Contacts of the strand formed by residues 159 - 163 (chain B) in PDB entry 4R7P
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 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B VAL* 3.6 10.5 - - + +
112B LYS* 3.9 16.4 - - + -
139B LEU* 4.6 2.9 - - + -
142B THR* 3.9 26.7 - - + -
143B VAL* 4.1 25.4 - - + +
146B ILE* 3.8 20.4 - - + -
157B VAL 4.0 1.2 + - - -
158B PRO* 1.3 73.7 - - - +
160B VAL* 1.3 59.5 + - - +
161B LEU* 3.9 21.1 - - + -
183B VAL* 3.7 16.4 - - + +
184B LYS 3.0 7.6 + - - +
185B ILE* 3.3 13.9 - - + -
186B TYR* 2.7 33.4 + - - +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 3.7 26.0 - - + -
110B VAL 2.8 14.4 + - - +
111B VAL* 3.5 9.2 - - + +
112B LYS 3.1 25.5 + - - +
159B LEU* 1.3 77.4 - - - +
161B LEU* 1.3 64.6 + - - +
162B MET 3.7 0.7 + - - -
186B TYR* 3.6 12.8 - - + +
188B PHE* 3.6 34.5 - - + -
230B PHE* 4.0 13.2 - - + -
235B LEU* 4.5 6.1 - - + -
239B PHE* 3.7 23.6 - - + -
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Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LYS* 3.6 23.3 - - + +
114B ASN* 4.4 9.9 - - + +
139B LEU* 3.6 34.5 - - + -
159B LEU* 3.9 18.4 - - + -
160B VAL* 1.3 71.0 - - - +
162B MET* 1.3 63.4 + - - +
163B ASN* 3.2 18.3 + - - +
171B THR* 4.2 12.3 - - + -
175B LEU* 4.1 17.5 - - + -
185B ILE* 3.9 20.0 - - + -
186B TYR 2.9 17.8 + - - +
187B THR* 3.5 4.4 + - - -
188B PHE* 3.4 20.1 + - - -
252B ILE* 5.1 1.6 - - + -
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Residues in contact with MET 162 (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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111B VAL* 4.8 3.6 - - + +
112B LYS 3.0 13.9 + - - +
113B LEU* 3.8 22.7 - - + -
114B ASN* 2.7 32.4 + - - +
115B GLY* 3.8 1.0 + - - -
160B VAL 3.7 2.2 + - - -
161B LEU* 1.3 69.5 - - - +
163B ASN* 1.3 64.3 + - - +
188B PHE* 3.5 35.7 - - + +
190B GLN* 2.9 46.7 - - + +
222B GLY 4.4 5.8 - - - +
223B HIS* 4.6 4.5 - - + +
225B ASP* 4.5 0.7 - - + -
226B ILE* 3.7 40.6 - - + +
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Residues in contact with ASN 163 (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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114B ASN* 3.1 29.6 + - - +
115B GLY* 4.5 1.6 - - - -
161B LEU* 3.5 14.9 - - - +
162B MET* 1.3 76.4 - - - +
164B SER* 1.3 61.3 + - - +
167B THR* 3.8 2.9 - - - +
168B ASP* 3.3 41.8 + - + +
171B THR* 3.8 15.7 - - - +
172B LYS* 4.8 1.4 - - - +
187B THR* 3.2 20.2 + - - +
188B PHE 2.8 14.0 + - - +
189B ASN* 3.9 2.7 - - - -
190B GLN* 2.9 30.2 + - - +
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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
------------------------------------------------------------
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