Contacts of the strand formed by residues 189 - 192 (chain B) in PDB entry 1WSQ
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 HIS 189 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LYS* 2.8 37.5 + - + +
102B ASN* 3.9 8.1 - - - -
157B ASP* 3.6 1.6 - - - -
184B LEU* 3.9 1.2 - - - +
185B HIS* 3.0 49.8 + + + +
186B ASP* 2.9 30.7 + - - +
187B ARG 4.3 2.2 - - - +
188B GLY* 1.3 79.9 - - - +
190B TYR* 1.3 73.4 + - - +
191B VAL* 3.7 5.2 - - + +
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Residues in contact with TYR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASN* 2.9 26.2 + - - +
134B VAL* 3.9 16.8 - - + -
137B LEU* 3.9 24.6 - - + +
146B PHE* 6.0 0.5 - - - -
150B GLU* 5.0 4.2 + - - +
153B GLN* 4.1 7.7 - - + +
154B ILE* 3.4 47.2 - - + +
157B ASP* 2.9 29.6 + - + +
158B THR* 5.5 0.2 - - - +
182B ILE* 4.0 10.8 - - + -
183B LEU 3.3 13.5 - - - +
184B LEU* 3.4 27.6 - - + +
188B GLY* 4.2 21.0 + - - -
189B HIS* 1.3 72.7 - - - +
191B VAL* 1.3 66.9 + - - +
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Residues in contact with VAL 191 (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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101B LYS 3.5 20.9 - - - +
102B ASN* 3.3 10.1 - - - +
103B ILE 4.5 3.6 - - - +
104B VAL* 3.7 19.5 - - + +
127B ASP* 6.2 0.2 - - - +
129B CYS* 3.5 30.7 - - - -
158B THR* 6.6 0.2 - - - -
182B ILE* 3.6 7.1 - - - -
183B LEU* 2.9 40.7 + - + +
185B HIS* 4.3 12.6 - - + -
189B HIS* 3.7 11.4 - - + +
190B TYR* 1.3 81.8 - - - +
192B LEU* 1.3 61.0 + - - +
193B CYS 4.0 0.2 + - - -
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Residues in contact with LEU 192 (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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102B ASN 2.7 17.0 + - - +
103B ILE* 3.7 2.9 - - - -
104B VAL* 3.1 23.9 + - - -
158B THR* 5.1 3.3 - - + +
161B ALA* 3.8 25.5 - - + +
162B VAL* 4.5 8.5 - - + -
165B LEU* 4.8 3.6 - - + -
174B HIS* 3.7 23.6 - - + +
177B LEU* 3.8 26.7 - - + -
181B ASN* 3.6 21.5 - - + +
182B ILE* 3.7 19.7 - - + -
191B VAL* 1.3 74.1 - - - +
193B CYS* 1.3 70.1 + - - +
195B PHE* 4.0 17.0 - - + -
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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