Contacts of the strand formed by residues 192 - 198 (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 TRP 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLN* 3.7 13.0 + - - +
132A ILE* 3.6 52.4 + - + +
135A LEU* 3.6 38.3 + - + -
136A ASP 3.5 19.3 - - - -
137A ARG* 3.6 34.0 - - + +
139A LEU 3.9 7.4 - - - -
141A TYR* 4.3 1.3 - + - -
185A LEU* 3.7 17.3 - - + -
186A VAL* 3.4 30.5 - - - -
187A TYR* 3.4 38.6 - + + -
191A LYS* 1.3 79.5 - - - +
193A ALA* 1.3 62.5 + - - +
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Residues in contact with ALA 193 (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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128A GLN* 4.6 2.2 - - - +
168A PHE* 3.2 13.9 - - + +
169A TRP 3.9 2.0 - - - +
170A HIS* 3.3 37.8 + - + +
185A LEU* 3.7 7.7 - - - +
186A VAL 3.0 33.0 + - - +
191A LYS* 4.4 12.3 - - - -
192A TRP* 1.3 76.1 - - - +
194A TRP* 1.3 68.3 + - - +
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Residues in contact with TRP 194 (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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122A ILE* 4.1 20.2 - - + +
128A GLN* 2.8 26.3 + - - -
143A LEU* 3.7 17.2 - - + +
145A LEU* 4.0 17.5 - - + -
156A TRP* 4.1 21.3 - + - -
162A PHE* 5.3 0.9 - + - -
166A ARG 4.0 6.7 - - - -
167A VAL* 3.6 34.3 - - + -
168A PHE* 2.7 47.1 + + + +
169A TRP* 3.6 35.8 - + + -
170A HIS* 2.9 27.1 + - - +
173A GLU* 3.9 1.7 - - - +
183A VAL* 4.0 13.2 - - + -
184A VAL 3.5 3.6 - - - -
185A LEU* 4.0 8.1 - - + -
193A ALA* 1.3 77.2 - - - +
195A ASN* 1.3 60.1 + - - +
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Residues in contact with ASN 195 (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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169A TRP* 4.1 4.3 - - - -
170A HIS* 4.6 2.5 - - + -
173A GLU* 2.9 19.5 + - - +
183A VAL* 3.3 3.3 - - - -
184A VAL* 2.9 38.5 + - + +
186A VAL* 3.6 24.5 - - + +
193A ALA 3.9 0.2 + - - -
194A TRP* 1.3 75.4 - - - +
196A ASP* 1.3 62.3 + - - +
197A VAL* 3.8 18.8 - - - +
501A CA 2.3 29.8 - - - -
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Residues in contact with ASP 196 (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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154A TRP* 3.9 26.7 - - + -
169A TRP* 3.9 6.3 - - + -
173A GLU* 2.8 9.8 + - - +
174A PRO* 3.4 14.7 - - + +
175A ASP 3.0 11.0 + - - -
176A ASN* 2.9 40.0 + - - +
181A ASN* 4.6 5.2 - - + +
182A CYS 3.3 4.7 - - - +
195A ASN* 1.3 79.0 - - - +
197A VAL* 1.3 61.1 + - - +
501A CA 2.4 50.3 - - - -
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Residues in contact with VAL 197 (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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140A SER* 6.3 0.2 - - - -
142A PHE* 3.9 20.6 - - + -
176A ASN* 3.9 5.2 - - - +
181A ASN* 3.4 1.0 - - - -
182A CYS 2.6 39.5 + - - +
184A VAL* 4.1 19.3 - - + -
195A ASN* 3.8 17.5 - - - +
196A ASP* 1.3 79.9 - - - +
198A PRO* 1.3 79.9 - - + +
201A PHE* 3.6 32.8 - - + -
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Residues in contact with PRO 198 (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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142A PHE* 4.4 0.3 - - - -
176A ASN* 3.8 13.2 - - - +
180A GLU 3.6 9.2 - - - +
181A ASN* 3.9 4.9 - - - +
197A VAL* 1.3 94.6 - - + +
199A CYS* 1.3 58.9 + - - +
200A ASN* 3.1 22.7 - - - +
201A PHE* 2.9 55.3 + - + +
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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