Contacts of the strand formed by residues 158 - 162 (chain A) in PDB entry 3QOW
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 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ASP 3.9 2.7 + - - +
157A ASP* 1.3 75.3 - - - +
159A PHE* 1.3 59.8 + - - +
160A VAL* 5.8 1.3 - - + -
180A LYS* 3.8 38.8 - - + +
181A HIS* 3.8 30.5 - - + +
183A TYR* 4.8 11.7 - - + +
234A ASN* 3.6 23.6 - - + +
235A THR* 3.2 8.1 - - + +
236A SER* 2.9 16.7 + - - +
237A VAL* 2.9 25.9 + - - -
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Residues in contact with PHE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A MET* 3.8 22.0 - - + -
153A MET* 4.1 22.4 - - + -
157A ASP 4.2 0.2 - - - -
158A LEU* 1.3 73.8 - - - +
160A VAL* 1.3 69.7 + - - +
161A ASP* 3.8 20.0 - - + -
169A VAL* 4.1 5.4 - - + -
170A VAL* 4.5 10.8 - - + -
173A VAL* 3.9 26.0 - - + -
179A CYS* 4.3 2.7 - - - -
181A HIS 3.4 6.5 + - - +
182A HIS* 3.3 31.8 - - + +
183A TYR* 2.9 26.5 + - - -
237A VAL* 3.3 28.5 - - + -
239A PHE* 3.6 28.3 - - + -
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 5.1 1.1 - - + -
159A PHE* 1.3 86.7 - - - +
161A ASP* 1.3 62.1 + - - +
162A LEU* 3.6 29.5 + - + -
183A TYR* 3.2 27.8 - - + +
185A VAL* 4.7 0.4 - - + -
228A TRP* 3.8 22.7 - - + -
231A ARG* 6.3 0.2 - - + -
235A THR* 3.4 31.9 - - + +
237A VAL 3.0 6.7 + - - -
238A ILE* 3.5 7.8 - - + +
239A PHE 2.8 32.9 + - - +
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Residues in contact with ASP 161 (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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159A PHE* 3.8 8.6 - - + -
160A VAL* 1.3 72.5 - - - +
162A LEU* 1.3 69.7 + - - +
163A GLY 3.5 0.7 + - - -
164A SER* 3.4 14.0 - - - +
169A VAL* 3.4 19.3 - - + +
170A VAL* 3.7 21.9 - - + +
183A TYR 2.9 8.5 + - - +
184A GLY* 3.5 0.7 - - - -
185A VAL* 3.2 26.7 + - - +
239A PHE* 3.3 24.9 - - + +
240A VAL* 4.6 0.3 - - - -
417A SAM 2.9 33.1 + - - -
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Residues in contact with LEU 162 (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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160A VAL* 3.6 20.0 - - + -
161A ASP* 1.3 72.5 - - - +
163A GLY* 1.3 65.2 + - - +
185A VAL* 4.0 6.1 - - + -
223A PHE* 3.7 33.7 - - + -
228A TRP* 4.4 2.9 - - + -
232A ILE* 4.2 17.7 - - + -
238A ILE* 3.7 38.6 - - + -
239A PHE 2.9 7.9 + - - +
240A VAL* 3.5 31.2 - - + +
241A ASN 4.4 1.7 + - - -
245A PHE* 4.3 3.1 - - - -
253A LEU* 3.8 26.2 - - + -
257A PHE* 4.2 4.9 - - + -
417A SAM 5.7 0.2 - - - +
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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