Contacts of the strand formed by residues 157 - 161 (chain B) in PDB entry 5WN0
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 VAL 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B SER* 4.4 3.1 + - - -
131B VAL* 3.7 2.1 - - - +
144B TYR* 3.6 6.6 - - - +
145B GLY* 3.2 43.7 + - - +
146B ILE* 4.4 9.9 - - + -
156B ARG* 1.3 87.3 - - + +
158B ILE* 1.3 70.9 + - - +
159B VAL* 4.0 18.6 - - + -
168B VAL* 4.0 10.3 - - + -
169B THR 3.2 9.4 - - - +
170B ALA* 4.1 7.6 - - + -
188B TRP* 4.1 15.0 - - + -
192B PHE* 4.0 21.3 - - + -
195B PHE* 5.0 0.2 - - + -
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Residues in contact with ILE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TYR* 3.2 33.7 - - + +
120B SER* 4.3 2.0 - - - -
131B VAL* 3.6 17.0 - - + +
132B GLY* 3.8 10.8 - - - -
133B LEU* 3.7 36.7 - - + +
142B VAL* 4.3 15.3 - - + -
143B SER 3.6 10.3 - - - +
144B TYR* 4.0 15.3 - - + -
157B VAL* 1.3 80.0 - - - +
159B VAL* 1.3 72.3 + - - +
160B ALA* 4.9 0.9 - - + -
167B LEU 3.7 1.4 - - - +
168B VAL* 3.3 5.2 - - - +
169B THR* 3.0 35.6 + - - +
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LYS 3.8 0.7 - - - +
142B VAL* 3.3 6.2 - - - -
143B SER* 3.0 48.2 + - - +
145B GLY 4.5 2.9 - - - +
157B VAL* 4.0 12.1 - - + -
158B ILE* 1.3 78.6 - - - +
160B ALA* 1.3 62.3 + - - +
161B GLU* 4.0 1.8 - - + +
166B VAL* 3.8 22.4 - - + -
167B LEU 3.6 2.2 - - - -
168B VAL* 4.0 7.0 - - + -
195B PHE* 3.8 31.0 - - + -
199B LEU* 3.9 23.6 - - + -
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Residues in contact with ALA 160 (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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133B LEU* 3.7 30.1 - - + -
139B PRO* 4.2 13.0 - - + -
141B LYS 3.5 6.3 - - - -
142B VAL* 4.8 2.7 - - + +
158B ILE* 4.1 1.8 - - + -
159B VAL* 1.3 72.7 - - - +
161B GLU* 1.3 60.7 + - - +
162B PHE* 3.3 22.7 + - + -
166B VAL* 4.0 1.1 - - - -
167B LEU 2.8 38.0 + - - +
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Residues in contact with GLU 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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139B PRO* 3.7 1.6 - - - +
140B LEU* 2.9 43.9 + - + +
141B LYS* 3.2 49.1 + - + +
159B VAL* 4.0 2.3 + - + +
160B ALA* 1.3 68.6 - - - +
162B PHE* 1.3 68.1 + - - +
165B PHE 4.1 1.1 - - - -
166B VAL* 3.9 17.7 - - + +
202B ARG* 4.9 12.5 + - - -
203B LYS* 3.3 30.4 + - + +
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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