Contacts of the strand formed by residues 1283 - 1287 (chain M) in PDB entry 3HOU
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 VAL1283 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706M HIS* 4.7 20.6 - - + +
707M GLY* 5.7 1.6 - - - -
1135M ARG* 5.3 0.7 - - - +
1281M ARG* 5.3 5.4 - - + -
1282M VAL* 1.3 85.9 - - - +
1284M MET* 1.3 77.0 + - - +
1285M MET* 4.7 9.6 - - + -
1306M LEU* 3.2 10.0 - - - -
1307M GLU* 2.9 40.5 + - + +
1308M THR 6.0 0.2 - - - +
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Residues in contact with MET1284 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128M GLN* 3.8 20.6 - - - +
1131M ALA* 3.6 24.7 - - + -
1132M LYS* 3.8 23.3 - - + +
1135M ARG* 3.4 33.4 - - - +
1283M VAL* 1.3 88.7 - - - +
1285M MET* 1.3 67.7 + - - +
1304M TRP* 3.9 22.1 - - + -
1305M VAL 3.7 3.8 - - - -
1306M LEU* 3.6 20.0 - - + -
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Residues in contact with MET1285 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1283M VAL* 4.7 11.0 - - + -
1284M MET* 1.3 84.4 - - - +
1286M LYS* 1.3 67.4 + - - +
1287M TYR* 3.5 28.2 + - + -
1303M GLU 3.5 1.0 - - - +
1304M TRP* 3.0 10.2 - - - -
1305M VAL* 2.5 45.3 + - - +
1307M GLU* 3.2 28.5 - - + +
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Residues in contact with LYS1286 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126M ALA* 6.6 0.4 - - - -
1285M MET* 1.3 79.0 - - - +
1287M TYR* 1.3 64.5 + - - +
1288M ASP 3.8 0.9 + - - -
1302M PRO* 4.2 29.8 - - + +
1303M GLU 3.3 9.2 - - - +
1304M TRP* 3.8 43.8 - - + +
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Residues in contact with TYR1287 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117M THR* 3.6 8.3 + - + +
1119M TYR* 4.0 22.9 - + - -
1285M MET* 3.5 22.1 + - + -
1286M LYS* 1.3 75.4 - - - +
1288M ASP* 1.3 64.9 + - - +
1289M ARG* 5.5 1.3 - - + -
1302M PRO* 3.1 4.6 - - - +
1303M GLU* 2.9 42.0 + - + +
1305M VAL* 3.5 35.9 - - + -
1307M GLU* 2.9 44.7 + - + +
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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