Contacts of the strand formed by residues 165 - 171 (chain B) in PDB entry 2W7U
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 LEU 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B VAL* 4.5 22.2 - - + -
29B VAL* 4.4 15.7 - - + -
35B VAL* 5.6 3.1 - - + -
101B THR* 4.0 18.1 - - + +
102B LYS 2.7 19.2 + - - +
103B PHE* 3.7 23.4 - - + -
104B ALA* 2.9 26.2 + - - +
157B PRO* 4.2 11.2 - - + -
158B VAL 3.8 4.7 - - - +
159B LEU* 3.8 10.9 - - + +
164B GLU* 1.3 69.2 - - - +
166B ILE* 1.3 62.1 + - - +
167B GLY 3.4 30.3 - - - +
186B PHE* 3.7 20.7 - - + +
191B LYS* 5.9 0.3 - - - -
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Residues in contact with ILE 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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104B ALA* 4.3 11.7 - - + -
106B GLY 5.4 0.9 - - - -
107B ALA* 3.8 22.9 - - + +
111B ASP* 5.9 1.6 - - + +
113B ILE* 3.7 22.7 - - + -
135B ILE* 4.4 1.3 - - + -
143B MET* 4.2 13.7 - - + -
158B VAL* 2.9 15.1 + - + +
159B LEU 4.1 0.7 - - - -
160B ASN* 3.7 32.5 - - + +
164B GLU 4.0 5.6 - - - +
165B LEU* 1.3 77.1 - - - +
167B GLY* 1.3 58.9 + - - +
185B TYR* 3.7 31.0 - - + -
186B PHE* 3.1 32.5 + - - +
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Residues in contact with GLY 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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143B MET* 3.8 8.1 - - - +
157B PRO 3.6 0.5 - - - -
158B VAL 2.7 33.1 + - - -
165B LEU* 3.4 8.9 - - - +
166B ILE* 1.3 82.2 - - - +
168B ILE* 1.3 59.8 + - - +
184B VAL 3.2 14.4 - - - -
186B PHE* 3.6 15.3 - - - -
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Residues in contact with ILE 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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27B VAL* 3.8 22.0 - - + -
35B VAL* 4.2 16.4 - - + +
36B THR* 3.6 31.4 - - - +
37B ASN* 4.0 8.3 - - + -
78B ASP 3.7 19.7 - - - +
79B LEU* 4.5 4.9 - - + -
155B GLY* 3.7 19.7 - - - +
156B SER 3.3 6.1 - - - +
158B VAL* 4.4 2.9 - - - -
165B LEU* 5.1 0.2 - - + -
167B GLY* 1.3 79.0 - - - +
169B LEU* 1.3 63.9 + - - +
183B GLY* 3.2 4.0 - - - -
184B VAL* 2.9 39.6 + - + +
186B PHE* 4.3 11.9 - - + -
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Residues in contact with LEU 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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37B ASN* 3.8 3.3 + - - +
115B VAL* 4.4 11.2 - - + -
145B PHE* 3.7 33.2 - - + -
149B ALA* 3.9 25.6 - - + -
153B ASN* 3.5 33.2 - - + +
154B SER* 4.3 4.5 - - - +
155B GLY* 2.9 25.3 + - - -
156B SER* 2.9 14.4 + - - +
158B VAL* 4.2 3.3 - - + +
168B ILE* 1.3 74.4 - - - +
170B TYR* 1.3 66.1 + - - +
171B ALA* 3.8 21.3 - - - +
172B GLY 5.0 0.4 - - - +
181B ASN* 4.0 7.0 - - + +
182B PHE 3.8 8.1 - - - +
183B GLY* 4.3 1.8 - - - -
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Residues in contact with TYR 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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37B ASN* 3.9 12.3 + - + +
78B ASP* 3.7 47.9 - - + +
142B PHE* 3.7 23.9 - + - -
154B SER* 4.0 11.3 + - - -
168B ILE* 5.4 0.2 - - + -
169B LEU* 1.3 79.9 - - - +
171B ALA* 1.3 73.6 + - + +
182B PHE* 3.1 44.7 + - + +
183B GLY 3.6 22.7 - - - -
184B VAL* 3.7 11.4 - - + -
172D GLY 5.5 1.4 + - - -
182D PHE* 5.2 3.5 - - - -
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Residues in contact with ALA 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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154B SER* 5.6 0.2 - - - -
169B LEU* 3.8 8.8 - - - +
170B TYR* 1.3 105.4 - - + +
172B GLY* 1.3 65.8 + - - +
181B ASN* 3.7 5.7 - - - +
182B PHE* 2.9 37.3 + - + +
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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