Contacts of the strand formed by residues 1278 - 1282 (chain B) in PDB entry 2QOM
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 PHE1278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1261B SER* 3.3 3.1 - - - -
1262B VAL* 2.8 53.8 + - + +
1263B GLY* 5.1 2.5 - - - -
1264B LEU* 6.4 2.2 - - + -
1276B LEU* 3.8 31.6 - - + -
1277B GLU* 1.3 73.9 - - - +
1279B GLU* 1.3 61.8 + - - +
1291B ALA 3.4 4.3 - - - +
1292B VAL* 3.8 34.8 - - + -
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Residues in contact with GLU1279 (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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1024B ASN* 4.8 7.7 + - - -
1027B LYS* 4.1 16.9 - - - +
1046B MET* 3.8 22.8 - - + +
1259B LEU* 5.1 16.3 - - + +
1260B MET 3.4 9.0 - - - +
1261B SER* 4.0 17.9 - - - -
1277B GLU* 4.6 10.7 - - + +
1278B PHE* 1.3 78.2 - - - +
1280B LYS* 1.3 67.9 + - - +
1288B VAL* 4.8 2.7 - - + -
1290B ASN* 3.8 3.8 - - - +
1291B ALA* 3.0 40.4 + - + +
1293B ASN* 5.4 1.0 - - + +
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Residues in contact with LYS1280 (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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1259B LEU* 4.0 3.7 - - - +
1260B MET* 3.1 51.5 + - + +
1279B GLU* 1.3 79.3 - - - +
1281B SER* 1.3 74.3 + - - +
1282B ALA* 6.0 2.0 - - - -
1288B VAL* 3.4 20.8 - - - +
1289B ASP* 3.8 16.2 - - - +
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Residues in contact with SER1281 (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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1257B ARG* 3.8 11.0 - - - -
1258B MET 3.1 14.1 - - - -
1259B LEU* 3.9 16.4 - - - -
1260B MET* 5.2 2.9 - - - -
1280B LYS* 1.3 87.9 - - - +
1282B ALA* 1.3 62.8 + - - +
1287B ASN* 2.6 27.2 + - - +
1288B VAL* 2.8 35.3 + - - +
1289B ASP* 5.5 0.3 - - - +
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Residues in contact with ALA1282 (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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1257B ARG* 3.5 0.9 - - - -
1258B MET* 2.8 34.1 + - + +
1260B MET* 4.7 13.7 - - - -
1280B LYS* 6.0 1.8 - - - -
1281B SER* 1.3 78.3 - - - +
1283B PHE* 1.3 89.3 + - + +
1284B GLY 3.1 5.2 + - - -
1287B ASN* 3.0 10.8 + - - +
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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