Contacts of the strand formed by residues 1308 - 1312 (chain A) in PDB entry 6A5T
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 ALA1308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119A THR* 5.3 2.2 - - + -
1120A VAL 3.9 11.2 - - - +
1121A TYR* 4.6 19.1 - - + +
1122A LEU* 5.3 3.4 - - - -
1287A MET* 4.3 1.3 - - - +
1288A VAL* 2.9 33.5 + - - +
1289A LYS* 4.8 0.2 - - - +
1290A HIS* 3.9 30.1 - - + +
1307A TRP* 1.3 76.5 - - - +
1309A LEU* 1.3 72.8 + - - +
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Residues in contact with LEU1309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1119A THR* 3.7 2.3 - - - +
1120A VAL* 2.8 48.4 + - + +
1122A LEU* 4.1 16.4 - - + -
1133A ALA 4.9 0.9 - - - +
1136A ILE* 4.0 27.8 - - + -
1137A GLN* 4.2 17.0 - - + +
1140A ILE* 4.5 10.5 - - + -
1285A VAL* 4.3 13.2 - - + -
1286A TYR 3.5 13.9 - - - +
1287A MET* 3.7 29.6 - - + -
1288A VAL* 5.2 0.2 - - - -
1308A ALA* 1.3 83.2 - - - +
1310A GLU* 1.3 70.0 + - - +
1311A THR* 5.4 0.4 - - + -
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Residues in contact with GLU1310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117A ALA* 6.2 0.9 - - + -
1118A LEU 3.3 17.3 - - - +
1119A THR* 4.3 14.0 + - + +
1285A VAL* 3.3 5.0 - - - +
1286A TYR* 2.9 39.7 + - + +
1288A VAL* 4.2 19.5 - - + +
1290A HIS* 3.1 33.6 + - + -
1309A LEU* 1.3 81.0 - - - +
1311A THR* 1.3 65.8 + - - +
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Residues in contact with THR1311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116A PRO 4.2 1.0 - - - +
1117A ALA* 3.9 9.7 - - - +
1118A LEU* 2.8 56.5 + - + +
1120A VAL* 4.5 13.0 - - + -
1140A ILE* 5.1 4.9 - - + -
1282A ILE* 3.7 25.8 - - + -
1284A LYS 3.6 5.6 - - - -
1285A VAL* 4.0 12.8 - - + -
1286A TYR* 5.3 0.4 - - - -
1309A LEU* 5.1 0.4 - - + -
1310A GLU* 1.3 85.9 - - - +
1312A ASP* 1.3 71.0 + - - +
1313A GLY 3.3 4.6 + - - -
1319A VAL* 6.2 0.7 - - + -
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Residues in contact with ASP1312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115A THR* 5.7 8.9 - - + +
1116A PRO 4.6 3.3 - - - +
1281A GLY 3.7 0.3 - - - +
1282A ILE* 3.5 2.6 - - - -
1283A SER* 3.1 39.2 + - - +
1284A LYS* 2.9 37.7 + - - +
1286A TYR* 3.4 29.5 + - - -
1311A THR* 1.3 81.6 - - - +
1313A GLY* 1.3 61.6 + - - +
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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