Contacts of the strand formed by residues 195 - 201 (chain B) in PDB entry 3WOR
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 ASP 195 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B SER* 5.4 0.5 + - - -
193B ILE* 3.7 2.5 - - - +
194B LYS* 1.3 76.5 - - - +
196B VAL* 1.3 63.9 + - - +
197B ARG* 2.8 40.5 + - - +
229B ARG 3.9 0.5 - - - +
230B ALA* 3.9 1.6 - - - -
231B TYR* 3.0 41.4 + - + +
239B ALA 3.4 17.3 + - - +
241B PHE* 3.5 22.5 - - - +
245B ASN* 2.7 27.3 + - - +
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Residues in contact with VAL 196 (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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117B SER* 3.8 3.6 + - - -
118B ALA* 2.9 26.8 + - + +
119B GLY 4.6 3.0 + - - +
122B ALA* 3.9 31.6 + - + +
123B ARG* 3.9 9.6 - - - +
124B VAL* 3.9 25.1 - - + -
193B ILE* 4.0 9.9 - - + +
194B LYS 3.9 1.2 + - - -
195B ASP* 1.3 77.8 - - - +
197B ARG* 1.3 68.3 + - - +
228B TYR* 3.7 42.6 - - + -
229B ARG 3.6 5.4 - - - +
230B ALA* 5.3 0.9 - - - -
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Residues in contact with ARG 197 (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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112B THR 4.9 2.6 + - - -
113B ALA* 5.8 0.2 - - - +
115B GLU* 3.9 27.8 + - + +
116B VAL 3.3 13.5 - - - +
117B SER* 4.3 3.8 - - - -
118B ALA* 4.0 0.4 - - - +
195B ASP* 2.8 36.9 + - - +
196B VAL* 1.3 81.8 - - - +
198B LEU* 1.3 59.8 + - - +
228B TYR* 3.0 9.2 - - - -
229B ARG 2.6 42.0 + - - +
231B TYR* 3.4 45.8 + - + -
241B PHE* 3.6 21.2 - - - -
242B SER 3.1 23.0 + - - -
243B LYS* 3.9 25.5 + - - +
245B ASN* 3.9 3.2 + - - +
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Residues in contact with LEU 198 (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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88B ALA* 4.7 4.5 - - + -
91B ALA* 4.6 5.8 - - + +
92B ILE* 3.8 43.3 - - + +
95B ASN* 4.9 0.2 - - - +
102B LEU* 4.8 5.4 - - + -
107B PHE* 3.3 43.5 - - + -
115B GLU* 3.5 6.6 - - - -
116B VAL* 2.8 38.5 + - + +
117B SER 5.2 2.2 - - - +
118B ALA* 4.3 6.4 - - - +
197B ARG* 1.3 70.3 - - - +
199B ALA* 1.3 58.7 + - - +
200B TYR 4.1 12.6 - - - +
201B ALA* 4.7 0.4 - - + -
227B PHE 3.7 15.3 - - - +
228B TYR* 4.2 19.4 - - + -
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Residues in contact with ALA 199 (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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80B LEU* 4.3 19.1 - - + -
107B PHE* 3.9 5.3 - - - -
108B ASN* 4.4 1.4 - - - +
109B ALA* 3.2 27.9 + - + +
115B GLU* 3.8 26.2 - - + +
197B ARG 3.6 0.6 + - - -
198B LEU* 1.3 74.6 - - - +
200B TYR* 1.3 62.8 + - - +
227B PHE* 2.8 18.0 + - + +
228B TYR 4.3 5.6 - - - -
229B ARG* 4.5 2.0 - - - +
714B LEU* 4.4 9.2 - - + +
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Residues in contact with TYR 200 (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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107B PHE* 3.2 16.7 - - - -
108B ASN* 4.0 8.7 - - - -
198B LEU* 3.8 5.4 - - - +
199B ALA* 1.3 79.0 - - - +
201B ALA* 1.3 63.6 + - - +
202B PRO* 3.6 15.3 - - + +
225B PHE* 3.4 23.3 - + - -
226B ALA* 3.5 3.1 - - - +
227B PHE* 2.8 51.9 + + + +
704B ILE* 3.8 9.4 - - - +
705B MET* 3.8 13.3 - - + +
709B TYR* 2.6 57.9 + + - +
710B PRO 4.4 1.8 - - - -
711B ALA* 3.6 24.7 - - + -
714B LEU* 3.7 16.4 - - + -
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Residues in contact with ALA 201 (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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85B HIS* 4.6 1.3 - - + +
92B ILE* 3.6 36.3 - - + -
102B LEU 5.7 0.2 - - - +
106B GLY* 3.2 2.4 - - - -
107B PHE* 2.7 45.7 + - + +
198B LEU* 4.7 1.6 - - + -
200B TYR* 1.3 79.3 - - - +
202B PRO* 1.3 76.6 - - + +
226B ALA* 4.4 4.0 - - + -
709B TYR* 3.5 3.1 - - - -
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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