Contacts of the strand formed by residues 160 - 170 (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 GLY 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B PHE* 3.9 13.9 - - - -
154B ALA* 3.7 0.3 - - - -
155B ASP* 2.8 29.0 + - - -
158B LYS* 3.4 4.2 - - - -
159B ASN* 1.3 79.3 - - - +
161B ILE* 1.3 67.4 + - - +
185B ASN 3.3 13.9 - - - -
187B PRO* 4.4 0.2 - - - -
195B LEU* 3.6 10.7 - - - +
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Residues in contact with ILE 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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83B PHE* 3.6 26.9 - - + -
84B PHE* 3.5 35.9 - - + -
152B ILE* 4.1 8.3 - - + -
153B MET 3.4 9.4 - - - +
154B ALA* 4.4 0.2 - - - -
155B ASP* 4.1 4.0 - - - +
160B GLY* 1.3 79.3 - - - +
162B LYS* 1.3 61.2 + - - +
163B VAL* 3.7 17.7 - - + -
184B GLN* 3.2 8.1 - - - +
185B ASN* 3.0 46.4 + - + +
196B PRO* 3.7 35.0 - - + -
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Residues in contact with LYS 162 (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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151B TYR 4.0 0.7 - - - +
152B ILE* 3.7 0.3 - - - -
153B MET* 2.8 63.1 + - + +
155B ASP* 3.7 29.5 + - + +
158B LYS* 5.5 1.4 - - - +
161B ILE* 1.3 71.9 - - - +
163B VAL* 1.3 62.3 + - - +
164B ASN* 5.0 7.4 - - - +
182B TYR* 6.6 0.4 - - - -
183B GLN 3.7 8.6 + - - -
184B GLN* 2.9 36.5 + - + +
243B GLN* 3.5 25.6 - - - +
6C LYS* 5.1 6.5 - - - +
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLN* 4.9 0.7 - - - +
84B PHE* 5.1 0.4 - - + -
150B VAL* 3.6 28.5 - - + -
151B TYR 3.2 12.8 - - - +
152B ILE* 4.4 10.1 - - + -
161B ILE* 3.7 33.2 - - + -
162B LYS* 1.3 81.2 - - - +
164B ASN* 1.3 66.8 + - - +
165B PHE* 4.1 4.5 - - + -
181B HIS 3.9 0.4 - - - +
183B GLN* 2.9 70.4 + - + +
185B ASN* 4.1 2.0 - - - +
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Residues in contact with ASN 164 (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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151B TYR* 2.9 34.1 + - - +
162B LYS* 5.0 7.0 - - - +
163B VAL* 1.3 83.8 + - - +
165B PHE* 1.3 67.5 + - - +
181B HIS 3.5 4.2 + - - -
182B TYR* 3.5 24.0 - - - +
183B GLN 4.5 0.6 - - - +
241B GLN* 3.6 29.4 - - + +
242B VAL* 4.9 1.7 - - - -
243B GLN* 3.6 18.8 + - - +
250B MET* 3.1 29.9 - - + +
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Residues in contact with PHE 165 (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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62B THR* 3.8 1.8 - - + -
66B CR2 3.7 22.9 - + - -
96B ARG* 3.8 15.5 - - - -
148B HIS* 5.1 1.6 - - + -
149B ASN 3.3 22.9 - - - +
150B VAL* 4.0 17.0 - - + -
163B VAL* 4.1 12.1 - - + -
164B ASN* 1.3 81.0 - - - +
166B LYS* 1.3 60.9 - - - +
167B ILE* 3.7 23.8 - - + -
181B HIS* 2.7 74.1 + + + +
183B GLN* 3.4 22.9 - - + -
241B GLN* 4.6 6.7 - - - -
250B MET* 3.4 7.7 - - - +
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Residues in contact with LYS 166 (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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148B HIS* 3.3 21.3 - - - +
165B PHE* 1.3 80.4 - - - +
167B ILE* 1.3 66.0 + - - +
168B ARG* 4.9 5.2 + - + +
178B LEU* 5.3 18.3 - - + +
179B ALA 3.5 4.7 - - - +
180B ASP* 3.2 33.7 + - - +
241B GLN* 3.9 25.0 - - - +
249B GLN* 5.6 1.0 + - - -
250B MET* 3.9 36.7 + - - -
251B MET* 5.0 1.6 - - - +
252B PRO* 5.6 1.3 - - - -
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Residues in contact with ILE 167 (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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62B THR* 4.0 0.7 - - + -
66B CR2 3.7 8.5 - - + +
145B TYR* 3.3 30.1 - - + +
148B HIS* 3.4 30.1 - - + +
165B PHE* 3.7 21.8 - - + -
166B LYS* 1.3 73.2 - - - +
168B ARG* 1.3 64.3 + - - +
169B HIS* 3.5 30.1 - - + +
177B GLN 3.7 0.9 - - - +
178B LEU* 3.4 9.2 - - - +
179B ALA* 2.9 32.0 + - + +
181B HIS* 3.2 34.1 - - + +
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Residues in contact with ARG 168 (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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146A ASN* 3.2 23.8 + - - +
168A ARG* 5.8 4.2 - - - +
170A ASN* 3.6 16.1 + - - +
145B TYR* 5.7 1.7 - - - -
146B ASN* 2.9 36.2 + - - +
147B SER 2.9 28.6 + - - -
148B HIS* 2.9 29.1 + - + +
166B LYS* 4.9 4.2 + - + +
167B ILE* 1.3 76.6 - - - +
169B HIS* 1.3 59.7 + - - +
170B ASN* 3.9 0.7 - - - +
176B VAL* 3.9 18.4 - - + -
178B LEU* 4.0 15.9 - - + -
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Residues in contact with HIS 169 (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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58B PRO* 3.2 37.3 - - - +
59B THR* 3.9 11.6 + - - -
100B PHE* 4.0 24.0 - + - -
141B LEU* 3.6 28.1 - - + +
144B ASN 5.5 0.8 + - - -
145B TYR* 3.8 10.5 - + - -
167B ILE* 3.5 28.6 + - + +
168B ARG* 1.3 70.0 + - - +
170B ASN* 1.3 64.1 + - - +
176B VAL* 3.5 2.4 - - - +
177B GLN* 2.8 53.4 + - + +
179B ALA* 4.1 8.3 - - + +
181B HIS* 5.4 2.2 - - - -
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Residues in contact with ASN 170 (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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147A SER 4.0 6.5 + - - -
168A ARG* 3.5 28.7 + - - +
141B LEU* 3.5 7.3 - - - +
142B GLU* 2.9 48.5 + - - +
144B ASN* 3.6 23.3 + - - +
146B ASN* 3.3 20.8 + - - +
168B ARG* 3.8 2.0 + - - +
169B HIS* 1.3 72.7 - - - +
171B ILE* 1.3 60.0 + - - +
175B SER 3.9 4.9 - - - +
176B VAL* 4.1 16.1 - - - +
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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