Contacts of the helix formed by residues 1131 - 1141 (chain B) 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 GLY1131 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A GLY* 4.6 3.1 - - - -
1129B ARG* 2.9 28.2 + - - -
1130B PHE* 1.3 73.5 - - - +
1132B GLU* 1.3 70.3 + - - +
1133B MET 3.2 2.7 - - - -
1134B GLU* 2.7 30.7 + - - +
1135B ARG* 3.2 3.2 + - - -
35T C 5.5 0.2 - - - -
36T C 4.1 13.7 - - - -
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Residues in contact with GLU1132 (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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338A ARG* 4.1 24.1 + - - +
342A MET* 4.4 24.1 - - + +
343A GLY* 4.5 8.2 - - - +
840A ARG* 3.6 38.5 + - - +
844A LYS* 6.1 2.3 - - - +
1404A SER 5.3 1.6 - - - +
1130B PHE 3.9 0.2 + - - -
1131B GLY* 1.3 67.8 - - - -
1133B MET* 1.3 63.0 + - + +
1135B ARG* 2.3 52.2 + - - +
1136B ASP* 2.9 12.2 + - - +
35T C 5.2 8.7 + - - +
36T C 4.6 5.1 + - - +
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Residues in contact with MET1133 (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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449A PRO* 4.9 11.4 - - - -
450A SER* 3.9 21.0 - - - +
451A LEU* 3.5 32.1 - - + -
836A GLY* 5.5 7.4 - - - +
839A GLN* 4.1 22.4 - - + +
840A ARG* 5.7 4.0 - - + +
1131B GLY 3.0 1.4 + - - -
1132B GLU* 1.3 82.5 - - + +
1134B GLU* 1.3 62.1 + - - +
1136B ASP* 3.0 20.9 - - - +
1137B CYS* 3.0 28.9 + - - -
35T C 4.5 26.2 - - - +
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Residues in contact with GLU1134 (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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446A ASN* 3.0 26.2 - - - +
448A GLN* 2.6 40.4 + - - +
450A SER* 3.6 15.6 + - - +
456A MET* 4.3 6.3 - - - -
491A HIS* 5.3 1.1 - - - +
1129B ARG 4.8 0.4 - - - +
1130B PHE* 4.0 27.8 - - + -
1131B GLY* 2.7 29.9 + - - +
1133B MET* 1.3 72.8 + - - +
1135B ARG* 1.3 64.8 + - - +
1137B CYS* 3.8 5.7 - - - +
1138B MET* 2.9 28.8 + - - +
36T C 5.7 0.5 - - - +
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Residues in contact with ARG1135 (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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342A MET* 4.4 28.7 + - - +
844A LYS* 3.3 23.4 - - - +
847A GLU* 2.7 35.3 + - - +
1427A VAL* 5.5 1.2 - - - +
1428A SER* 4.5 9.8 + - - +
1431A VAL* 4.3 27.6 - - - -
1130B PHE* 4.4 10.8 - - + +
1131B GLY 3.2 5.0 + - - +
1132B GLU* 2.3 46.1 + - - +
1134B GLU* 1.3 67.6 - - - +
1136B ASP* 1.3 70.8 + - - +
1138B MET* 3.8 0.5 - - - +
1139B ILE* 2.9 53.6 + - + +
1147B LEU* 4.2 16.8 - - + +
1151B LEU* 5.4 2.2 - - + -
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Residues in contact with ASP1136 (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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450A SER 5.6 0.2 - - - +
839A GLN* 4.8 3.3 + - - +
840A ARG* 6.0 1.6 - - - -
843A VAL* 3.0 38.2 - - + +
844A LYS* 5.8 0.3 - - - +
1068A VAL* 3.7 10.0 - - + +
1072A GLN* 3.7 17.5 - - - +
1132B GLU* 2.9 9.4 + - - +
1133B MET* 3.0 37.2 + - + +
1135B ARG* 1.3 92.0 + - - +
1137B CYS* 1.3 66.9 + - - +
1139B ILE* 3.2 9.3 + - - +
1140B ALA* 2.9 14.7 + - - +
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Residues in contact with CYS1137 (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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450A SER* 3.5 34.5 - - - -
452A HIS 4.4 4.0 - - - -
453A LYS* 4.3 13.9 - - - +
455A SER* 4.9 0.7 - - - -
456A MET* 3.6 29.8 - - + -
1072A GLN* 3.8 17.5 - - - +
1133B MET 3.0 8.5 + - - +
1134B GLU 3.8 2.5 - - - +
1136B ASP* 1.3 78.8 - - - +
1138B MET* 1.3 56.2 + - - +
1140B ALA* 2.5 28.8 + - - +
1141B HIS* 2.9 20.2 + - + -
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Residues in contact with MET1138 (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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444A LEU* 4.9 3.4 - - + -
456A MET* 3.6 36.6 - - + +
502A LEU* 5.0 10.5 - - + -
506A CYS* 5.4 2.2 - - - -
1439A MET* 4.0 3.4 - - - +
1130B PHE* 3.9 17.5 - - + -
1134B GLU 2.9 20.5 + - - +
1135B ARG 4.4 1.3 - - - +
1137B CYS* 1.3 73.8 - - - +
1139B ILE* 1.3 63.0 + - - +
1141B HIS* 4.2 17.3 - - + +
1142B GLY 3.5 9.7 + - - -
1143B ALA* 3.7 35.9 + - + +
1146B PHE* 3.6 28.3 - - + -
1147B LEU* 4.5 16.0 - - + +
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Residues in contact with ILE1139 (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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847A GLU* 4.8 9.4 - - + +
1065A MET* 4.0 14.6 - - + +
1068A VAL* 3.7 23.8 - - + -
1427A VAL* 4.7 10.8 - - + -
1439A MET* 3.4 34.5 - - + +
1135B ARG* 2.9 61.1 + - + +
1136B ASP* 3.3 11.4 - - - +
1137B CYS 2.8 0.2 + - - -
1138B MET* 1.3 76.1 - - - +
1140B ALA* 1.3 57.6 + - - +
1142B GLY* 2.3 31.2 + - - -
1147B LEU* 4.3 6.5 - - + -
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Residues in contact with ALA1140 (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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453A LYS* 4.0 26.0 + - + +
1064A GLU* 4.4 13.2 - - - +
1065A MET* 5.1 7.2 + - - -
1068A VAL* 3.8 19.5 - - + -
1069A ILE* 4.3 21.5 - - + +
1072A GLN* 4.5 4.3 - - - +
1136B ASP 2.9 11.3 + - - +
1137B CYS* 2.5 14.7 + - - +
1139B ILE* 1.3 74.9 - - - +
1141B HIS* 1.3 62.2 + - - +
1142B GLY* 3.0 1.6 + - - -
88F TYR* 4.5 2.3 + - - -
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Residues in contact with HIS1141 (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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453A LYS* 2.4 45.3 + - + +
456A MET* 3.1 18.3 + - + +
505A LEU* 4.2 8.7 + - - +
506A CYS* 2.6 37.3 - - + -
511A GLN* 3.4 27.9 + - - -
1137B CYS* 2.9 26.0 + - + +
1138B MET* 4.4 16.6 - - + +
1140B ALA* 1.3 75.6 - - - +
1142B GLY* 1.3 57.4 + - - +
1143B ALA* 2.9 12.6 + - + +
88F TYR* 3.7 17.5 + - - -
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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