Contacts of the helix formed by residues 1341 - 1345 (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 ASP1341 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 4.9 0.7 - - - -
187A ASP* 3.3 10.7 - - - +
189A THR* 5.3 1.6 + - - -
1339B PRO 3.0 4.0 + - - +
1340B TYR* 1.3 78.6 - - - +
1342B GLN* 1.3 66.2 + - - +
1343B TYR* 2.9 42.3 + - - +
1344B LEU* 3.0 40.8 + - + +
1345B HIS 3.9 0.5 + - - -
1382B PRO* 3.9 10.6 - - - +
1383B GLY 4.2 3.0 + - - -
1406B LEU 5.6 0.2 - - - +
1408B PRO* 3.8 24.6 - - + +
1412B GLN* 6.1 1.2 - - - +
1481B LEU* 3.7 15.3 - - - +
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Residues in contact with GLN1342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A ASN* 3.1 29.0 + - - +
187A ASP* 2.7 21.1 + - + +
189A THR* 3.9 16.4 - - + -
190A HIS* 4.0 44.1 + - + +
1341B ASP* 1.3 70.0 + - - +
1343B TYR* 1.3 65.9 + - + +
1345B HIS* 3.1 42.9 + - + +
1382B PRO* 4.6 9.7 - - - +
1385B ASN* 4.4 2.9 + - - -
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Residues in contact with TYR1343 (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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189A THR* 3.5 35.6 - - + +
193A LYS* 2.7 38.4 + - + +
1165B MET 4.6 0.7 - - - +
1168B GLU* 3.3 19.8 - - - +
1169B ALA* 3.2 39.4 + - - +
1171B LYS* 3.6 19.7 - - + -
1172B PRO* 3.2 30.4 - - + +
1341B ASP* 2.9 17.1 + - - +
1342B GLN* 1.3 78.7 - - - +
1344B LEU* 1.3 56.4 + - - +
1345B HIS* 3.2 11.1 + + - -
1346B ARG 4.8 0.5 + - - -
1412B GLN* 4.1 11.2 - - + -
1413B HIS* 2.8 14.3 + + - -
1481B LEU* 4.6 3.8 - - + -
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Residues in contact with LEU1344 (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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1165B MET* 4.9 2.2 - - - -
1169B ALA* 3.8 17.9 - - + -
1339B PRO* 3.7 30.9 - - + +
1341B ASP* 3.0 24.6 + - + +
1342B GLN 3.1 1.0 - - - -
1343B TYR* 1.3 77.1 - - - +
1345B HIS* 1.3 55.3 + - - -
1346B ARG 3.1 6.1 - - - +
1347B PHE* 3.0 46.9 + - + +
1348B ALA 4.5 0.5 + - - -
1406B LEU* 5.5 4.0 - - + +
1478B PHE* 4.6 11.9 - - + -
1481B LEU* 3.5 37.9 - - + -
1486B LEU* 4.0 15.7 - - + -
1489B LEU* 5.5 3.6 - - + -
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Residues in contact with HIS1345 (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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1168B GLU* 2.6 36.6 + - + +
1342B GLN* 3.1 36.1 + - + +
1343B TYR* 3.2 12.4 - + - -
1344B LEU* 1.3 76.5 - - - +
1346B ARG* 1.3 104.8 + - + +
1348B ALA* 5.2 3.4 + - - +
1349B ALA* 5.5 1.0 + - - +
1381B GLU* 4.6 5.0 - - - +
1382B PRO* 3.9 31.3 - - + +
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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