Contacts of the helix formed by residues 82 - 95 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A GLN* 3.0 28.0 + - - +
80B ALA* 2.9 11.7 + - + +
81B ALA* 1.3 75.6 - - - +
83B GLN* 1.3 58.7 + - - +
85B GLY 2.8 19.9 + - - -
86B ASP* 2.9 34.7 + - - -
106B ALA* 4.2 6.3 - - + +
109B PRO* 3.5 8.5 - - - +
110B THR* 2.6 46.7 + - - -
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Residues in contact with GLN 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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82A ASP* 3.0 28.5 + - - +
83A GLN* 3.1 20.0 + - + +
84A LEU* 3.0 43.8 + - + +
109A PRO* 4.0 5.7 - - - +
112A ARG* 3.9 20.8 - - - +
82B ASP* 1.3 76.3 - - - +
84B LEU* 1.3 58.9 + - + +
86B ASP* 3.2 13.7 + - - +
87B ILE* 3.0 34.6 + - + +
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Residues in contact with LEU 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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83A GLN* 2.9 28.2 + - + +
84A LEU* 6.3 0.4 - - + -
87A ILE* 4.5 21.5 - - + -
12B VAL* 3.5 35.7 - - + +
14B ILE* 5.8 5.4 - - + -
53B GLU* 5.4 3.4 - - + -
83B GLN* 1.3 72.5 - - - +
85B GLY* 1.3 61.2 + - - +
87B ILE* 3.3 13.5 + - + +
88B PHE* 3.0 24.9 + - - +
110B THR* 3.8 20.4 - - + +
111B ALA 5.1 0.7 - - - +
112B ARG* 3.6 44.0 - - + +
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Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 3.8 14.3 - - - +
80B ALA 3.5 11.7 - - - -
82B ASP* 2.8 14.4 + - - -
84B LEU* 1.3 78.0 - - - +
86B ASP* 1.3 56.7 + - - +
88B PHE* 3.4 2.3 + - - +
89B THR* 2.9 35.6 + - - -
110B THR* 3.2 16.7 + - - -
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Residues in contact with ASP 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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45A TYR* 4.1 9.0 + - + -
80B ALA 5.3 0.5 - - - +
81B ALA* 5.3 2.8 - - - -
82B ASP 2.9 25.7 + - - +
83B GLN* 3.2 15.0 + - - +
85B GLY* 1.3 74.4 - - - +
87B ILE* 1.3 59.2 + - + +
89B THR* 3.8 6.1 + - - -
90B HIS* 2.9 30.0 + - - +
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Residues in contact with ILE 87 (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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14A ILE* 5.9 3.6 - - + -
45A TYR* 3.6 17.9 - - + +
53A GLU* 3.5 40.4 - - + +
84A LEU* 4.4 19.5 - - + -
87A ILE* 5.8 1.6 - - + -
12B VAL* 4.6 11.9 - - + -
53B GLU* 6.0 1.6 - - + -
55B SER* 3.8 5.8 - - - +
83B GLN* 3.0 22.2 + - + +
84B LEU* 3.3 20.4 + - + +
86B ASP* 1.3 73.3 - - + +
88B PHE* 1.3 66.6 + - - +
90B HIS* 3.2 2.1 + - - +
91B ASP* 3.0 45.4 + - - +
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Residues in contact with PHE 88 (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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10B ALA* 3.6 11.7 - - + -
11B ILE 3.4 34.5 - - - -
12B VAL* 4.1 4.9 - - + -
55B SER* 3.3 18.0 + - - -
56B GLY 3.4 22.9 - - - -
60B GLY* 4.9 0.2 - - - -
75B TYR* 3.5 37.9 - + - -
79B VAL* 3.8 20.0 - - + -
84B LEU 3.0 17.7 + - - +
85B GLY 3.6 4.3 - - - +
87B ILE* 1.3 77.4 - - - +
89B THR* 1.3 65.8 + - - +
91B ASP* 3.3 1.4 + - - +
92B ILE* 3.2 41.9 + - + +
99B TYR* 4.2 11.2 - + - -
110B THR* 5.1 0.2 - - + -
313B ARG* 3.8 6.3 - - - -
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Residues in contact with THR 89 (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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79B VAL* 4.0 8.1 - - - +
85B GLY 2.9 23.5 + - - -
86B ASP* 3.8 7.1 + - - -
88B PHE* 1.3 76.8 - - - +
90B HIS* 1.3 63.7 + - - +
92B ILE* 3.6 0.5 - - - +
93B ARG* 3.2 52.3 + - - +
99B TYR* 3.5 27.6 - - + +
103B PRO* 5.8 1.2 - - - +
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Residues in contact with HIS 90 (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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45A TYR* 2.8 79.1 + + + +
46A SER* 5.0 3.4 - - - -
48A MSE 3.0 16.9 + - + +
49A GLY 2.9 23.7 + - - -
51A ALA* 4.7 1.3 - - + +
86B ASP 2.9 13.5 + - - +
87B ILE 3.6 0.9 - - - +
89B THR* 1.3 79.5 - - - +
91B ASP* 1.3 82.2 - - - +
93B ARG* 3.9 2.2 - - - +
94B ALA* 2.8 35.7 + - + +
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Residues in contact with ASP 91 (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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45A TYR* 4.6 1.2 + - - -
50A PRO* 3.6 19.2 - - + +
51A ALA* 3.2 34.2 + - - +
53A GLU* 4.6 0.7 - - - +
55B SER* 2.6 39.7 + - - +
87B ILE* 3.0 26.0 + - - +
90B HIS* 1.3 98.0 - - - +
92B ILE* 1.3 63.2 + - - +
95B GLN* 3.2 19.2 + - - +
313B ARG* 4.0 6.0 + - - +
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Residues in contact with ILE 92 (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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60B GLY* 4.0 24.7 - - - +
63B ALA* 4.7 0.4 - - + -
64B ALA* 5.3 1.8 - - + +
75B TYR* 3.5 41.5 - - + -
88B PHE* 3.2 25.6 + - + +
89B THR 3.6 0.9 - - - +
91B ASP* 1.3 80.4 - - - +
93B ARG* 1.3 63.5 + - - +
95B GLN* 3.3 13.4 + - - +
96B GLY 3.6 0.2 + - - -
97B VAL* 3.4 41.1 + - + +
99B TYR* 3.6 32.5 - - + -
313B ARG* 3.9 14.3 - - - +
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Residues in contact with ARG 93 (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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89B THR* 3.2 36.8 + - - +
90B HIS* 4.0 2.5 - - - +
92B ILE* 1.3 75.8 - - - +
94B ALA* 1.3 57.5 + - - +
96B GLY* 2.9 21.8 + - - -
97B VAL 3.7 11.0 + - - +
99B TYR* 3.8 36.4 + - + +
100B GLN* 6.1 2.4 - - - +
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Residues in contact with ALA 94 (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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46A SER 6.0 0.9 - - - +
48A MSE 3.5 24.7 - - - +
49A GLY* 4.2 1.8 - - - -
50A PRO* 3.8 19.6 - - + +
90B HIS* 2.8 34.0 + - + +
91B ASP 3.9 1.6 - - - +
93B ARG* 1.3 74.1 - - - +
95B GLN* 1.3 59.6 + - - +
96B GLY* 3.2 1.4 + - - -
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Residues in contact with GLN 95 (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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50A PRO* 3.8 21.2 - - + +
64B ALA* 3.4 43.6 + - + +
67B ALA* 3.4 14.5 - - + +
68B ASN* 3.5 36.1 + - - +
91B ASP 3.2 13.7 + - - +
92B ILE* 3.6 10.5 - - - +
93B ARG 3.2 0.8 - - - -
94B ALA* 1.3 76.0 - - - +
96B GLY* 1.3 57.3 + - - +
97B VAL* 3.5 1.1 - - + -
313B ARG* 6.0 2.6 - - - +
314B PRO 4.9 5.3 + - - -
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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