Contacts of the strand formed by residues 168 - 179 (chain B) in PDB entry 5V8V
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 ILE 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B THR* 5.1 7.0 - - - -
74B SER* 3.4 24.7 - - - +
163B ILE 3.6 0.7 - - - +
164B THR* 3.3 4.0 - - - -
165B VAL* 2.7 41.9 + - + +
166B GLY 3.3 1.2 + - - -
167B GLY* 1.3 81.8 - - - +
169B THR* 1.3 72.7 + - - +
170B VAL* 4.3 2.9 - - + -
213B ILE* 4.0 36.8 - - + -
216B GLN* 4.3 7.2 - - - +
218B VAL* 4.1 12.6 - - + -
219B LEU* 3.8 27.8 - - + -
244B LEU* 4.5 7.2 - - + -
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Residues in contact with THR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 5.6 7.4 - - + -
163B ILE 3.3 5.4 - - - +
164B THR* 3.4 30.7 - - + -
167B GLY 4.4 1.1 + - - +
168B ILE* 1.3 74.0 - - - +
170B VAL* 1.3 57.7 + - - +
216B GLN* 2.8 32.1 + - - +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B ILE* 3.4 4.4 - - - -
163B ILE* 2.9 38.7 + - + +
165B VAL* 5.2 1.3 - - + -
168B ILE* 4.3 3.4 - - + -
169B THR* 1.3 80.9 - - - +
171B THR* 1.3 65.9 + - - +
172B GLN* 3.3 10.6 + - + +
209B ILE* 3.8 31.9 - - + -
212B ASN* 4.2 7.6 - - + -
213B ILE* 3.5 36.6 - - + +
216B GLN* 3.4 19.3 - - - +
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Residues in contact with THR 171 (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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160B GLN* 3.2 31.9 - - + +
161B ASP* 3.9 8.3 - - - +
162B ILE* 4.6 4.1 - - + +
170B VAL* 1.3 70.5 - - - +
172B GLN* 1.3 59.3 + - - +
212B ASN* 3.6 19.6 + - - +
216B GLN* 4.9 2.0 - - - +
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Residues in contact with GLN 172 (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 VAL* 4.3 12.9 - - + +
159B SER 3.8 0.2 - - - +
160B GLN* 3.6 6.0 - - - -
161B ASP 3.0 30.7 + - - +
163B ILE* 3.6 33.2 - - + -
170B VAL* 3.3 10.5 + - + +
171B THR* 1.3 74.5 - - - +
173B MET* 1.3 87.6 + - - +
174B PHE* 3.8 4.3 + - - -
206B VAL* 4.5 0.4 - - - +
207B THR 3.2 20.2 + - - -
208B PRO* 4.7 0.2 - - - +
209B ILE* 3.3 30.9 - - + +
212B ASN* 2.5 29.7 + - - +
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Residues in contact with MET 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL* 4.7 3.3 + - - +
141B ASN* 3.1 39.9 - - + +
158B LEU* 3.8 21.1 - - + -
159B SER 3.5 22.4 - - - +
160B GLN* 4.1 18.6 - - + +
172B GLN* 1.3 98.0 + - - +
174B PHE* 1.3 60.3 + - - +
206B VAL* 3.4 34.1 - - + +
207B THR* 6.5 0.4 - - - -
212B ASN* 4.9 1.4 - - - +
501B NAG 3.3 19.7 - - - +
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Residues in contact with PHE 174 (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 ILE* 4.0 12.3 - - + -
110B VAL* 3.3 30.1 - - + +
112B VAL* 3.9 22.7 - - + -
130B PHE* 3.5 30.1 - + - -
158B LEU* 3.5 7.9 - - - -
159B SER* 2.8 55.1 + - - +
161B ASP* 3.9 23.6 - - + -
163B ILE* 4.4 14.6 - - + -
172B GLN 3.8 9.2 - - - -
173B MET* 1.3 74.2 - - - +
175B GLY* 1.3 69.0 + - - +
176B GLU* 3.8 20.4 + - + -
206B VAL* 5.7 0.2 - - - -
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Residues in contact with GLY 175 (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 VAL 2.7 15.3 + - - -
111B TRP* 3.2 8.0 - - - +
112B VAL 3.1 28.1 + - - +
145B LEU* 3.9 23.6 - - - +
157B PHE 3.4 7.9 - - - -
158B LEU* 4.6 0.4 - - - -
174B PHE* 1.3 76.9 - - - +
176B GLU* 1.3 60.9 - - - -
177B VAL* 3.7 1.6 - - - -
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Residues in contact with GLU 176 (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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112B VAL 3.7 3.6 - - - +
114B SER* 2.7 28.7 + - - +
116B LYS* 4.5 2.6 - - - +
130B PHE* 3.4 37.9 - - + +
132B ALA* 3.9 10.5 + - - +
138B TYR* 3.9 10.9 + - - -
156B GLY* 3.1 4.4 - - - -
157B PHE* 2.7 54.9 + - + +
159B SER* 2.5 27.6 + - - +
174B PHE* 3.8 10.7 + - + -
175B GLY* 1.3 70.2 - - - -
177B VAL* 1.3 62.7 + - - +
178B THR* 3.8 4.7 - - - +
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Residues in contact with VAL 177 (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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111B TRP* 3.4 42.2 - - + -
112B VAL 2.9 16.8 + - - +
113B PRO* 3.9 1.1 - - + +
114B SER* 2.9 24.7 + - - +
117B CYS* 3.7 6.2 - - - +
124B CYS* 5.9 0.4 - - - -
145B LEU* 6.1 1.8 - - + -
147B LEU* 5.2 2.2 - - + -
154B VAL* 4.2 15.0 - - + -
155B SER 3.4 10.8 - - - +
156B GLY* 4.1 1.3 - - - +
175B GLY* 4.3 2.2 - - - +
176B GLU* 1.3 71.7 - - - +
178B THR* 1.3 61.4 + - - +
179B GLU 3.6 13.0 - - - +
180B MET* 3.5 34.3 - - + -
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Residues in contact with THR 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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114B SER* 4.4 1.1 - - - -
116B LYS* 4.2 18.4 - - + +
117B CYS* 3.5 25.8 - - - +
118B SER* 3.9 6.1 + - - -
121B TYR* 3.8 6.8 - - - -
144B GLU* 5.1 3.1 + - - -
155B SER* 2.5 22.5 + - - -
156B GLY* 3.3 7.6 - - - -
157B PHE* 3.4 35.4 - - + -
176B GLU 3.8 2.7 - - - +
177B VAL* 1.3 78.3 - - - +
179B GLU* 1.3 66.9 + - - +
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Residues in contact with GLU 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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121B TYR* 3.6 32.9 + - + -
153B THR* 5.6 2.8 - - - +
154B VAL* 3.6 24.0 - - - +
155B SER* 3.1 31.0 + - - +
177B VAL* 3.6 5.4 - - - +
178B THR* 1.3 90.8 + - - +
180B MET* 1.3 62.0 + - - +
181B PRO* 3.7 5.6 - - + +
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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