Contacts of the strand formed by residues 176 - 187 (chain B) in PDB entry 3VHT
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 VAL 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ARG* 6.6 0.2 - - - -
168B ARG* 3.9 24.9 - - + -
169B HIS 3.5 11.2 - - - +
170B ASN* 4.1 13.5 - - - +
171B ILE* 3.3 3.8 - - - +
174B GLY 4.6 4.0 - - - +
175B SER* 1.3 82.8 - - - +
177B GLN* 1.3 61.0 + - - +
178B LEU* 3.8 29.5 + - + +
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Residues in contact with GLN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 3.8 9.9 - - + +
101B LYS* 3.1 31.8 + - - +
103B ASP* 4.9 3.5 - - - +
135B ASN* 3.0 31.0 + - + +
136B ILE* 3.8 20.9 - - + +
141B LEU* 4.7 3.8 - - + -
169B HIS* 2.8 52.3 + - + +
171B ILE* 2.9 21.2 - - + +
176B VAL* 1.3 72.5 - - - +
178B LEU* 1.3 87.3 + - - +
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Residues in contact with LEU 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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100B PHE* 3.5 0.9 - - - -
101B LYS* 3.0 51.4 + - + +
166B LYS* 5.3 19.7 - - + +
167B ILE 3.4 5.2 - - - +
168B ARG* 4.0 18.6 - - + -
176B VAL* 3.8 29.0 + - + +
177B GLN* 1.3 81.9 + - - +
179B ALA* 1.3 61.9 + - - +
180B ASP* 4.2 10.3 - - - +
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Residues in contact with ALA 179 (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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98B ILE* 3.8 14.6 - - + -
99B PHE 3.3 5.4 - - - +
100B PHE* 3.7 29.6 - - + -
166B LYS* 5.3 0.2 - - - +
167B ILE* 2.9 36.8 + - + +
169B HIS* 4.1 11.4 - - + -
178B LEU* 1.3 75.8 - - - +
180B ASP* 1.3 62.2 + - - +
181B HIS* 2.9 20.9 + - + -
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Residues in contact with ASP 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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97B THR 3.6 2.6 - - - +
98B ILE* 3.3 3.6 - - - -
99B PHE* 2.9 42.2 + - + +
101B LYS* 6.1 2.4 - - - +
165B PHE 3.8 4.9 - - - -
166B LYS* 3.2 41.8 + - - +
178B LEU* 4.8 6.8 - - - +
179B ALA* 1.3 72.6 + - - +
181B HIS* 1.3 60.5 + - - +
182B TYR* 3.7 30.0 + - + -
249B GLN* 4.2 9.2 - - - +
250B MET* 4.3 5.9 - - + +
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Residues in contact with HIS 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B THR 5.5 0.9 + - - -
62B THR* 2.8 30.0 + - - -
96B ARG* 3.7 11.0 - - - -
97B THR 3.8 3.6 - - - -
98B ILE* 3.4 38.9 - - + +
100B PHE* 5.9 0.4 - + - -
163B VAL 3.9 0.9 - - - +
164B ASN* 3.5 4.7 - - - -
165B PHE* 2.7 58.4 + + + +
167B ILE* 3.2 28.2 - - + +
169B HIS* 5.4 2.2 - - - -
179B ALA* 2.9 25.0 + - + -
180B ASP* 1.3 71.6 - - - +
182B TYR* 1.3 58.7 + - - +
183B GLN 3.9 0.2 - - - -
250B MET* 2.9 20.0 - - - +
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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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95B GLU 3.9 0.2 - - - +
96B ARG* 3.3 3.6 - - - -
97B THR* 2.9 41.6 + - - +
99B PHE* 3.6 36.6 - + + -
162B LYS* 6.6 0.4 - - - -
164B ASN* 3.5 18.4 - - - +
180B ASP* 3.7 22.0 + - + -
181B HIS* 1.3 73.1 - - - +
183B GLN* 1.3 59.9 + - - +
243B GLN* 3.7 17.7 - - - +
248B GLN* 3.4 20.4 - - + -
249B GLN* 3.6 20.1 + - - -
250B MET* 3.1 38.8 + - + +
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Residues in contact with GLN 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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69B GLN* 3.0 25.0 + - - -
94B GLN* 3.2 11.1 + - + -
95B GLU 3.2 9.9 - - - +
96B ARG* 2.8 42.6 + - + +
162B LYS* 3.7 9.6 + - - +
163B VAL* 2.9 50.5 + - + +
164B ASN* 4.5 0.4 - - - +
165B PHE* 3.4 16.5 - - + -
182B TYR* 1.3 74.8 - - - +
184B GLN* 1.3 69.1 + - - +
185B ASN* 2.7 24.5 + - - +
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Residues in contact with GLN 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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93B VAL 3.7 0.9 - - - +
94B GLN* 3.7 0.2 - - - -
95B GLU* 3.0 63.4 + - + +
155B ASP* 4.8 1.2 - - - +
158B LYS* 4.2 26.6 - - + +
161B ILE 3.2 13.7 - - - +
162B LYS* 2.9 31.3 + - + +
163B VAL 4.7 0.2 - - - +
183B GLN* 1.3 77.8 - - - +
185B ASN* 1.3 69.3 + - - +
186B THR* 5.1 8.0 + - - +
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Residues in contact with ASN 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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83B PHE* 3.7 13.3 - - + -
84B PHE* 4.2 3.8 - - - -
92B TYR* 3.2 26.7 - - + -
93B VAL 3.3 4.3 - - - +
94B GLN* 2.9 30.1 + - - +
158B LYS* 5.8 0.7 - - - +
160B GLY* 3.3 6.4 - - - -
161B ILE* 3.0 55.3 + - + +
163B VAL* 4.1 0.5 - - - +
183B GLN* 2.7 25.9 + - - +
184B GLN* 1.3 79.8 - - - +
186B THR* 1.3 63.0 + - - +
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Residues in contact with THR 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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83B PHE* 4.4 0.2 - - - -
92B TYR* 3.2 4.2 - - - -
93B VAL* 2.7 47.2 + - - +
95B GLU* 5.2 4.1 + - - -
158B LYS* 4.1 24.4 + - + +
160B GLY* 4.8 0.7 - - - -
184B GLN* 5.1 10.7 + - - +
185B ASN* 1.3 76.7 + - - +
187B PRO* 1.3 83.9 - - + +
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Residues in contact with PRO 187 (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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83B PHE* 3.9 11.1 - - + -
87B ALA* 4.3 7.2 - - + +
91B GLY 3.6 8.5 - - - +
92B TYR* 4.1 3.1 - - + -
93B VAL* 5.5 1.2 - - - +
159B ASN* 2.9 46.0 - - + +
186B THR* 1.3 104.9 - - + +
188B ILE* 1.3 62.2 + - - +
189B GLY 4.0 17.6 - - - +
191B GLY 5.3 1.8 - - - +
193B VAL* 4.2 22.7 - - + -
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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
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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