.4 - - - -
50B PRO* 3.9 19.2 - - + +
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Residues in contact with GLN 95 (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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64A ALA* 3.4 45.2 + - + +
67A ALA* 3.3 15.3 - - + +
68A ASN* 3.6 33.8 + - - +
91A ASP 3.3 12.4 + - - +
92A ILE 3.3 11.3 + - - +
93A ARG 3.1 1.2 - - - -
94A ALA* 1.3 76.4 - - - +
96A GLY* 1.3 57.6 + - - +
97A VAL* 3.5 2.7 - - + -
313A ARG* 6.0 3.6 - - - +
314A PRO 4.8 5.3 + - - -
50B PRO* 3.9 19.1 - - + +
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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