Contacts of the helix formed by residues 176 - 186 (chain B) in PDB entry 1VRR
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 TYR 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A VAL* 4.2 8.6 - - + +
112A LEU* 4.4 8.7 - - + +
113A LYS 4.7 2.6 + - - -
114A SER* 3.8 13.3 + - - -
161B LEU* 4.9 0.4 - - - -
162B PRO* 3.1 10.1 - - - +
164B LYS* 3.8 36.3 - - + -
167B SER* 3.3 22.4 - - - +
174B ILE 4.7 3.8 - - - -
175B SER* 1.3 78.9 - - - +
177B TYR* 1.3 69.9 + - - +
178B GLU* 3.7 17.0 - - + -
179B GLY* 3.0 35.0 + - - -
180B GLU* 3.3 12.1 + - - +
3D A 4.0 2.8 + - - -
4D T 2.7 39.8 + - - -
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Residues in contact with TYR 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA* 4.2 5.6 + - - -
86A PRO* 5.8 0.7 - - - +
5B GLU* 3.4 24.0 + - + +
6B VAL 3.6 5.9 + - - -
7B TYR* 3.2 30.8 + - - +
161B LEU* 4.1 24.2 - - + +
162B PRO 2.9 12.7 + - - +
163B MET* 3.5 29.4 - - + -
176B TYR* 1.3 68.4 - - - +
178B GLU* 1.3 81.9 + - + +
180B GLU* 3.0 4.3 + - - +
181B LEU* 2.8 50.1 + - + +
198B LEU* 3.7 23.6 - - + -
199B ILE 3.9 4.0 - - - -
200B GLY* 3.4 32.1 - - - -
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Residues in contact with GLU 178 (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 VAL* 4.0 13.3 - - + +
83A THR* 4.4 10.2 - - - +
84A ALA* 4.1 21.7 - - + +
110A GLU* 4.8 5.7 - - - +
112A LEU* 3.8 15.9 - - + +
163B MET* 3.5 32.1 - - + +
164B LYS* 3.0 43.0 + - - +
165B GLU 4.9 0.3 + - - -
176B TYR* 3.2 10.9 + - + -
177B TYR* 1.3 78.6 + - - +
179B GLY* 1.3 63.7 + - - +
181B LEU* 3.3 5.9 - - - +
182B TYR* 3.2 17.8 + - - +
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Residues in contact with GLY 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 4.2 10.1 - - - -
114A SER* 6.0 0.4 - - - -
176B TYR* 3.0 30.2 + - - -
178B GLU* 1.3 77.0 - - - +
180B GLU* 1.3 63.1 + - - +
182B TYR* 2.8 29.2 + - - +
183B ASN* 3.1 9.9 + - - -
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Residues in contact with GLU 180 (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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139A TYR* 5.1 2.0 - - - -
134B TYR* 4.1 19.8 - - - +
137B VAL* 3.6 48.2 - - + +
138B ALA* 4.4 7.8 + - - +
141B LEU* 5.5 1.1 - - + +
161B LEU* 3.9 13.5 - - + -
175B SER* 4.0 20.2 - - - +
176B TYR 3.3 6.3 + - - +
177B TYR 3.0 8.6 + - - +
179B GLY* 1.3 68.9 - - - +
181B LEU* 1.3 67.2 + - - +
183B ASN* 3.0 39.5 + - - +
184B VAL* 3.2 15.9 + - - +
198B LEU* 5.2 2.2 - - + -
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Residues in contact with LEU 181 (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 THR 4.1 3.4 - - - +
84A ALA* 3.4 26.7 - - - +
86A PRO* 4.3 9.4 - - + -
89A ILE* 3.8 18.8 - - + -
7B TYR* 4.0 27.6 - - + -
161B LEU* 5.6 0.2 - - - +
177B TYR* 2.8 42.5 + - + +
178B GLU 3.3 9.4 - - - +
180B GLU* 1.3 72.4 - - - +
182B TYR* 1.3 57.7 + - - +
184B VAL* 3.1 3.9 + - + +
185B ILE* 2.8 45.2 + - + +
198B LEU* 4.3 12.3 - - + +
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Residues in contact with TYR 182 (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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80A TYR* 3.4 52.2 - + - +
81A TYR 3.8 13.9 - - - -
82A VAL* 3.4 26.5 - - + -
89A ILE* 3.3 36.5 - - + +
92A THR* 5.4 2.2 - - - -
93A LEU* 3.7 22.4 + - + +
100A GLN* 4.5 8.1 + - - -
178B GLU 3.2 3.8 + - - +
179B GLY 2.8 14.2 + - - +
181B LEU* 1.3 79.6 - - - +
183B ASN* 1.3 56.3 + - - +
184B VAL 3.0 0.2 + - - -
185B ILE* 4.3 1.8 - - - +
186B ARG* 2.6 66.2 + - + +
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Residues in contact with ASN 183 (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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80A TYR* 4.2 7.7 + - - -
139A TYR* 4.0 15.0 + - - -
143A VAL* 4.0 23.0 - - + +
138B ALA* 6.2 0.2 - - + -
142B PHE* 5.4 2.2 - - + -
179B GLY 3.1 8.6 + - - +
180B GLU* 3.0 38.9 + - - +
182B TYR* 1.3 80.8 - - - +
184B VAL* 1.3 55.3 + - + +
186B ARG* 2.9 39.9 + - - +
187B GLN* 2.7 33.1 + - - +
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Residues in contact with VAL 184 (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 TYR* 4.5 9.6 - - + +
9B HIS* 3.7 26.9 - - + +
141B LEU* 3.5 32.1 - - + -
142B PHE* 5.2 3.6 - - + -
180B GLU 3.2 10.3 + - - +
181B LEU* 3.1 6.4 + - + +
182B TYR 3.0 0.6 - - - -
183B ASN* 1.3 79.4 - - + +
185B ILE* 1.3 66.6 + - + +
186B ARG 3.3 0.2 + - - -
187B GLN* 3.3 22.4 + - - +
188B GLY 3.6 6.6 - - - +
191B VAL 3.7 17.3 - - - +
192B PRO* 4.3 7.2 - - + -
196B LEU* 5.6 1.3 - - + -
198B LEU* 4.3 13.0 - - + -
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Residues in contact with ILE 185 (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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86A PRO* 4.2 12.6 - - + +
89A ILE* 3.8 28.3 - - + -
90A ARG* 3.3 41.8 + - + +
93A LEU* 4.3 9.2 - - + +
7B TYR* 3.5 35.9 - - + +
181B LEU* 2.8 35.3 + - + +
182B TYR* 3.9 2.2 - - - +
184B VAL* 1.3 77.8 - - + +
186B ARG* 1.3 63.6 + - - +
187B GLN 2.9 1.7 + - - -
188B GLY* 3.0 18.7 + - - +
189B ARG* 5.5 0.7 - - + -
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Residues in contact with ARG 186 (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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78A THR* 5.7 4.2 - - - +
80A TYR* 3.6 12.1 + - - -
93A LEU* 4.1 23.8 - - + +
116A ASN* 2.9 33.1 + - - +
143A VAL* 3.8 12.6 + - - +
147A ALA* 3.7 32.5 - - + +
150A VAL* 5.2 9.5 - - + +
182B TYR* 2.6 47.0 + - + +
183B ASN* 2.9 36.1 + - - +
184B VAL 3.3 0.2 - - - -
185B ILE* 1.3 74.2 - - - +
187B GLN* 1.3 60.8 + - + +
188B GLY 3.5 3.6 + - - -
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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