Contacts of the helix formed by residues 1138 - 1150 (chain I) in PDB entry 6PSU
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 VAL1138 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137I GLU* 1.3 78.7 - - - +
1139I ALA* 1.3 67.1 + - + +
1140I LYS 3.4 1.1 - - - -
1141I LEU* 3.7 5.7 - - - +
1142I ARG* 2.9 35.5 + - - +
1166I ASP* 3.0 38.6 - - - +
1169I VAL* 4.8 6.9 - - + +
1170I MET* 4.0 14.8 - - + -
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Residues in contact with ALA1139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1137I GLU* 3.9 3.7 - - + +
1138I VAL* 1.3 86.4 - - + +
1140I LYS* 1.3 58.3 + - - +
1142I ARG* 3.2 14.6 + - - +
1143I GLU* 2.9 32.1 + - - +
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Residues in contact with LYS1140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131I MET* 3.5 28.1 - - + +
1136I GLN* 3.0 38.9 - - - +
1137I GLU* 3.0 35.0 + - + +
1138I VAL 3.4 0.4 - - - -
1139I ALA* 1.3 75.3 - - - +
1141I LEU* 1.3 65.1 + - - +
1143I GLU* 3.2 12.9 + - + +
1144I PHE* 2.9 25.0 + - + +
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Residues in contact with LEU1141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128I ILE* 4.3 12.1 - - + +
1131I MET* 3.3 52.2 - - + +
1132I LEU* 3.6 26.0 - - + -
1136I GLN* 5.3 0.9 - - + -
1137I GLU* 4.1 15.0 - - - +
1138I VAL* 3.7 8.0 - - - +
1139I ALA 3.3 0.2 - - - -
1140I LYS* 1.3 80.5 - - - +
1142I ARG* 1.3 61.7 + - - +
1144I PHE* 3.9 1.0 - - - +
1145I ILE* 3.0 36.0 + - + +
1169I VAL* 4.2 8.5 - - + +
1170I MET* 3.8 19.7 - - + -
1173I ALA* 3.8 17.0 - - + -
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Residues in contact with ARG1142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138I VAL* 2.9 23.8 + - - +
1139I ALA* 3.4 11.9 - - - +
1140I LYS 3.2 0.2 - - - -
1141I LEU* 1.3 74.8 - - - +
1143I GLU* 1.3 59.4 + - - +
1145I ILE* 4.7 1.6 - - - -
1146I GLN* 2.9 35.3 + - + +
1161I LEU* 3.2 47.5 + - + +
1164I PHE 4.7 1.1 + - - -
1165I SER* 3.1 39.4 - - - +
1166I ASP* 4.0 15.1 + - - +
1169I VAL* 4.3 11.6 - - + +
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Residues in contact with GLU1143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1139I ALA* 2.9 15.9 + - - +
1140I LYS* 3.4 16.4 - - + +
1142I ARG* 1.3 77.7 - - - +
1144I PHE* 1.3 62.8 + - - +
1146I GLN* 3.6 5.0 - - - +
1147I ARG* 3.0 29.9 + - - +
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Residues in contact with PHE1144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124I ILE* 3.9 22.0 - - + -
1127I LYS* 3.5 36.1 - - + -
1128I ILE* 3.4 33.0 - - + -
1131I MET* 3.7 24.5 - - + -
1140I LYS* 2.9 16.7 + - + +
1141I LEU 3.9 1.6 - - - +
1143I GLU* 1.3 74.8 - - - +
1145I ILE* 1.3 71.7 + - + +
1147I ARG* 2.9 27.5 - - - +
1148I ALA* 2.9 21.1 + - + +
1201I LEU* 4.1 25.6 - - + -
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Residues in contact with ILE1145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128I ILE* 3.6 37.0 - - + -
1141I LEU* 3.0 27.0 + - + +
1142I ARG* 4.0 3.8 - - - +
1144I PHE* 1.3 78.9 - - - +
1146I GLN* 1.3 60.1 + - - +
1148I ALA* 3.1 6.2 + - - +
1149I TYR* 2.9 56.1 + - + -
1161I LEU* 4.7 11.0 - - + -
1169I VAL* 4.8 6.7 - - + +
1172I LEU* 3.8 31.0 - - + +
1173I ALA* 4.4 13.9 - - + -
1176I LEU* 4.8 0.4 - - + -
1180I MET* 5.7 0.4 - - + -
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Residues in contact with GLN1146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142I ARG* 2.9 21.5 + - + +
1143I GLU* 3.6 6.1 - - - +
1145I ILE* 1.3 79.3 - - - +
1147I ARG* 1.3 53.3 + - - +
1149I TYR* 3.1 13.9 + - - +
1150I ASP* 2.7 38.5 + - - +
1159I VAL 3.3 17.9 + - - -
1160I ASP* 3.0 30.7 - - - +
1161I LEU* 3.0 25.3 + - + +
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Residues in contact with ARG1147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143I GLU* 3.0 22.1 + - - +
1144I PHE* 2.9 37.5 - - + +
1146I GLN* 1.3 77.2 - - - +
1148I ALA* 1.3 57.3 + - - +
1150I ASP* 2.9 28.9 - - - +
1151I LEU* 4.1 6.4 - - - +
1201I LEU* 3.7 29.2 - - + +
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Residues in contact with ALA1148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I LYS* 3.8 15.8 - - - +
1124I ILE* 4.3 10.5 - - + -
1144I PHE* 2.9 15.9 + - + +
1145I ILE* 3.1 10.7 + - - +
1147I ARG* 1.3 80.8 - - - +
1149I TYR* 1.3 60.5 + - - +
1150I ASP 3.2 1.6 + - - -
1151I LEU* 4.0 9.8 - - - +
1180I MET* 3.8 23.3 - - + +
1198I LEU* 5.4 3.0 - - + +
1201I LEU* 3.7 27.1 - - + -
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Residues in contact with TYR1149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I ILE* 2.6 48.0 + - + +
12I ARG 4.4 0.2 - - - -
13I LYS* 3.7 38.7 + - + -
1145I ILE* 2.9 47.5 + - + +
1146I GLN* 3.1 10.9 + - - +
1148I ALA* 1.3 75.4 - - - +
1150I ASP* 1.3 59.1 + - - +
1155I VAL* 5.6 2.8 - - - +
1157I GLN* 4.1 12.1 + - - +
1159I VAL* 3.4 39.1 - - + +
1161I LEU* 5.5 3.1 - - + -
1172I LEU* 4.0 9.0 - - + -
1176I LEU* 3.0 24.2 - - + +
1180I MET* 3.8 14.2 - - + +
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Residues in contact with ASP1150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I LYS* 5.2 0.2 - - - +
1146I GLN* 2.7 31.5 + - - +
1147I ARG* 2.9 23.1 - - - +
1148I ALA 3.1 0.4 - - - -
1149I TYR* 1.3 78.0 - - - +
1151I LEU* 1.3 64.5 + - - +
1155I VAL* 5.4 6.7 - - + -
1158I LYS* 5.8 9.6 - - + -
1159I VAL 5.6 2.0 - - - +
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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