Contacts of the strand formed by residues 1284 - 1289 (chain B) in PDB entry 4Z4Q
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 ILE1284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272B ILE* 4.9 5.6 - - + -
1275B VAL* 4.5 21.3 - - + -
1276B ARG* 3.2 51.6 + - + +
1281B VAL* 4.5 9.7 + - + +
1283B GLY* 1.3 79.2 - - - +
1285B ALA* 1.3 57.8 + - - +
1286B GLU 4.0 6.1 - - - +
1287B VAL* 4.4 7.0 - - + -
1300B ILE* 4.3 22.2 - - + -
1301B GLU 4.2 1.6 - - - -
1302B LEU* 4.3 4.5 - - + -
1303B LYS* 3.5 14.0 - - - +
1311B VAL* 4.1 31.0 - - + -
1315B LEU* 4.4 10.1 - - + -
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Residues in contact with ALA1285 (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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1276B ARG* 3.7 12.9 + - - -
1283B GLY 3.4 3.2 + - - -
1284B ILE* 1.3 73.7 - - - +
1286B GLU* 1.3 60.9 + - + +
1301B GLU* 2.8 34.2 + - + +
1302B LEU 3.6 16.8 - - - +
1303B LYS* 3.8 12.5 - - + +
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Residues in contact with GLU1286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A GLN* 5.9 0.7 - - - +
1276B ARG* 4.2 6.7 - - - +
1284B ILE* 3.6 3.5 - - - +
1285B ALA* 1.3 85.2 - - + +
1287B VAL* 1.3 71.9 + - - +
1288B ARG* 3.0 40.6 + - + +
1299B ALA 3.8 1.4 - - - +
1300B ILE* 3.7 2.3 - - - +
1301B GLU* 2.9 43.2 + - + +
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Residues in contact with VAL1287 (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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420A GLN* 5.3 0.2 + - - -
1269B VAL* 3.7 34.5 - - + +
1272B ILE* 3.8 24.2 - - + +
1273B ASP* 3.8 40.4 + - + +
1276B ARG* 4.9 0.2 - - + -
1284B ILE* 4.4 13.5 - - + -
1286B GLU* 1.3 79.8 - - - +
1288B ARG* 1.3 70.7 + - - +
1298B ILE* 4.4 14.1 - - + -
1299B ALA 3.7 4.5 - - - +
1300B ILE* 4.7 6.5 - - + -
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Residues in contact with ARG1288 (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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420A GLN* 3.7 29.4 - - + +
1253B GLN* 3.0 20.0 + - - -
1269B VAL* 5.6 0.2 - - - -
1286B GLU* 3.0 35.7 + - - +
1287B VAL* 1.3 80.1 - - - +
1289B ASP* 1.3 62.6 + - - +
1290B GLU* 2.1 43.9 + - + +
1298B ILE* 3.6 4.2 - - - -
1299B ALA* 3.0 39.2 + - - +
1301B GLU* 3.0 33.5 + - - +
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Residues in contact with ASP1289 (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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420A GLN* 3.3 17.9 + - - +
447A ARG* 3.3 42.5 + - - +
1109B ASP* 4.1 6.1 - - - +
1265B LYS* 3.2 29.9 - - - +
1266B ALA* 5.5 1.7 - - - -
1269B VAL* 4.3 26.3 - - + +
1288B ARG* 1.3 71.7 - - - +
1290B GLU* 1.3 60.8 + - - +
1291B SER* 2.8 26.7 + - - -
1297B ARG 3.5 3.9 - - - +
1298B ILE* 4.1 5.2 - - - +
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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