Contacts of the strand formed by residues 1186 - 1191 (chain B) in PDB entry 1W21
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 SER1186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140B LEU* 3.8 2.8 - - - +
1184B GLY 3.7 0.4 - - - -
1185B TRP* 1.3 100.6 - - - +
1187B SER* 1.3 62.6 + - - +
1200B CYS* 3.2 6.1 - - - +
1201B MET* 2.9 29.7 + - - +
1231B ARG* 3.7 9.1 - - - +
1232B THR* 3.0 24.9 + - - -
1234B GLU* 2.5 27.3 + - - -
2477B SIA 4.2 3.1 - - - -
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Residues in contact with SER1187 (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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1127B TYR* 3.1 20.8 + - - -
1140B LEU* 4.0 14.8 - - - +
1164B LEU* 3.4 22.5 - - - +
1186B SER* 1.3 77.6 + - - +
1188B THR* 1.3 59.4 + - - +
1199B ILE 3.1 15.0 - - - -
1200B CYS* 4.1 4.3 - - - -
1232B THR* 3.5 8.9 - - - +
1234B GLU* 2.8 42.1 + - - -
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Residues in contact with THR1188 (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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1127B TYR* 3.4 8.0 + - - -
1164B LEU* 4.3 1.7 - - - +
1187B SER* 1.3 76.2 - - - +
1189B SER* 1.3 68.3 + - - +
1198B SER* 3.5 0.2 - - - -
1199B ILE* 2.9 51.1 + - + +
1232B THR* 4.1 8.5 - - + +
1233B GLN* 3.8 10.5 + - - -
1235B SER 2.8 24.0 + - - -
1237B CYS* 3.4 17.9 + - - +
1246B VAL* 3.9 30.1 - - + -
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Residues in contact with SER1189 (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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1127B TYR* 3.6 16.5 + - - -
1129B SER* 3.9 0.3 + - - -
1138B PHE* 3.7 12.8 - - - -
1164B LEU* 4.4 0.9 - - - -
1188B THR* 1.3 81.8 + - - +
1190B CYS* 1.3 59.0 + - - +
1196B ARG* 2.8 28.9 + - - -
1197B MET 2.9 15.9 + - - -
1198B SER* 3.0 17.2 + - - -
1235B SER 4.1 2.2 + - - -
1236B GLU* 3.0 14.6 - - - +
1237B CYS* 2.9 22.9 + - - -
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Residues in contact with CYS1190 (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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1129B SER* 3.9 4.3 - - - +
1189B SER* 1.3 71.9 + - - +
1191B HIS* 1.3 58.2 + - - +
1192B ASP 4.1 0.7 + - - -
1196B ARG* 3.3 11.0 - - - +
1197B MET* 2.8 51.1 + - - +
1236B GLU* 5.2 1.1 - - - +
1237B CYS* 2.0 69.8 - - - +
1238B VAL* 3.9 1.1 - - - +
1239B CYS* 3.8 19.4 - - - -
1244B CYS* 4.0 1.3 - - - -
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Residues in contact with HIS1191 (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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1091B LEU* 4.7 2.6 - - - +
1129B SER* 4.5 0.2 + - - -
1130B CYS 3.6 21.7 + - - +
1131B ASP* 3.3 23.1 - - + +
1132B PRO* 3.5 18.3 - - + +
1190B CYS* 1.3 74.5 - - - +
1192B ASP* 1.3 61.1 + - - +
1193B GLY* 2.9 31.7 + - - -
1194B MET 3.3 28.7 + - - -
1195B SER* 3.5 24.4 - - - -
1196B ARG* 3.5 19.5 + - + +
1239B CYS* 3.8 10.9 + - - +
1420B TRP* 3.4 17.7 - - + -
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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