Contacts of the helix formed by residues 1130 - 1141 (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 ILE1130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1128A LEU 4.0 0.8 + - - +
1129A ASP* 1.3 78.1 + - - +
1131A GLU* 1.3 85.8 + - + +
1132A LYS 3.4 0.4 - - - -
1133A ALA* 3.0 10.6 + - + +
1134A LYS* 2.8 38.8 + - + +
1287A MET* 5.4 4.9 - - + -
1307A TRP* 3.9 39.7 - - + +
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Residues in contact with GLU1131 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1129A ASP* 2.8 12.3 + - - +
1130A ILE* 1.3 89.2 - - + +
1132A LYS* 1.3 64.5 + - + +
1134A LYS* 3.0 35.2 + - - +
1135A VAL* 3.0 28.1 + - + +
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Residues in contact with LYS1132 (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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1125A GLU* 3.8 20.4 + - - +
1126A ILE* 3.5 35.0 - - + -
1129A ASP* 2.6 27.7 + - - +
1131A GLU* 1.3 73.8 - - + +
1133A ALA* 1.3 60.4 + - - +
1135A VAL* 3.2 8.6 + - - +
1136A ILE* 2.9 26.7 + - - +
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Residues in contact with ALA1133 (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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1122A LEU* 4.5 10.1 - - + -
1126A ILE* 3.3 20.7 - - + +
1129A ASP 4.2 3.4 - - - +
1130A ILE* 3.0 18.4 + - + +
1132A LYS* 1.3 80.2 - - - +
1134A LYS* 1.3 62.0 + - - +
1136A ILE* 3.2 7.0 + - - +
1137A GLN* 2.9 20.3 + - - +
1287A MET* 3.6 29.3 - - + +
1307A TRP* 5.0 5.6 - - + -
1309A LEU* 4.9 1.4 - - - +
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Residues in contact with LYS1134 (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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1130A ILE* 2.8 26.1 + - + +
1131A GLU* 3.0 36.6 + - - +
1133A ALA* 1.3 73.7 - - - +
1135A VAL* 1.3 63.8 + - + +
1137A GLN* 3.4 3.6 + - - +
1138A SER* 3.0 25.2 + - - -
1208A GLN* 5.2 11.8 + - - +
1287A MET* 4.0 15.3 - - + -
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Residues in contact with VAL1135 (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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1131A GLU 3.0 15.0 + - - +
1132A LYS* 3.7 8.7 - - - +
1134A LYS* 1.3 76.4 - - + +
1136A ILE* 1.3 65.7 + - + +
1138A SER* 2.6 24.9 + - - +
1139A SER* 2.9 12.0 + - - -
1208A GLN* 5.2 9.9 - - - +
1277A ARG* 6.3 0.7 - - - +
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Residues in contact with ILE1136 (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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1122A LEU* 4.0 18.2 - - + -
1126A ILE* 4.3 18.6 - - + -
1132A LYS 2.9 16.7 + - - +
1133A ALA* 3.6 9.0 - - - +
1135A VAL* 1.3 77.4 - - + +
1137A GLN* 1.3 66.9 + - - +
1139A SER* 2.4 29.3 + - - +
1140A ILE* 3.0 17.4 + - + +
1309A LEU* 4.0 18.8 - - + -
1322A VAL* 5.1 2.9 - - + -
1323A PRO* 3.4 26.0 - - + +
1324A GLY* 4.6 6.5 - - - +
1325A VAL* 4.6 3.6 - - + -
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Residues in contact with GLN1137 (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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1133A ALA 2.9 16.4 + - - +
1134A LYS* 3.8 4.7 - - - +
1136A ILE* 1.3 76.0 - - - +
1138A SER* 1.3 56.8 + - - +
1140A ILE* 2.5 29.0 + - - +
1141A GLU* 2.9 18.3 + - + +
1285A VAL* 2.4 58.9 + - + +
1286A TYR* 4.3 0.6 - - - +
1287A MET* 3.8 27.7 - - + +
1309A LEU* 4.2 17.0 - - + -
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Residues in contact with SER1138 (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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1134A LYS 3.0 10.0 + - - -
1135A VAL* 2.6 30.0 + - - +
1137A GLN* 1.3 80.0 - - - +
1139A SER* 1.3 60.7 + - - +
1141A GLU* 3.7 22.5 + - - +
1207A LYS* 5.7 4.0 - - - -
1208A GLN* 3.4 27.9 + - - -
1277A ARG* 3.5 24.8 + - - +
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Residues in contact with SER1139 (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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1135A VAL* 2.9 13.0 + - - -
1136A ILE* 2.4 30.8 + - - +
1138A SER* 1.3 77.8 + - - +
1140A ILE* 1.3 61.6 + - - +
1277A ARG* 4.2 13.8 - - - +
1278A GLY* 3.2 25.6 + - - -
1279A ILE* 5.2 1.6 - - - +
1322A VAL* 4.3 16.1 - - - +
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Residues in contact with ILE1140 (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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1120A VAL* 4.6 11.4 - - + -
1136A ILE* 3.0 28.5 + - + +
1137A GLN* 2.5 15.9 + - - +
1139A SER* 1.3 76.2 - - - +
1141A GLU* 1.3 65.1 + - - +
1142A TYR 2.7 5.4 + - - -
1278A GLY* 3.4 8.0 - - - -
1279A ILE* 3.4 13.8 + - + +
1282A ILE* 4.4 14.6 - - + +
1285A VAL* 4.0 20.0 - - + -
1309A LEU* 4.5 12.3 - - + -
1311A THR* 5.1 4.3 - - + -
1319A VAL* 4.9 20.9 - - + -
1322A VAL* 4.5 17.9 - - + -
1325A VAL* 4.6 14.8 - - + -
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Residues in contact with GLU1141 (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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1137A GLN* 2.9 15.8 + - + +
1138A SER* 3.9 22.3 - - - +
1139A SER 3.5 0.4 - - - -
1140A ILE* 1.3 72.6 - - - +
1142A TYR* 1.3 69.3 + - - +
1143A THR* 3.0 21.2 + - - +
1147A ASN* 5.9 0.9 - - - +
1206A ASP 5.0 1.7 - - - +
1207A LYS* 2.6 42.9 + - - +
1277A ARG* 3.5 3.6 - - - +
1278A GLY* 3.4 10.6 + - - -
1282A ILE 4.6 0.7 - - - -
1283A SER 4.8 10.0 - - - +
1284A LYS* 5.5 10.1 - - - +
1285A VAL* 4.4 16.5 - - + +
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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