Contacts of the helix formed by residues 83 - 99 (chain B) in PDB entry 2VZE
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 PHE 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 4.0 24.2 - - + +
54B TRP* 3.7 21.3 - + + -
55B ALA* 3.5 18.1 - - - +
58B GLU* 3.3 19.0 + - - +
63B ARG* 4.0 11.4 - - - -
66B SER 3.3 17.5 - - - -
67B PRO 3.5 16.2 - - - -
68B ALA* 3.5 18.6 - - + -
82B ASN* 1.3 76.3 - - - +
84B ARG* 1.3 57.4 + - - +
86B LEU* 3.7 3.2 - - + +
87B SER* 2.9 28.1 + - - -
277B TRP* 3.8 15.9 - + + -
280B GLY* 3.3 30.7 - - - -
281B ALA 3.4 22.7 - - - -
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A GLU* 4.8 13.7 - - - +
186A LYS* 4.2 23.0 - - - +
55B ALA* 3.9 12.0 - - + +
58B GLU* 3.3 18.3 + - + +
59B LYS* 3.4 58.3 + - + +
82B ASN* 3.1 8.7 + - - +
83B PHE* 1.3 76.4 - - - +
85B GLU* 1.3 57.0 + - + +
87B SER* 3.2 2.1 + - - -
88B GLU* 2.8 56.4 + - - +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B MET* 3.9 9.0 - - - +
81B TRP* 3.5 21.6 - - + -
82B ASN* 2.8 58.7 + - - +
84B ARG* 1.3 74.3 - - + +
86B LEU* 1.3 57.1 + - - +
88B GLU* 3.9 12.7 - - - +
89B ASN* 2.8 32.9 + - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 3.8 22.0 - - + -
68B ALA* 3.9 11.7 - - + -
69B LEU* 4.5 15.7 - - + -
81B TRP* 3.9 12.9 - - + -
82B ASN 2.8 16.3 + - - +
83B PHE* 3.7 6.3 - - + +
85B GLU* 1.3 72.5 - - - +
87B SER* 1.3 67.7 + - - +
89B ASN* 4.6 0.4 - - - -
90B SER* 2.9 28.6 + - - -
120B TRP* 5.6 0.9 - - + -
121B LEU* 3.9 22.2 - - + -
124B LEU* 4.0 13.7 - - + -
277B TRP* 3.5 43.7 - - + -
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.9 4.9 - - - +
52B ASP* 3.0 24.1 + - - -
55B ALA* 3.6 17.5 - - - +
59B LYS* 5.2 5.1 + - - -
83B PHE 2.9 18.9 + - - -
84B ARG* 3.2 6.0 + - - -
86B LEU* 1.3 77.4 - - - +
88B GLU* 1.3 64.7 + - - +
90B SER* 3.2 4.0 + - - -
91B GLN* 3.0 41.1 + - - +
128B ARG* 3.7 8.5 + - - +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LYS* 4.5 14.2 - - - +
59B LYS* 5.4 8.4 + - - +
84B ARG* 2.8 52.1 + - + +
85B GLU* 3.9 14.1 - - - +
87B SER* 1.3 75.8 - - - +
89B ASN* 1.3 63.4 + - - +
91B GLN* 3.1 7.5 + - - +
92B GLN* 3.0 25.7 + - - +
203B THR* 4.0 37.6 + - + +
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Residues in contact with ASN 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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81B TRP* 3.1 28.3 - - + +
85B GLU 2.8 22.4 + - - +
86B LEU 4.1 0.4 - - - +
88B GLU* 1.3 74.0 - - - +
90B SER* 1.3 57.6 + - - +
92B GLN* 2.9 25.8 - - - +
93B ALA* 3.0 20.6 + - - +
121B LEU* 2.9 37.1 - - + +
198B LEU* 3.8 19.6 - - - +
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LEU 2.9 22.7 + - - -
87B SER 3.2 4.2 + - - -
89B ASN* 1.3 74.7 - - - +
91B GLN* 1.3 59.5 + - - +
93B ALA* 3.3 10.1 + - - +
94B ALA* 3.0 25.6 + - - +
121B LEU* 4.1 10.5 - - - +
124B LEU* 3.7 35.6 - - - +
125B GLY* 3.9 2.4 - - - -
128B ARG* 3.1 27.5 + - - -
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 4.7 3.4 + - - -
59B LYS* 5.3 7.9 - - - +
87B SER* 3.0 40.5 + - - +
88B GLU* 3.5 6.6 - - - +
90B SER* 1.3 73.6 - - - +
92B GLN* 1.3 65.2 + - - +
94B ALA* 3.3 3.8 + - - +
95B ASN* 3.0 26.6 + - - -
128B ARG* 3.6 28.8 - - - +
202B SER 3.9 2.7 - - - -
203B THR 3.4 24.4 + - - +
204B THR* 3.5 4.7 - - - +
205B HIS* 2.9 42.8 + - + +
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Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 3.0 12.8 + - - +
89B ASN* 2.9 37.5 + - - +
91B GLN* 1.3 76.7 - - - +
93B ALA* 1.3 62.1 + - - +
95B ASN 3.0 1.6 + - - -
96B VAL* 2.9 21.3 + - - +
198B LEU* 3.3 31.7 + - + +
199B ASN* 4.1 10.1 + - - +
201B ALA* 3.2 28.1 + - + +
202B SER 3.2 22.9 - - - +
203B THR* 3.7 19.0 - - - +
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Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ASN 3.0 13.5 + - - +
90B SER* 3.3 8.3 - - - +
91B GLN 3.2 0.4 - - - -
92B GLN* 1.3 75.7 - - - +
94B ALA* 1.3 62.2 + - - +
96B VAL* 3.2 6.9 + - - +
97B LEU* 3.1 27.5 + - + +
121B LEU* 3.3 33.9 - - + +
122B VAL* 4.6 2.0 - - - +
125B GLY* 4.1 5.6 - - - -
194B PHE* 4.5 8.0 - - + -
198B LEU* 3.4 16.7 - - + +
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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
----------------------------------------------------------
90B SER 3.0 14.0 + - - +
91B GLN 3.3 8.3 + - - +
93B ALA* 1.3 76.2 - - - +
95B ASN* 1.3 57.6 + - - +
97B LEU* 3.9 1.5 - - - +
98B SER* 2.9 33.4 + - - -
125B GLY* 3.6 24.8 - - - +
128B ARG* 3.8 7.0 - - + -
129B ALA* 4.3 3.1 - - + +
205B HIS* 3.6 31.4 - - + +
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Residues in contact with ASN 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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91B GLN 3.0 13.0 + - - +
92B GLN 3.0 6.9 + - - +
94B ALA* 1.3 73.1 - - - +
96B VAL* 1.3 58.8 + - - +
98B SER* 4.1 3.9 + - - -
99B GLY* 2.7 32.9 + - - +
100B ALA 3.3 2.4 + - - -
201B ALA* 4.0 13.0 - - + -
202B SER* 3.0 29.0 + - - +
204B THR 2.9 28.5 + - - +
205B HIS* 3.3 19.8 - - - +
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Residues in contact with VAL 96 (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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92B GLN 2.9 13.4 + - - +
93B ALA* 3.5 9.6 - - - +
95B ASN* 1.3 78.0 - - - +
97B LEU* 1.3 59.6 + - + +
100B ALA* 3.4 7.7 + - + +
101B CYS* 3.0 33.6 + - - -
181B LEU* 4.1 28.9 - - + -
194B PHE* 4.2 15.3 - - + +
197B LEU* 3.5 21.3 - - + +
198B LEU* 3.5 39.0 - - + +
201B ALA* 4.1 4.2 - - + +
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Residues in contact with LEU 97 (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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93B ALA* 3.1 22.1 + - + +
94B ALA* 4.0 2.9 - - - +
96B VAL* 1.3 79.0 - - + +
98B SER* 1.3 57.3 + - - +
101B CYS* 3.4 6.2 - - - +
102B GLY 3.3 7.8 + - - -
103B LEU* 3.0 40.3 + - + +
109B VAL* 4.8 6.5 - - + -
122B VAL* 4.0 15.7 - - + +
125B GLY* 3.8 6.3 - - - -
126B CYS* 3.8 36.6 - - - +
129B ALA* 5.1 0.2 - - + -
131B LEU* 3.7 16.2 - - + -
158B VAL* 4.5 12.3 - - + -
181B LEU* 3.7 28.3 - - + -
194B PHE* 5.4 4.3 - - + -
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ALA 2.9 21.4 + - - -
95B ASN* 4.1 3.1 + - - -
97B LEU* 1.3 77.0 - - - +
99B GLY* 1.3 60.1 + - - +
102B GLY* 3.3 16.9 - - - -
103B LEU* 3.5 18.8 - - - +
104B GLN* 5.4 2.1 + - - -
129B ALA* 4.1 17.3 - - - -
205B HIS* 4.0 16.4 + - - -
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ASN* 2.7 20.1 + - - -
98B SER* 1.3 75.8 + - - +
100B ALA* 1.3 65.1 + - - +
101B CYS 3.4 0.7 - - - -
102B GLY* 3.4 8.7 + - - -
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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
------------------------------------------------------------
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