Contacts of the strand formed by residues 141 - 147 (chain A) in PDB entry 3WHD
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 TYR 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A PRO* 4.0 12.7 - - + +
99A LEU 4.3 2.9 - - - -
100A THR* 3.9 10.4 - - + +
134A PHE 4.6 1.6 + - - -
135A LEU* 3.6 40.8 - - + -
136A ASP* 2.8 47.1 + - - +
139A LEU* 3.8 22.7 - - + +
140A SER* 1.3 77.0 - - - +
142A PHE* 1.3 64.2 + - - +
143A LEU* 3.4 0.9 + - - +
184A VAL* 3.1 3.7 - - - +
185A LEU* 2.7 44.9 + - + +
192A TRP* 4.3 1.1 - + - -
204A SER* 3.5 19.1 - - - -
205A ARG 3.6 20.0 - - - +
206A ILE* 3.9 19.3 - - + -
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Residues in contact with PHE 142 (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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103A LYS 3.4 9.9 - - - -
105A TRP* 3.4 55.2 - + + -
108A SER* 3.7 14.8 - - - -
119A LEU* 3.8 17.4 - - + +
141A TYR* 1.3 70.7 - - - +
143A LEU* 1.3 63.6 + - - +
182A CYS* 4.0 8.3 - - + -
183A VAL 3.6 7.2 - - - -
184A VAL* 3.4 22.8 - - + +
197A VAL* 3.9 18.4 - - + -
198A PRO 4.4 0.2 - - - -
199A CYS 4.3 2.7 - - - -
201A PHE* 3.3 26.9 - - + -
203A ALA* 3.9 10.3 - - + -
204A SER 2.8 24.5 + - - +
205A ARG* 3.8 1.1 - - + -
206A ILE 3.3 23.0 + - - +
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Residues in contact with LEU 143 (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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105A TRP* 2.9 23.6 + - - -
119A LEU* 3.7 6.5 - - - +
120A MET* 3.6 20.0 - - + +
122A ILE* 3.9 26.2 - - + -
141A TYR 4.1 6.3 - - - +
142A PHE* 1.3 79.7 - - - +
144A GLY* 1.3 60.6 + - - +
145A LEU 3.2 5.1 + - - +
156A TRP* 4.3 8.3 - - + -
183A VAL* 3.0 29.6 + - + +
185A LEU* 4.2 11.4 - - + +
194A TRP* 3.7 33.4 - - + +
206A ILE* 4.1 22.9 - - + -
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Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A TRP* 3.4 12.6 - - - -
119A LEU* 3.5 21.2 - - - +
120A MET 2.9 17.8 + - - -
121A THR* 5.5 0.2 - - - -
143A LEU* 1.3 72.2 - - - +
145A LEU* 1.3 60.4 + - - +
155A ARG 3.3 2.8 - - - +
156A TRP* 3.6 9.8 - - - -
157A VAL* 3.0 32.0 + - - -
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Residues in contact with LEU 145 (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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105A TRP* 4.2 2.0 + - - -
143A LEU 3.2 3.0 - - - -
144A GLY* 1.3 77.3 - - - +
146A ARG* 1.3 60.3 + - - +
154A TRP* 3.8 27.6 - - + -
155A ARG 3.6 22.7 - - - +
156A TRP* 3.5 29.2 - - + +
162A PHE* 3.7 27.4 - - + -
169A TRP* 4.4 4.7 - - + -
182A CYS* 3.5 3.1 - - - +
183A VAL* 3.1 49.7 + - + +
194A TRP* 4.0 24.9 - - + -
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Residues in contact with ARG 146 (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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105A TRP* 3.5 41.2 - - + -
145A LEU* 1.3 76.9 - - - +
147A ASP* 1.3 65.9 + - - +
148A GLU* 3.6 33.6 + - - +
153A GLN 3.6 1.6 - - - +
154A TRP* 3.4 5.2 - - - -
155A ARG* 2.8 40.4 + - - +
180A GLU* 2.7 41.3 + - - +
181A ASN 3.5 6.1 - - - +
182A CYS* 3.6 17.7 - - - -
199A CYS* 4.0 0.9 - - - -
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Residues in contact with ASP 147 (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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146A ARG* 1.3 72.4 - - - +
148A GLU* 1.3 65.0 + - - +
149A ASN 3.3 0.9 + - - -
150A ALA* 3.3 12.0 + - - -
151A LYS 3.2 10.3 + - - -
152A GLY* 2.7 30.3 + - - -
153A GLN* 2.8 36.0 + - - +
154A TRP* 3.4 33.6 - - + -
181A ASN* 2.8 31.6 + - + +
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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