Contacts of the strand formed by residues 174 - 185 (chain A) in PDB entry 2WV4
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 ASP 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ARG* 4.9 6.7 - - - +
170A LYS* 3.4 3.0 - - - -
171A ASP* 2.4 47.2 + - + +
173A ALA* 1.3 81.2 - - - +
175A THR* 1.3 60.2 + - - +
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Residues in contact with THR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.7 29.5 - - + +
102A HIS* 5.1 5.5 + - - -
104A ARG* 4.2 6.5 + - - -
168A LEU* 3.8 22.0 - - + -
169A ALA 3.2 14.8 - - - +
170A LYS* 3.7 21.8 - - - +
173A ALA 5.0 0.3 + - - -
174A ASP* 1.3 77.7 - - - +
176A PHE* 1.3 66.9 + - - +
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.2 4.7 - - - -
102A HIS* 3.4 12.1 - - - +
104A ARG* 3.4 46.9 - - + +
106A THR 5.1 1.1 - - - -
108A ARG* 3.7 16.4 - - + -
109A MET* 3.7 26.7 - - + -
168A LEU* 3.2 4.5 - - - +
169A ALA* 2.8 52.1 + - + +
170A LYS 3.5 20.6 - - - -
171A ASP* 3.3 20.4 - - + -
175A THR* 1.3 78.3 - - - +
177A ILE* 1.3 77.7 + - - +
178A VAL* 4.1 12.6 - - + -
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Residues in contact with ILE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.5 6.1 - - + -
12A VAL* 4.3 9.9 - - + -
34A THR* 6.0 1.3 - - + -
99A ILE* 3.8 23.6 - - + +
102A HIS* 2.6 34.6 + - + +
103A PHE* 3.5 57.2 - - + -
104A ARG 4.4 1.6 + - - -
166A ALA* 4.6 8.5 - - + -
167A VAL 3.7 10.1 - - - +
168A LEU* 3.6 20.6 - - + -
176A PHE* 1.3 82.7 - - - +
178A VAL* 1.3 65.4 + - - +
179A GLY* 4.0 10.5 - - - +
194A VAL 5.0 0.2 - - - +
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PHE* 4.4 0.4 - - - -
109A MET* 4.8 7.2 - - + -
152A PHE* 3.8 28.9 - - + -
167A VAL* 2.8 20.3 + - + +
168A LEU 4.4 0.2 - - - -
169A ALA* 3.5 32.5 - - + +
176A PHE* 4.1 13.7 - - + -
177A ILE* 1.3 75.6 - - - +
179A GLY* 1.3 58.6 + - - +
191A CYS* 3.7 23.8 - - - -
193A CYS* 4.1 13.8 - - + +
194A VAL* 3.1 28.2 + - - +
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Residues in contact with GLY 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 5.4 1.1 - - - -
103A PHE* 4.7 2.5 - - - -
166A ALA* 3.5 4.4 - - - +
167A VAL* 2.8 29.3 + - - +
177A ILE* 3.7 8.3 - - - +
178A VAL* 1.3 83.7 - - - +
180A THR* 1.3 60.0 + - - -
191A CYS* 4.3 4.0 - - - -
192A SER 3.3 13.2 - - - -
194A VAL* 4.1 11.4 - - - -
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Residues in contact with THR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A THR* 3.8 13.2 - - + +
42A LEU* 3.9 30.4 - - + +
43A VAL 4.8 4.6 + - - -
44A PRO* 5.6 1.1 - - - +
84A ASP 5.3 0.2 + - - -
85A ALA* 3.9 24.4 - - - +
164A GLY* 3.3 33.0 - - - +
165A GLY 3.1 4.3 - - - +
166A ALA* 4.7 0.4 - - - -
179A GLY* 1.3 76.6 - - - +
181A HIS* 1.3 66.6 + - - +
182A SER* 3.6 3.6 + - - -
191A CYS* 3.5 2.7 - - - -
192A SER* 3.0 26.6 + - - -
194A VAL* 4.7 1.0 - - - +
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Residues in contact with HIS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PRO* 4.8 1.2 - - - +
129A PHE* 4.3 8.1 - + + -
154A TYR* 2.9 23.0 + - - +
158A THR* 3.3 28.9 - - + +
162A TYR* 3.5 34.0 - - + +
163A ALA* 3.1 12.7 - - - +
164A GLY 2.9 22.4 + - - +
165A GLY* 2.7 15.2 + - - +
167A VAL* 3.8 6.6 - - + +
180A THR* 1.3 74.0 - - - +
182A SER* 1.3 62.4 + - - +
183A ALA 3.2 25.9 + - - -
190A TYR 3.9 2.8 + - - -
191A CYS* 3.6 10.4 - - - +
6C GLN* 2.5 28.4 + - + -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A PRO* 5.5 1.3 - - - +
46A HIS* 3.8 8.8 - - - -
84A ASP* 2.7 28.6 + - - -
148A MET* 3.9 14.6 - - - +
151A LEU* 5.6 0.2 - - - -
163A ALA* 4.1 4.7 - - - +
180A THR* 3.4 5.4 + - - -
181A HIS* 1.3 82.0 + - - +
183A ALA* 1.3 64.0 + - - +
190A TYR 2.9 11.1 + - - -
191A CYS 4.8 0.2 - - - -
192A SER* 2.7 26.4 + - - -
5C LYS* 3.6 4.7 - - - -
6C GLN 3.1 19.9 + - - -
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 3.9 10.5 - - + -
148A MET* 3.6 22.7 - - + -
181A HIS* 3.2 8.4 + - - -
182A SER* 1.3 79.8 - - - +
184A GLY* 1.3 60.7 + - - +
190A TYR* 2.8 34.8 + - + -
3C PRO* 4.3 5.6 - - + -
4C ALA 3.2 20.9 - - - +
5C LYS* 4.2 1.1 - - - -
6C GLN* 3.5 8.5 - - - +
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Residues in contact with GLY 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR* 3.7 4.7 - - - -
183A ALA* 1.3 77.7 - - - +
185A GLY* 1.3 58.1 + - - -
188A VAL 3.4 11.7 - - - -
190A TYR* 4.3 3.3 - - - -
3C PRO* 4.0 3.8 - - - -
4C ALA* 3.0 34.0 + - - +
6C GLN* 3.4 25.1 + - - -
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Residues in contact with GLY 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A THR* 4.5 4.5 + - - -
184A GLY* 1.3 75.8 - - - -
186A ASN* 1.3 73.0 + - - +
187A GLY 3.3 3.1 + - - -
188A VAL* 3.1 26.1 + - - +
190A TYR* 5.1 0.2 - - - -
1C ACE 4.9 3.3 - - - +
2C ALA 5.3 2.5 - - - -
3C PRO* 4.5 10.8 - - - +
6C GLN* 4.6 1.3 - - - +
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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