Contacts of the helix formed by residues 1087 - 1100 (chain A) in PDB entry 3MPX
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 GLN1087 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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998A ASP* 5.1 3.4 + - - +
1037A LEU* 3.8 36.1 - - + +
1085A MSE 3.1 5.8 - - + +
1086A GLU* 1.3 84.3 - - + +
1088A GLY* 1.3 55.4 + - - +
1089A GLU 3.5 1.8 - - - -
1090A ASN* 3.5 28.5 + - - +
1091A LEU* 2.8 36.7 + - - +
1111A GLY* 6.0 2.6 - - - +
1112A ARG 4.6 6.1 + - - -
1113A GLU* 6.2 0.4 - - - +
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Residues in contact with GLY1088 (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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1044A PHE* 3.8 5.4 - - - -
1081A ALA* 3.6 27.4 - - - -
1082A ASN* 3.7 8.3 - - - +
1085A MSE 3.2 19.0 + - - +
1087A GLN* 1.3 73.6 - - - +
1089A GLU* 1.4 63.1 + - - +
1091A LEU* 3.4 6.7 + - - +
1092A GLN* 3.1 24.1 + - - +
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Residues in contact with GLU1089 (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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8A UNX 3.6 15.3 - - - -
1082A ASN* 3.6 19.8 + - + +
1086A GLU 5.1 1.3 + - - +
1088A GLY* 1.4 72.5 - - - +
1090A ASN* 1.3 57.2 + - - +
1092A GLN* 3.4 7.4 + - - +
1093A LYS* 3.0 40.5 + - - +
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Residues in contact with ASN1090 (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 GLU 5.4 2.1 + - - +
1087A GLN* 3.5 26.1 + - - +
1088A GLY 3.4 0.2 - - - -
1089A GLU* 1.3 76.3 - - - +
1091A LEU* 1.4 64.3 + - - +
1093A LYS* 3.2 21.6 + - - +
1094A LEU* 3.0 47.3 + - - +
1112A ARG 3.0 24.4 + - - -
1113A GLU* 3.4 11.7 - - - +
1114A PHE* 3.0 23.6 + - - +
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Residues in contact with LEU1091 (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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1037A LEU* 3.5 36.6 - - + +
1040A VAL* 4.1 10.1 - - + -
1041A GLN* 3.7 30.1 - - + +
1044A PHE* 3.7 24.2 - - + -
1085A MSE 4.8 2.7 - - + -
1087A GLN* 2.8 23.8 + - - +
1088A GLY 3.7 4.9 - - - +
1090A ASN* 1.4 70.3 - - - +
1092A GLN* 1.3 57.8 + - - +
1094A LEU* 3.6 5.1 + - + -
1095A VAL* 3.0 35.6 + - + +
1108A LEU* 3.6 31.2 - - + -
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Residues in contact with GLN1092 (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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1044A PHE* 3.7 24.8 - - + -
1047A GLN* 3.8 19.9 + - - -
1078A THR* 5.2 0.9 + - - -
1082A ASN* 3.0 26.2 + - - +
1088A GLY 3.1 13.0 + - - +
1089A GLU* 3.5 9.1 + - - +
1090A ASN 3.2 0.2 - - - -
1091A LEU* 1.3 73.6 - - - +
1093A LYS* 1.4 66.3 + - + +
1095A VAL* 3.0 2.9 + - - -
1096A HIS* 3.0 47.1 + - + +
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Residues in contact with LYS1093 (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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1089A GLU* 3.0 37.2 + - - +
1090A ASN* 3.3 25.9 + - - +
1092A GLN* 1.4 76.7 - - + +
1094A LEU* 1.4 53.4 + - - +
1096A HIS* 3.3 4.7 + - - +
1097A ILE* 2.8 46.0 + - + +
1114A PHE* 3.5 51.5 + - + -
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Residues in contact with LEU1094 (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 ASN* 3.0 41.4 + - - +
1091A LEU* 4.1 6.5 - - + +
1093A LYS* 1.4 72.6 - - - +
1095A VAL* 1.4 60.7 + - + +
1097A ILE* 4.5 2.7 - - + -
1098A GLU* 3.0 28.1 + - - +
1107A LEU* 3.3 49.3 + - + +
1108A LEU* 4.5 14.1 - - + +
1109A GLN 5.1 1.1 - - - +
1112A ARG* 4.3 13.0 - - + +
1114A PHE* 4.1 22.2 - - + +
1136A MSE 4.2 20.2 - - + -
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Residues in contact with VAL1095 (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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1041A GLN* 3.8 33.4 - - + +
1044A PHE* 3.7 42.8 - - + +
1045A GLN* 3.9 14.1 - - + +
1048A VAL* 4.2 9.2 - - + -
1091A LEU* 3.0 23.4 + - + +
1092A GLN 3.0 5.7 + - - +
1094A LEU* 1.4 75.8 - - + +
1096A HIS* 1.4 62.9 + - + +
1098A GLU* 3.5 4.8 + - - +
1099A HIS* 3.2 22.5 + - - +
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Residues in contact with HIS1096 (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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1044A PHE* 4.7 2.7 + - + +
1047A GLN* 4.2 15.8 + - + -
1048A VAL* 3.3 35.2 - - + +
1092A GLN* 3.0 54.7 + - + +
1093A LYS* 3.8 4.7 - - - +
1095A VAL* 1.4 79.6 - - + +
1097A ILE* 1.4 55.8 + - + +
1099A HIS* 3.6 3.6 + - - +
1100A SER* 3.1 29.3 + - - -
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Residues in contact with ILE1097 (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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1093A LYS* 2.8 32.9 + - + +
1094A LEU* 4.5 4.5 - - + +
1096A HIS* 1.4 69.7 - - + +
1098A GLU* 1.3 67.5 + - - +
1100A SER* 3.0 17.8 + - - -
1101A VAL* 3.1 17.9 - - + +
1107A LEU* 3.6 19.5 - - + -
1114A PHE* 3.4 39.9 - - + -
1117A GLU* 5.2 2.9 - - - +
1134A PHE* 3.7 37.7 - - + -
1136A MSE 5.3 2.5 - - + -
1141A LEU* 4.0 13.0 - - + -
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Residues in contact with GLU1098 (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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1094A LEU 3.0 19.8 + - - +
1095A VAL* 3.9 5.4 - - - +
1096A HIS 3.4 0.4 - - - -
1097A ILE* 1.3 77.3 - - - +
1099A HIS* 1.3 57.4 + - - +
1101A VAL* 3.1 24.9 - - - +
1104A GLN* 3.5 14.1 - - - +
1105A GLY 3.9 21.1 - - - +
1106A ASP* 4.8 1.1 - - - -
1107A LEU* 3.5 19.8 - - + +
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Residues in contact with HIS1099 (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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899A GLU* 5.1 15.5 + - - -
1048A VAL* 3.5 42.0 + - + +
1049A LEU* 4.9 4.5 - - + +
1052A ASP* 2.8 34.8 + - + -
1095A VAL 3.2 15.6 + - - +
1096A HIS 3.8 4.9 - - - +
1098A GLU* 1.3 77.9 - - - +
1100A SER* 1.4 56.6 + - - +
1101A VAL 4.6 2.1 - - - +
1150A LYS* 2.7 50.0 + - - +
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Residues in contact with SER1100 (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 HIS 3.1 15.2 + - - -
1097A ILE* 3.0 18.7 + - - +
1098A GLU 3.2 0.2 + - - -
1099A HIS* 1.4 76.0 - - - +
1101A VAL* 1.3 63.0 + - - +
1102A ARG 3.5 0.9 + - - -
1134A PHE* 4.1 3.1 - - - -
1149A GLY 4.9 2.2 - - - -
1150A LYS* 3.4 25.5 - - - +
1151A TYR* 3.1 47.1 + - - -
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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