Contacts of the helix formed by residues 75 - 92 (chain B) in PDB entry 2VK8
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 GLY 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A TRP* 4.0 9.4 - - - -
73B THR 3.4 0.8 + - - -
74B PHE* 1.3 67.8 - - - +
76B VAL* 1.3 59.0 + - - -
77B GLY 3.3 0.7 - - - -
78B GLU* 2.9 16.2 + - - +
79B LEU* 3.0 37.2 + - - +
115B HIS 3.8 6.7 - - - -
125B PHE* 3.6 28.9 - - - -
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ASN* 3.4 12.6 + - - -
412A TRP* 3.3 50.9 - - + +
414A SER* 3.7 14.8 - - - +
1564A TPP 3.3 31.3 - - - +
73B THR* 3.6 10.1 - - + -
74B PHE 2.8 5.9 + - - -
75B GLY* 1.3 72.5 - - - -
77B GLY* 1.3 61.4 + - - +
80B SER* 2.8 26.3 + - - -
115B HIS* 3.5 27.4 - - + +
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLU* 3.6 30.4 - - - +
72B THR* 3.6 10.3 - - - -
73B THR* 3.0 18.2 + - - -
76B VAL* 1.3 81.2 - - - +
78B GLU* 1.3 65.1 + - - +
80B SER* 3.2 13.7 + - - -
81B ALA* 3.3 10.4 + - - +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 3.3 17.4 + - - +
73B THR 3.1 5.9 + - - +
74B PHE* 3.6 11.3 - - - -
75B GLY* 2.9 31.0 + - - +
77B GLY* 1.3 76.4 - - - +
79B LEU* 1.3 66.8 + - + +
81B ALA* 3.1 11.8 + - - +
82B LEU* 3.3 21.8 + - + +
97B HIS* 3.7 16.6 - - + -
99B VAL* 3.7 10.4 - - + +
125B PHE* 3.4 31.4 - - + +
129B SER* 4.6 1.0 + - - -
164B TYR* 2.6 35.4 + - + -
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 4.4 8.3 - - - +
80A SER 5.6 0.3 - - - +
82A LEU* 4.3 9.0 - - + +
83A ASN* 4.0 20.9 + - + +
86A ALA* 3.5 32.3 - - + -
412A TRP* 4.1 3.8 - - + -
75B GLY 3.0 20.7 + - - +
78B GLU* 1.3 79.3 - - + +
80B SER* 1.3 61.8 + - - +
81B ALA 3.3 0.3 + - - -
82B LEU* 3.3 30.7 + - + +
125B PHE* 3.7 36.6 - - + +
128B MET* 3.7 31.6 - - + -
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.1 17.6 - - - +
79A LEU 5.5 0.9 - - - +
80A SER* 5.3 7.0 - - - +
83A ASN* 3.1 23.3 + - - +
1564A TPP 4.3 2.8 - - - +
51B GLU* 3.7 21.4 + - - -
52B LEU* 3.5 27.5 - - - +
76B VAL 2.8 18.5 + - - -
77B GLY 3.2 11.1 + - - -
79B LEU* 1.3 78.9 - - - +
81B ALA* 1.3 59.2 + - - +
82B LEU 3.5 0.3 + - - -
83B ASN* 4.7 1.0 + - - +
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Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B GLU* 3.9 18.8 - - + +
52B LEU* 4.3 2.0 - - - +
55B ALA* 3.7 9.7 - - + +
70B ILE* 4.3 9.6 - - + -
72B THR* 4.4 2.2 - - + -
77B GLY 3.3 8.1 + - - +
78B GLU 3.1 11.2 + - - +
80B SER* 1.3 78.3 - - - +
82B LEU* 1.3 64.1 + - - +
83B ASN 3.3 2.2 - - - -
84B GLY* 2.9 16.0 + - - -
85B ILE* 3.1 12.9 + - + +
97B HIS* 4.1 17.7 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.6 11.0 - - + +
82A LEU* 5.6 3.8 - - + -
128A MET* 3.9 27.1 - - + -
78B GLU 3.3 22.0 - - - +
79B LEU* 3.3 35.4 + - + +
80B SER 3.3 0.8 - - - -
81B ALA* 1.3 78.4 - - - +
83B ASN* 1.3 58.0 + - - +
85B ILE* 3.2 12.7 + - + -
86B ALA* 2.8 31.1 + - - +
97B HIS* 4.5 4.0 - - + -
125B PHE 5.4 0.2 - - - +
128B MET* 4.5 10.8 - - + -
129B SER* 3.4 27.4 - - - +
132B ILE* 3.6 15.1 - - + +
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Residues in contact with ASN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLY 4.0 1.4 - - - +
76A VAL* 3.3 13.7 + - - -
79A LEU* 3.9 12.0 + - + +
80A SER* 3.1 37.4 + - - +
52B LEU* 3.9 8.4 - - + +
56B TYR* 2.9 15.4 + - - -
80B SER 4.7 0.6 + - - -
81B ALA 3.3 1.0 - - - -
82B LEU* 1.3 77.7 - - - +
84B GLY* 1.3 61.7 + - - +
86B ALA* 3.6 0.3 + - - +
87B GLY* 3.2 16.3 + - - -
412B TRP* 3.0 35.0 + - - -
414B SER* 2.8 29.5 + - - -
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Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.5 6.0 - - - +
55B ALA* 3.8 20.5 - - - +
56B TYR* 3.9 21.7 - - - -
59B ASP* 4.6 1.4 - - - +
81B ALA 2.9 8.6 + - - -
83B ASN* 1.3 77.1 - - - +
85B ILE* 1.3 66.1 + - - +
87B GLY* 3.2 3.5 + - - -
88B SER* 3.1 24.7 + - - -
409B GLN* 5.8 0.3 + - - -
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA* 4.3 7.2 - - + +
70B ILE* 4.3 6.7 - - + -
81B ALA* 3.1 18.0 + - + +
82B LEU* 3.7 11.0 - - + +
84B GLY* 1.3 78.0 - - - +
86B ALA* 1.3 57.2 + - - +
88B SER* 3.1 7.5 + - - +
89B TYR* 2.9 24.9 + - - +
95B VAL* 4.1 23.3 - - + -
97B HIS* 3.9 40.8 - - + +
129B SER* 5.7 1.6 - - - +
132B ILE* 3.8 23.8 - - + +
133B SER* 4.9 3.8 - - - +
162B PRO* 3.4 22.2 - - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 3.4 26.0 - - + -
117A LEU* 3.8 4.7 - - + +
82B LEU 2.8 20.8 + - - +
83B ASN 3.9 0.7 - - - +
84B GLY 3.3 0.2 - - - -
85B ILE* 1.3 74.1 - - - +
87B GLY* 1.3 57.5 + - - +
89B TYR* 3.1 4.3 + - - +
90B ALA* 2.9 28.8 + - - +
132B ILE* 4.0 23.1 - - + -
412B TRP* 3.6 17.7 - - + -
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Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ASP* 4.2 5.0 - - - +
83B ASN 3.2 12.1 + - - -
84B GLY 3.2 3.5 + - - -
86B ALA* 1.3 75.7 - - - +
88B SER* 1.3 57.2 + - - +
90B ALA* 4.4 0.2 - - - -
91B GLU* 3.0 36.3 + - - +
409B GLN* 4.2 4.9 - - - -
412B TRP* 3.3 34.2 - - - +
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA 4.8 1.0 + - - -
59B ASP* 2.7 33.6 + - - +
84B GLY 3.1 12.8 + - - -
85B ILE* 3.1 10.4 + - - +
87B GLY* 1.3 74.2 - - - +
89B TYR* 1.3 65.7 + - - +
92B HIS* 3.0 4.5 + - - -
93B VAL* 2.8 40.2 + - - +
95B VAL* 3.6 13.7 - - - +
162B PRO* 3.6 15.8 - - - +
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 4.1 36.3 - - + -
119A ASN* 4.8 10.6 + - + -
85B ILE 2.9 9.5 + - - +
86B ALA* 3.5 10.1 - - - +
88B SER* 1.3 79.3 - - - +
90B ALA* 1.3 63.7 + - - +
91B GLU 3.3 0.7 + - - -
92B HIS 3.3 4.2 + - - -
131B ASN 5.2 3.8 - - - -
132B ILE* 3.4 34.3 - - + +
133B SER 4.0 21.9 + - - -
134B GLU* 4.1 7.8 + - - -
161B ARG* 2.8 62.2 + - + +
162B PRO* 3.5 13.4 - - + +
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A THR 3.6 24.0 - - - +
117A LEU* 3.8 21.1 - - - +
86B ALA 2.9 15.2 + - - +
87B GLY 3.9 4.3 - - - +
88B SER 3.4 0.2 - - - -
89B TYR* 1.3 76.6 - - - +
91B GLU* 1.3 58.9 + - - +
92B HIS* 3.4 15.8 + - - -
288B LEU* 4.4 2.6 - - - +
411B LEU* 3.4 22.2 - - + +
412B TRP* 3.9 16.8 - - + -
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ARG* 2.9 32.0 + - - +
87B GLY 3.0 18.5 + - - +
90B ALA* 1.3 77.9 - - - +
92B HIS* 1.3 73.4 + - - +
93B VAL* 3.6 3.6 - - + -
224B ARG* 3.0 20.7 - - - +
247B MET* 3.4 25.9 - - + +
288B LEU* 5.6 0.8 - - - +
408B SER 4.0 1.9 - - - +
409B GLN* 3.2 25.4 - - + -
411B LEU* 2.9 29.6 + - + -
412B TRP* 2.9 19.4 + - + +
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Residues in contact with HIS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU 5.9 0.2 + - - -
88B SER 3.0 5.4 + - - -
89B TYR 3.3 3.6 + - - -
90B ALA 3.4 16.7 + - - -
91B GLU* 1.3 79.8 - - - +
93B VAL* 1.3 56.7 + - - +
160B GLN* 2.8 24.9 - - - +
161B ARG* 3.3 39.9 + - - +
221B CYS* 4.7 2.9 - - - -
224B ARG* 2.9 29.8 + - + +
225B HIS* 2.8 30.0 + + - +
288B LEU* 4.6 10.7 - - + +
311B SER* 5.1 0.7 - - - -
1566B 2OP 3.6 32.8 - - + +
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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
------------------------------------------------------------
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