Contacts of the helix formed by residues 151 - 161 (chain B) in PDB entry 3VAS
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 GLN 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B ALA 3.4 14.2 + - - +
148B HIS* 3.2 39.8 + - - +
149B ILE 3.2 0.4 - - - -
150B GLU* 1.3 76.8 - - - +
152B PRO* 1.3 64.5 - - + +
153B HIS* 3.5 33.4 + - + -
154B VAL* 2.9 5.0 + - + +
155B TRP* 2.7 32.7 + - - +
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Residues in contact with PRO 152 (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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150B GLU 3.4 5.8 - - - +
151B GLN* 1.3 87.1 - - + +
153B HIS* 1.3 59.3 + - - +
155B TRP* 4.6 4.0 - - + +
156B SER* 3.0 31.4 + - - -
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Residues in contact with HIS 153 (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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110B GLU* 3.8 28.7 + - - +
148B HIS* 5.3 1.8 - - - -
151B GLN* 3.5 38.5 + - + +
152B PRO* 1.3 81.2 - - + +
154B VAL* 1.3 73.9 + - + +
156B SER* 4.3 9.0 + - - -
157B LEU* 3.9 15.9 - - - +
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Residues in contact with VAL 154 (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 PHE* 4.8 2.1 - - + -
86B VAL* 3.9 26.7 - - + -
110B GLU* 4.1 14.1 - - + -
148B HIS* 3.3 39.5 - - + +
149B ILE* 3.8 14.6 - - + +
151B GLN* 2.9 10.4 + - + +
153B HIS* 1.3 103.8 - - + +
155B TRP* 1.3 64.8 + - - +
156B SER 3.1 1.3 - - - -
157B LEU* 3.0 23.9 + - - +
158B VAL* 3.7 5.5 + - + +
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Residues in contact with TRP 155 (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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149B ILE* 3.3 42.2 + - + +
150B GLU* 4.4 9.6 - - - +
151B GLN 2.7 17.6 + - - +
152B PRO* 4.3 3.6 - - + +
154B VAL* 1.3 72.4 - - - +
156B SER* 1.3 57.5 + - - +
158B VAL* 2.9 43.2 + - + +
159B GLU* 3.0 43.5 + - + +
180B LYS* 4.1 47.8 - - + -
181B ILE* 4.1 7.9 - - + -
184B HIS* 4.0 23.8 + + + -
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Residues in contact with SER 156 (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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152B PRO 3.0 20.9 + - - -
153B HIS* 4.3 10.5 + - - -
155B TRP* 1.3 77.3 - - - +
157B LEU* 1.3 63.5 + - - +
159B GLU* 3.4 10.8 + - - +
160B LYS* 3.2 37.1 + - - +
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Residues in contact with LEU 157 (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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7B GLY 4.4 0.9 - - - +
10B PHE* 3.8 21.8 - - + -
84B SER* 4.2 26.2 + - - +
85B TYR 5.4 0.4 - - - +
86B VAL* 4.8 3.8 - - + -
108B VAL* 4.3 18.8 - - + -
109B THR 5.0 0.2 - - - -
110B GLU* 3.6 35.0 - - + +
153B HIS 3.9 10.5 - - - +
154B VAL 3.0 13.8 + - - +
156B SER* 1.3 79.6 - - - +
158B VAL* 1.3 62.8 + - - +
160B LYS* 3.5 37.2 - - + +
161B ALA* 3.5 12.6 + - - +
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Residues in contact with VAL 158 (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 PHE* 3.8 28.3 - - + -
149B ILE* 4.9 3.6 - - + -
154B VAL* 4.2 5.6 - - + +
155B TRP* 2.9 46.9 + - + +
157B LEU* 1.3 76.4 - - - +
159B GLU* 1.3 61.3 + - - +
161B ALA 3.3 6.4 + - - -
164B TYR* 2.4 48.8 + - + +
181B ILE* 4.1 16.2 - - + -
184B HIS* 3.8 16.2 - - + +
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Residues in contact with GLU 159 (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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155B TRP* 3.0 48.3 + - + +
156B SER* 3.4 9.1 + - - +
157B LEU 3.4 0.2 - - - -
158B VAL* 1.3 77.9 - - - +
160B LYS* 1.3 57.1 + - - +
162B GLN* 4.2 3.8 + - - -
184B HIS* 4.1 15.9 + - + -
190B LYS* 2.9 22.1 + - - +
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Residues in contact with LYS 160 (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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5B SER* 4.9 5.7 + - - -
6B GLU* 3.6 25.8 + - - +
7B GLY* 3.8 18.5 - - - +
8B TYR* 4.5 2.1 - - - -
84B SER* 5.2 0.2 - - - +
156B SER* 3.2 23.2 + - - +
157B LEU* 3.5 35.1 - - + +
159B GLU* 1.3 75.0 - - - +
161B ALA* 1.3 63.3 + - - +
162B GLN* 3.2 18.8 + - - +
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Residues in contact with ALA 161 (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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7B GLY 3.1 19.7 - - - +
8B TYR 3.5 6.1 - - - +
10B PHE* 3.5 31.9 - - + +
157B LEU 3.6 6.5 - - - +
158B VAL 3.3 6.4 + - - +
159B GLU 3.3 1.2 - - - -
160B LYS* 1.3 81.6 - - - +
162B GLN* 1.3 61.0 + - - +
163B VAL 4.0 1.1 - - - +
164B TYR* 3.4 7.9 + - + -
190B LYS* 2.8 30.0 + - - +
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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