Contacts of the strand formed by residues 1298 - 1302 (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 ILE1298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254B ILE 3.7 1.0 - - - +
1255B VAL* 3.5 1.4 - - - -
1256B ILE* 2.8 57.2 + - + +
1259B ILE* 4.3 22.2 - - + -
1265B LYS* 4.1 16.4 - - + -
1268B LEU* 4.4 11.0 - - + -
1269B VAL* 3.8 29.8 - - + -
1272B ILE* 5.0 4.7 - - + -
1287B VAL* 4.4 14.6 - - + -
1288B ARG 3.6 9.4 - - - +
1289B ASP* 4.1 11.2 - - - +
1296B LEU* 4.2 9.4 - - + -
1297B ARG* 1.3 78.1 - - - +
1299B ALA* 1.3 61.2 + - - +
1300B ILE* 3.8 4.8 + - + -
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Residues in contact with ALA1299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253B GLN* 4.8 10.8 - - - -
1254B ILE 3.5 5.2 - - - -
1255B VAL* 4.6 9.4 - - - +
1286B GLU 3.8 1.4 - - - +
1287B VAL* 3.7 2.3 - - - +
1288B ARG* 3.0 42.5 + - - +
1290B GLU* 5.0 7.3 - - - +
1297B ARG* 3.9 8.0 + - - +
1298B ILE* 1.3 71.0 - - - +
1300B ILE* 1.3 63.2 + - - +
1301B GLU 3.9 0.9 - - - -
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Residues in contact with ILE1300 (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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1253B GLN* 3.6 2.1 - - - +
1254B ILE* 2.6 56.3 + - + +
1256B ILE* 4.0 27.8 - - + -
1272B ILE* 4.0 17.3 - - + -
1284B ILE* 4.3 33.7 - - + -
1286B GLU 3.7 3.6 - - - +
1287B VAL* 4.7 7.6 - - + +
1298B ILE* 4.6 6.5 - - + +
1299B ALA* 1.3 74.3 - - - +
1301B GLU* 1.3 62.7 + - - +
1302B LEU* 3.6 7.8 + - + +
1311B VAL* 5.2 1.3 - - + -
1315B LEU* 3.5 28.5 - - + -
1321B LEU* 5.2 0.7 - - + -
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Residues in contact with GLU1301 (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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1247B LEU* 4.1 19.5 - - + +
1251B LYS* 6.1 1.3 - - + -
1253B GLN* 3.6 13.2 - - - +
1284B ILE* 3.9 2.4 - - - +
1285B ALA* 2.8 38.1 + - + +
1286B GLU* 2.9 33.1 + - + +
1288B ARG* 3.0 28.9 + - - +
1299B ALA 3.9 1.2 - - - -
1300B ILE* 1.3 70.2 - - - +
1302B LEU* 1.3 69.5 + - - +
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Residues in contact with LEU1302 (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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1244B ILE* 6.2 0.2 - - + -
1251B LYS* 4.3 6.9 - - - +
1252B GLU* 3.3 31.8 + - + +
1254B ILE* 4.1 21.3 - - + +
1283B GLY 3.2 17.5 - - - +
1284B ILE* 4.3 5.6 - - + -
1285B ALA* 3.6 8.2 - - - +
1300B ILE* 3.6 8.5 + - + +
1301B GLU* 1.3 83.4 - - - +
1303B LYS* 1.3 66.6 + - - +
1306B ALA* 4.2 9.6 - - + +
1308B THR* 3.6 35.9 - - - +
1311B VAL* 3.5 35.4 - - + -
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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