Contacts of the helix formed by residues 1090 - 1102 (chain A) in PDB entry 2DQZ
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 ASP1090 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1089A GLN* 1.3 74.2 - - - +
1091A PRO* 1.3 62.6 - - - +
1092A LYS* 3.1 21.6 + - - +
1093A ALA* 3.3 26.4 + - + +
1094A GLY* 2.7 35.2 + - - -
1145A MET 4.9 0.2 + - - -
1146A VAL* 4.3 7.0 - - + +
1295A LEU* 4.4 1.3 - - - +
1298A THR* 5.2 8.9 - - + +
1299A LEU* 3.7 26.6 - - + +
1304A LEU* 5.6 3.5 - - - +
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Residues in contact with PRO1091 (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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1086A MET* 5.5 4.0 - - + +
1089A GLN* 2.9 13.1 - - + +
1090A ASP* 1.3 87.6 - - - +
1092A LYS* 1.3 68.6 + - + +
1094A GLY* 4.6 0.9 - - - +
1095A GLN* 3.1 26.2 + - - +
1112A LEU* 3.9 24.9 - - + -
1295A LEU* 4.5 12.8 - - + -
1299A LEU* 5.0 6.7 - - + -
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Residues in contact with LYS1092 (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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1090A ASP* 3.1 10.5 + - - +
1091A PRO* 1.3 81.5 - - + +
1093A ALA* 1.3 67.2 + - - +
1095A GLN* 3.3 3.3 + - - +
1096A LEU* 3.1 23.7 + - - +
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Residues in contact with ALA1093 (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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111A PLM 3.6 33.3 - - + +
1090A ASP* 3.2 29.5 + - + +
1092A LYS* 1.3 79.2 - - - +
1094A GLY* 1.3 62.0 + - - +
1096A LEU* 3.4 7.1 + - - +
1097A LEU* 3.2 19.8 + - - +
1146A VAL* 4.4 7.4 - - + -
1304A LEU* 4.4 11.0 - - + -
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Residues in contact with GLY1094 (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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1086A MET* 5.0 8.3 - - - +
1089A GLN* 3.2 28.2 - - - +
1090A ASP 2.7 18.0 + - - -
1091A PRO* 4.0 1.1 - - - -
1093A ALA* 1.3 75.4 - - - +
1095A GLN* 1.3 60.3 + - - +
1097A LEU* 3.4 2.9 + - - +
1098A SER* 3.2 21.8 + - - -
1146A VAL* 4.2 7.5 - - - +
1147A GLY* 5.0 3.3 + - - -
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Residues in contact with GLN1095 (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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1086A MET* 5.1 9.9 - - + +
1091A PRO 3.1 17.9 + - - +
1092A LYS* 4.0 2.9 - - - +
1094A GLY* 1.3 72.2 - - - +
1096A LEU* 1.3 65.0 + - - +
1098A SER* 3.8 6.6 - - - -
1099A GLU* 3.0 42.4 + - + +
1107A ASN* 4.5 7.6 - - - +
1109A PRO* 4.1 23.4 - - + +
1110A LEU 5.1 2.1 + - - +
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Residues in contact with LEU1096 (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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111A PLM 4.7 3.6 - - + -
1092A LYS 3.1 17.1 + - - +
1093A ALA* 3.6 7.2 - - - +
1094A GLY 3.2 0.2 - - - -
1095A GLN* 1.3 78.4 - - - +
1097A LEU* 1.3 61.6 + - - +
1099A GLU* 3.1 16.9 + - - +
1100A LEU* 3.1 42.6 + - + +
1361A MET* 5.0 8.7 - - + -
1363A LEU* 3.3 31.6 - - + -
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Residues in contact with LEU1097 (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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111A PLM 4.0 14.4 - - + -
1093A ALA 3.2 13.6 + - - +
1094A GLY 3.9 3.6 - - - +
1096A LEU* 1.3 80.8 - - - +
1098A SER* 1.3 57.3 + - - +
1100A LEU* 3.2 9.7 + - + -
1101A PHE* 2.9 64.6 + - + +
1141A GLY 4.2 7.6 - - - +
1142A GLY* 3.8 19.1 - - - +
1146A VAL* 3.8 24.9 - - + -
1147A GLY* 4.8 7.0 - - - -
1152A TYR* 6.0 0.2 - - - +
1358A LEU* 5.1 1.3 - - + -
1363A LEU* 4.3 21.5 - - + -
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Residues in contact with SER1098 (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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1086A MET* 6.5 0.9 - - - -
1094A GLY 3.2 17.0 + - - -
1095A GLN* 3.8 7.6 - - - -
1096A LEU 3.2 0.2 - - - -
1097A LEU* 1.3 78.7 - - - +
1099A GLU* 1.3 57.6 + - - +
1102A THR* 2.8 35.7 + - - -
1107A ASN* 2.6 25.8 + - - -
1108A ILE 4.7 5.0 + - - -
1110A LEU* 5.8 3.1 - - - +
1148A ALA* 6.1 0.9 - - - -
1151A THR* 2.7 36.6 + - - -
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Residues in contact with GLU1099 (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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1095A GLN* 3.0 36.6 + - - +
1096A LEU* 3.1 19.7 + - + +
1098A SER* 1.3 76.9 - - - +
1100A LEU* 1.3 63.5 + - + +
1101A PHE 3.6 0.2 + - - -
1102A THR* 3.7 14.1 - - - +
1107A ASN* 3.4 29.4 + - + +
1482A LYS* 5.5 1.7 + - - -
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Residues in contact with LEU1100 (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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1096A LEU* 3.1 42.3 + - + +
1097A LEU* 3.2 8.5 + - + +
1099A GLU* 1.3 80.1 - - + +
1101A PHE* 1.3 72.0 + - + +
1102A THR 5.0 0.2 - - - -
1357A TRP* 4.5 10.8 - - + -
1358A LEU* 4.0 22.9 - - + -
1361A MET* 4.2 14.4 - - + -
1363A LEU* 4.4 7.2 - - + -
1455A PHE 5.4 0.7 - - - +
1457A SER* 4.1 28.7 - - - +
1473A PHE* 3.5 19.2 - - - -
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Residues in contact with PHE1101 (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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111A PLM 6.2 1.8 - - + -
1097A LEU* 2.9 40.2 + - + +
1100A LEU* 1.3 89.7 - - + +
1102A THR* 1.3 68.6 + - - +
1103A ASN* 3.3 4.2 + - - +
1141A GLY 5.8 4.3 - - - -
1142A GLY 6.0 0.2 - - - -
1151A THR* 4.2 7.2 - - + -
1152A TYR* 3.4 34.6 - - + +
1220A GLU* 3.4 24.9 - - - -
1221A SER* 5.6 2.0 - - - -
1358A LEU* 3.5 38.6 - - + -
1468A HIS* 4.0 11.0 - + - -
1469A GLY* 4.2 14.4 - - - -
1472A LEU* 3.6 20.7 - - + +
1473A PHE* 4.1 10.8 - + - -
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Residues in contact with THR1102 (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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1098A SER 2.8 21.7 + - - +
1099A GLU* 3.7 16.3 - - - +
1101A PHE* 1.3 79.8 - - - +
1103A ASN* 1.3 57.8 + - - +
1104A ARG* 2.9 38.5 - - - +
1107A ASN* 3.6 23.9 + - + +
1151A THR* 2.9 28.4 + - - +
1473A PHE* 3.7 7.4 - - - -
1482A LYS* 3.3 17.0 + - - +
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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