Contacts of the strand formed by residues 175 - 184 (chain B) in PDB entry 2W3B
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 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B TRP* 4.6 2.5 - - + -
25B PRO* 3.7 36.3 - - + -
27B LEU* 4.1 25.8 - - + -
138B ILE* 3.8 28.3 - - + -
140B GLN* 4.1 18.8 - - - +
142B PHE* 3.9 12.8 - - + -
171B GLU* 3.4 4.2 - - - +
172B GLU 2.9 29.5 + - - +
173B LYS* 3.8 10.8 - - + +
174B GLY* 1.3 79.6 - - - +
176B LYS* 1.3 67.1 + - - +
177B TYR* 3.7 6.4 - - + -
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Residues in contact with LYS 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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138B ILE* 3.9 1.0 - - - -
139B MET* 3.0 43.0 + - + +
140B GLN* 4.7 4.1 + - - +
169B VAL* 3.9 22.0 - - + -
170B GLN 3.2 6.1 - - - +
171B GLU* 3.5 38.2 + - + -
174B GLY 3.8 5.5 + - - -
175B ILE* 1.3 75.4 - - - +
177B TYR* 1.3 63.3 + - - +
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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
----------------------------------------------------------
27B LEU* 4.2 19.1 - - + -
29B ASN* 4.0 5.9 - - - +
30B GLU* 3.6 15.7 + - + -
136B THR* 3.5 21.1 - - + -
137B ARG 3.1 15.0 - - - +
138B ILE* 3.9 11.9 - - + -
139B MET* 4.0 4.9 - - - -
169B VAL* 3.6 1.7 - - - -
170B GLN* 2.7 61.1 + - + +
172B GLU* 2.5 45.2 + - + +
175B ILE* 3.7 15.9 - - + -
176B LYS* 1.3 75.3 - - - +
178B LYS* 1.3 63.9 + - - +
179B PHE* 3.6 27.6 - + - -
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Residues in contact with LYS 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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18A LYS* 5.4 3.8 - - - +
19A ASN* 2.4 38.7 + - - +
145A ASP* 5.2 0.6 + - - -
135B VAL 3.7 0.5 - - - +
136B THR* 3.4 3.0 - - - -
137B ARG* 2.8 51.5 + - + +
139B MET* 4.0 22.2 - - - +
167B SER 5.1 5.2 - - - +
168B ASP 4.7 6.5 - - - +
169B VAL* 4.6 15.9 - - + +
170B GLN* 5.1 1.1 - - - -
177B TYR* 1.3 77.6 - - - +
179B PHE* 1.3 64.7 + - - +
180B GLU* 3.4 27.4 + - + +
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Residues in contact with PHE 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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29B ASN* 5.0 1.3 - - + -
30B GLU* 4.2 5.4 - - + -
33B TYR* 3.4 58.8 - + + +
135B VAL 3.9 2.9 - - - -
136B THR* 3.4 22.9 - - + -
165B VAL* 3.5 22.8 - - + +
166B LEU* 3.8 40.6 + - + +
167B SER* 5.1 4.9 + - - +
168B ASP 5.2 1.0 + - - -
170B GLN* 3.8 25.8 - - + -
177B TYR* 3.6 27.4 - + - -
178B LYS* 1.3 73.7 - - - +
180B GLU* 1.3 61.8 + - - +
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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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19A ASN* 4.8 4.3 - - - +
33B TYR* 5.0 1.9 + - - -
134B PHE* 3.5 5.2 - - - +
135B VAL* 2.8 36.7 + - - +
137B ARG* 2.9 32.8 + - + +
158B LEU* 3.8 26.6 - - + +
178B LYS* 3.4 27.8 + - + +
179B PHE* 1.3 75.9 - - - +
181B VAL* 1.3 66.1 + - - +
182B TYR* 2.8 34.6 + - + -
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Residues in contact with VAL 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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132B LYS* 4.3 6.7 - - + -
133B LEU 3.3 5.6 - - - +
134B PHE* 3.8 36.8 - - + -
158B LEU* 3.6 5.0 - - - +
159B LEU* 2.8 52.4 + - + +
161B GLU 5.8 0.7 - - - -
162B TYR* 3.8 30.3 - - + -
165B VAL* 4.0 15.0 - - + -
180B GLU* 1.3 80.9 - - - +
182B TYR* 1.3 70.2 + - - +
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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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132B LYS* 3.2 7.6 - - - +
133B LEU* 2.8 46.7 + - + +
135B VAL* 4.0 14.8 - - + -
137B ARG* 3.0 17.6 + - - -
151B ILE* 3.6 36.1 - - + -
153B LEU* 4.1 16.4 - - + -
156B TYR* 4.1 7.6 - - + -
157B LYS 3.2 6.7 - - - -
158B LEU* 3.6 40.6 - - + +
159B LEU* 4.7 0.2 - - - -
180B GLU* 2.8 36.5 + - + -
181B VAL* 1.3 79.2 - - - +
183B GLU* 1.3 62.3 + - - +
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Residues in contact with GLU 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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130B HIS* 2.7 36.2 + - + +
131B LEU 3.3 6.1 - - - +
132B LYS* 3.6 14.1 - - + +
155B LYS 3.9 0.7 - - - +
156B TYR* 3.4 6.1 - - - -
157B LYS* 3.0 33.6 + - - +
159B LEU* 3.8 34.7 - - + +
162B TYR* 5.0 3.5 + - - -
182B TYR* 1.3 77.3 - - - +
184B LYS* 1.3 65.5 + - - +
185B ASN* 4.3 13.1 + - - +
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Residues in contact with LYS 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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125B MET 3.4 10.5 - - - +
126B ASN* 4.8 2.4 + - - +
127B HIS 2.6 29.8 + - - -
128B PRO* 4.0 1.0 - - - +
129B GLY 2.9 29.7 + - - +
130B HIS* 3.3 8.0 - - - -
131B LEU* 3.0 39.3 + - + +
155B LYS* 3.3 36.6 - - + +
156B TYR* 3.4 39.4 - - + -
183B GLU* 1.3 72.8 - - - +
185B ASN* 1.3 61.3 + - - +
186B ASP* 4.5 9.1 - - - +
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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