Contacts of the helix formed by residues 1101 - 1105 (chain J) in PDB entry 4XLR
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 VAL1101 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1097J LYS 3.7 9.2 - - - +
1098J LEU* 3.1 19.3 + - - +
1099J VAL 3.4 0.8 - - - -
1100J ASP* 1.3 80.1 - - - +
1102J ALA* 1.3 64.3 + - - +
1103J HIS* 3.1 13.4 + - - -
1104J GLU* 4.1 7.6 - - - +
1371J VAL* 4.5 8.7 - - + -
1374J GLN* 3.4 39.1 + - + +
1378J TYR* 5.8 0.4 - - - +
1424J VAL* 3.9 32.5 - - + +
1427J SER* 3.7 26.2 - - - -
1428J ALA* 4.5 2.2 - - - +
1431J THR* 5.3 3.2 + - - -
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Residues in contact with ALA1102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098J LEU 3.7 5.1 + - - +
1101J VAL* 1.3 80.7 - - + +
1103J HIS* 1.3 62.5 + - - +
1104J GLU 3.2 3.4 - - - -
1105J ILE* 3.0 19.9 + - - +
1222J GLY* 3.2 20.4 - - - +
1225J ALA* 5.9 0.9 - - + -
1370J ILE* 3.9 20.0 - - + +
1371J VAL* 4.7 9.2 - - + -
1374J GLN* 3.6 30.3 - - + +
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Residues in contact with HIS1103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098J LEU 4.7 1.4 + - - -
1099J VAL* 3.1 23.5 + - + +
1100J ASP* 3.3 31.5 + - - -
1101J VAL 3.1 6.3 + - - +
1102J ALA* 1.3 77.6 - - - +
1104J GLU* 1.3 65.8 + - + +
1105J ILE 3.0 9.8 + - - +
1106J VAL* 4.6 1.7 - - - +
1222J GLY* 4.5 9.5 - - - -
1223J VAL* 4.9 0.7 - - + +
1431J THR* 4.6 4.0 + - - -
1436J SER* 3.2 16.4 + - - -
1461J GLY* 4.0 2.0 - - - -
1462J LEU* 3.1 50.1 + - + +
1463J LYS* 3.4 17.6 - - + +
1464J GLU* 3.1 42.6 + - + -
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Residues in contact with GLU1104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101J VAL 4.1 12.1 - - - +
1103J HIS* 1.3 86.2 + - + +
1105J ILE* 1.3 67.6 + - + +
1106J VAL* 3.7 2.7 + - - +
1108J ARG* 4.0 3.6 + - - -
1198J TYR* 3.3 22.3 - - - +
1374J GLN* 4.3 1.6 - - - +
1377J LYS* 3.1 25.6 + - - -
1398J TRP* 3.8 13.5 - - - -
1431J THR* 2.7 27.8 + - - -
1432J LYS* 3.4 20.6 - - - +
1460J ILE* 4.2 14.8 - - + +
1461J GLY* 3.9 25.1 - - - +
1462J LEU 4.7 0.2 - - - +
1464J GLU* 3.6 4.5 - - - +
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Residues in contact with ILE1105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102J ALA* 3.2 15.2 - - + +
1103J HIS 3.0 3.0 - - - +
1104J GLU* 1.3 84.3 - - + +
1106J VAL* 1.3 70.1 + - - +
1198J TYR 4.0 0.7 - - - -
1199J GLY* 3.5 32.3 - - - +
1200J VAL* 3.7 22.4 - - + -
1220J ALA 4.4 0.2 - - - -
1221J VAL* 3.9 5.6 - - + -
1222J GLY 3.3 19.4 + - - -
1370J ILE* 4.4 11.2 - - + -
1373J ARG* 3.3 21.5 - - - +
1374J GLN* 3.5 33.2 - - + +
1398J TRP* 3.8 11.9 - - + -
1462J LEU* 5.5 0.2 - - - +
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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