Contacts of the helix formed by residues 1098 - 1103 (chain B) in PDB entry 1XTB
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 LEU1098 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1083B MET 3.3 25.4 - - - +
1084B PHE 4.1 3.1 - - - +
1086B GLY* 3.8 8.7 - - - +
1096B ALA* 3.9 9.4 - - + -
1097B VAL* 1.3 75.1 - - - +
1099B HIS* 1.3 65.2 + - - +
1100B VAL* 3.0 14.6 - - + +
1101B ALA* 3.2 13.3 + - + +
1102B LEU* 3.7 1.4 + - - +
1110B ILE* 3.7 28.9 - - + -
1112B VAL* 3.4 32.8 - - + -
1117B VAL* 4.5 7.0 - - + -
1268B TRP* 3.0 50.7 + - + -
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Residues in contact with HIS1099 (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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1083B MET* 4.2 14.2 - - - -
1097B VAL* 3.6 30.4 - - + +
1098B LEU* 1.3 76.5 + - - +
1100B VAL* 1.3 73.1 + - + +
1102B LEU* 3.1 29.0 + - + +
1103B ARG* 3.5 25.2 + - - +
1268B TRP 4.2 3.7 + - - +
1269B VAL* 5.4 2.5 - - + -
1270B GLY 5.5 2.0 + - - -
1273B TYR* 3.4 57.8 - + + +
1276B TRP* 4.6 0.8 - - + +
1494B GLU* 3.8 25.6 + - - +
1495B HIS* 4.8 5.1 + - - -
1509B PHE* 3.9 10.5 - + - -
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Residues in contact with VAL1100 (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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1083B MET* 4.4 7.2 - - + +
1084B PHE* 3.9 50.3 - - + -
1097B VAL 4.8 2.5 - - - +
1098B LEU* 4.1 24.0 - - + -
1099B HIS* 1.3 86.8 - - + +
1101B ALA* 1.3 63.6 + - - +
1103B ARG* 3.3 20.4 + - - +
1104B ASN* 3.2 20.2 + - - +
1110B ILE* 4.9 5.8 - - + -
1300B HIS* 5.2 0.7 + - - -
1303B ASP* 3.9 19.4 - - - +
1495B HIS* 4.1 8.1 - - + -
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Residues in contact with ALA1101 (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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1098B LEU* 3.2 23.9 + - + +
1099B HIS 3.2 0.2 - - - -
1100B VAL* 1.3 80.1 - - - +
1102B LEU* 1.3 64.7 + - - +
1103B ARG 3.2 0.7 + - - -
1104B ASN* 3.2 9.0 + - - -
1110B ILE* 3.6 28.7 - - + -
1117B VAL* 4.1 19.3 - - + -
1118B MET* 3.3 20.5 - - - +
1121B VAL* 3.8 3.7 - - + +
1268B TRP* 4.2 6.3 - - + -
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Residues in contact with LEU1102 (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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1098B LEU 4.0 7.0 - - - +
1099B HIS* 3.1 22.4 + - - +
1101B ALA* 1.3 79.4 - - - +
1103B ARG* 1.3 55.3 + - - +
1104B ASN 4.0 0.2 + - - -
1105B ARG* 5.5 0.2 + - - -
1118B MET* 5.5 0.2 - - - -
1121B VAL* 3.9 20.4 - - + +
1125B LEU* 4.3 6.8 - - - +
1266B TRP* 4.0 23.8 - - + -
1268B TRP* 4.1 5.8 - - + -
1269B VAL* 3.8 27.8 - - + -
1273B TYR 4.2 4.3 - - - +
1276B TRP* 3.8 22.2 - - + +
1277B SER* 3.5 41.7 - - - +
1296B LEU* 4.2 13.5 - - - +
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Residues in contact with ARG1103 (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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1099B HIS* 3.5 29.9 + - - -
1100B VAL* 3.7 6.5 - - - +
1101B ALA 3.1 0.4 - - - -
1102B LEU* 1.3 77.4 - - - +
1104B ASN* 1.3 59.9 + - - +
1105B ARG* 2.8 16.2 + - - +
1276B TRP* 3.0 34.2 - - - +
1296B LEU* 3.5 35.0 - - + +
1299B ALA* 3.6 15.9 - - - +
1300B HIS* 3.1 26.8 - - - +
1303B ASP* 2.6 44.3 + - - +
1491B ALA* 3.8 5.3 - - - +
1494B GLU* 2.8 30.9 + - - -
1495B HIS* 3.7 12.5 + - - -
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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