Contacts of the strand formed by residues 174 - 178 (chain A) in PDB entry 4WLQ
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 ARG 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ARG* 4.1 7.1 - - - +
170A PRO* 3.4 1.7 - - - +
171A VAL 2.8 31.2 + - - +
172A ASN* 4.2 6.7 - - + +
173A GLY* 1.3 83.6 - - - +
175A LEU* 1.3 61.2 + - - +
176A TYR* 3.4 31.3 - - + +
187A ASP* 2.7 39.7 + - - +
189A GLY* 3.4 12.9 - - - +
190A ALA* 3.1 30.7 - - - +
191A CYS* 3.6 3.8 - - - -
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Residues in contact with LEU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A TYR* 4.6 5.8 - - + -
169A VAL 3.8 24.5 - - - +
170A PRO* 4.5 1.1 - - + -
174A ARG* 1.3 73.0 - - - +
176A TYR* 1.3 61.4 + - - +
187A ASP* 4.1 0.2 - - - +
188A LEU* 2.8 62.8 + - + +
189A GLY 2.7 16.5 + - - +
190A ALA 5.1 0.7 - - - +
191A CYS* 3.7 14.1 - - + -
196A TRP* 4.2 20.2 - - + +
199A ALA* 4.1 8.3 - - + +
200A VAL* 3.5 37.2 - - + +
203A VAL* 4.7 2.7 - - + -
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A VAL* 4.1 9.2 - - + -
73A ARG* 3.1 44.4 + - - -
77A ILE* 3.5 28.9 - - + +
168A TYR* 3.7 2.6 - - - +
169A VAL* 3.1 36.3 + - + +
171A VAL* 3.3 43.7 + - + +
172A ASN* 5.2 2.9 - - - +
174A ARG* 3.4 27.5 - - + +
175A LEU* 1.3 77.8 - - - +
177A GLU* 1.3 60.1 + - - +
178A LEU* 4.0 18.7 + - + -
185A PRO* 4.7 1.8 - - + -
186A ILE 3.2 16.6 - - - +
187A ASP* 4.0 13.7 - - - -
188A LEU* 4.6 1.1 - - - -
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Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 4.9 7.6 + - - +
166A VAL* 4.0 10.7 - - + +
167A SER 3.6 7.0 - - - +
168A TYR* 3.2 35.4 + - + -
175A LEU 4.2 0.6 + - - -
176A TYR* 1.3 72.4 - - - +
178A LEU* 1.3 71.2 + - - +
179A ASP* 3.9 6.0 + - + +
182A ARG* 5.7 1.4 + - - -
185A PRO* 3.8 0.3 - - - +
186A ILE* 3.0 59.4 + - + +
188A LEU* 4.1 14.7 - - + +
203A VAL* 5.4 0.7 - - - +
207A ARG* 2.6 34.0 + - - -
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 4.4 7.9 - - + -
78A PHE 3.5 9.2 - - - +
79A PHE* 4.0 14.8 - - + -
95A SER* 3.8 18.4 - - - +
99A ASN* 3.5 27.4 - - - +
165A PHE 4.7 0.5 - - - +
166A VAL* 3.5 7.3 - - - +
167A SER* 2.9 49.8 + - - +
169A VAL* 4.1 15.7 - - + -
176A TYR* 4.2 11.0 - - + -
177A GLU* 1.3 76.0 - - - +
179A ASP* 1.3 60.9 + - - +
185A PRO* 3.7 26.5 - - + -
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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
------------------------------------------------------------
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