Contacts of the helix formed by residues 1091 - 1109 (chain A) in PDB entry 5M64
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 VAL1091 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1086A ILE* 6.1 3.1 - - - +
1089A LEU 5.3 3.6 - - - +
1090A ASP* 1.3 85.9 + - - +
1092A GLU* 1.3 78.3 + - + +
1093A SER 3.2 3.1 + - - -
1095A LEU* 3.2 36.8 + - + +
1133A LEU* 3.8 35.6 - - + +
1168A ALA* 6.5 0.9 - - + -
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Residues in contact with GLU1092 (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* 3.0 28.2 - - - +
1091A VAL* 1.3 85.3 - - + +
1093A SER* 1.3 62.4 + - - +
1095A LEU* 3.9 7.6 - - - -
1096A LYS* 3.0 31.0 + - - +
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Residues in contact with SER1093 (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* 3.7 29.9 + - - +
1091A VAL 3.2 0.2 - - - -
1092A GLU* 1.3 83.0 - - - +
1094A ALA* 1.3 72.3 + - - +
1096A LYS* 3.8 4.5 - - - +
1097A TYR* 3.3 23.0 + - - +
1127A TYR* 5.7 11.5 - - - -
1132A TYR* 4.0 15.5 - - - +
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Residues in contact with ALA1094 (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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1091A VAL 3.8 1.8 + - - -
1093A SER* 1.3 83.3 + - - +
1095A LEU* 1.3 57.3 + - - +
1097A TYR* 4.1 3.8 - - - +
1098A SER* 3.1 27.1 + - - -
1123A VAL* 4.5 8.5 - - + +
1127A TYR* 5.6 14.1 - - + -
1132A TYR* 5.3 4.7 - - + -
1133A LEU 3.3 23.1 + - - +
1134A GLY* 3.6 4.3 - - - +
1135A SER* 3.6 25.4 - - - +
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Residues in contact with LEU1095 (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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1091A VAL* 3.2 31.5 + - + +
1092A GLU* 4.3 4.5 - - - +
1093A SER 3.2 0.6 - - - -
1094A ALA* 1.3 78.5 - - - +
1096A LYS* 1.3 64.1 + - - +
1098A SER* 3.6 6.7 - - - +
1099A LYS* 3.1 33.3 + - + +
1133A LEU 5.0 0.2 - - - +
1134A GLY* 4.1 21.3 - - - +
1167A ARG* 5.3 18.4 - - + -
1171A GLN* 4.9 10.5 - - + +
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Residues in contact with LYS1096 (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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1092A GLU* 3.0 20.8 + - + +
1093A SER* 3.8 5.2 - - - +
1095A LEU* 1.3 77.0 - - - +
1097A TYR* 1.3 65.7 + - + +
1099A LYS* 3.3 8.6 + - - +
1100A LYS* 3.1 58.4 + - - +
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Residues in contact with TYR1097 (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 SER 3.3 13.3 + - - +
1094A ALA* 4.6 3.6 - - - +
1096A LYS* 1.3 81.8 - - + +
1098A SER* 1.3 61.5 + - - +
1100A LYS* 3.2 12.6 + - + +
1101A THR* 2.9 40.5 + - + +
1119A LYS 4.7 0.3 + - - -
1120A TYR* 3.5 27.7 - + - -
1121A ASP* 2.7 51.1 + - - -
1123A VAL* 3.5 22.9 - - + -
1126A LYS* 3.2 29.2 - - - -
1127A TYR* 5.1 8.3 - + + -
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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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1094A ALA 3.1 22.8 + - - -
1095A LEU* 3.6 12.2 - - - +
1096A LYS 3.2 0.2 - - - -
1097A TYR* 1.3 77.8 - - - +
1099A LYS* 1.3 58.7 + - - +
1101A THR* 2.7 21.5 + - - -
1102A LEU* 2.7 27.1 + - - +
1123A VAL* 3.9 11.6 - - - +
1134A GLY 5.0 7.0 + - - -
1136A VAL* 5.2 1.9 - - - +
1141A GLN* 3.5 20.8 + - - -
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Residues in contact with LYS1099 (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 LEU* 3.1 20.4 + - + +
1096A LYS* 3.3 8.5 + - - +
1098A SER* 1.3 84.7 - - - +
1100A LYS* 1.3 60.7 + - + +
1102A LEU* 3.9 9.9 - - + +
1103A LYS* 2.9 30.7 + - - +
1145A GLU* 3.4 23.2 + - - -
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Residues in contact with LYS1100 (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 LYS* 3.1 43.6 + - - +
1097A TYR* 3.4 18.4 - - + +
1098A SER 3.2 0.4 - - - -
1099A LYS* 1.3 79.3 - - + +
1101A THR* 1.3 56.7 + - - +
1103A LYS* 3.4 12.2 + - + +
1104A TYR* 2.9 31.7 + - - +
1120A TYR* 4.1 28.0 - - + +
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Residues in contact with THR1101 (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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1097A TYR* 2.9 48.4 + - + +
1098A SER* 2.7 25.1 + - - -
1100A LYS* 1.3 72.5 - - - +
1102A LEU* 1.3 63.9 + - - +
1104A TYR* 4.2 4.3 - - - +
1105A ARG* 2.9 54.2 + - - +
1120A TYR* 4.3 13.0 - - + +
1121A ASP 3.9 8.7 - - - +
1123A VAL* 4.1 10.3 - - + +
1141A GLN* 5.1 1.6 + - - -
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Residues in contact with LEU1102 (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* 2.7 32.8 + - - +
1099A LYS* 3.9 14.6 - - + +
1100A LYS 3.3 0.2 - - - -
1101A THR* 1.3 74.9 + - - +
1103A LYS* 1.3 57.9 + - - +
1105A ARG* 3.7 13.4 - - - +
1106A LYS* 3.0 36.5 + - + +
1141A GLN* 3.3 39.0 - - + +
1142A ASP* 4.7 12.1 - - - +
1145A GLU* 3.8 34.1 - - - +
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Residues in contact with LYS1103 (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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1099A LYS 2.9 18.8 + - - +
1100A LYS* 3.8 13.5 - - + +
1102A LEU* 1.3 74.1 - - - +
1104A TYR* 1.3 64.7 + - - +
1106A LYS* 3.2 14.0 - - + +
1107A LYS* 3.1 53.2 + - + +
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Residues in contact with TYR1104 (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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1100A LYS 2.9 18.4 + - - +
1101A THR* 4.2 2.9 - - - +
1103A LYS* 1.3 77.4 - - - +
1105A ARG* 1.3 62.4 + - + +
1107A LYS* 3.7 28.3 + - - +
1108A HIS* 4.0 12.7 + - + +
1116A GLN* 3.8 15.4 + - + +
1117A SER* 3.4 31.2 + - - -
1118A VAL* 5.3 0.4 - - - -
1119A LYS* 2.4 40.9 + - + -
1120A TYR* 3.5 47.1 - + + -
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Residues in contact with ARG1105 (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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1101A THR* 2.9 57.1 + - - +
1102A LEU* 3.7 25.9 - - + +
1104A TYR* 1.3 80.3 - - + +
1106A LYS* 1.3 63.7 + - - +
1107A LYS 3.2 1.1 + - - -
1108A HIS* 3.5 9.0 + - - +
1109A SER* 3.2 15.4 + - - -
1116A GLN* 5.8 4.7 - - - +
1120A TYR 5.5 0.4 + - - -
1122A PRO* 5.1 3.4 - - - +
1138A GLU* 3.1 39.9 + - - -
1141A GLN* 4.4 2.0 - - - +
1142A ASP* 5.3 1.6 - - - -
207E ARG* 3.0 42.7 - - - +
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Residues in contact with LYS1106 (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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1102A LEU* 3.0 25.5 + - + +
1103A LYS* 3.2 20.2 - - + +
1105A ARG* 1.3 73.8 - - - +
1107A LYS* 1.3 66.3 + - + +
1109A SER* 2.7 22.5 + - - +
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Residues in contact with LYS1107 (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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1103A LYS* 3.1 47.0 + - + +
1104A TYR* 3.7 31.1 - - - +
1105A ARG 3.2 0.6 - - - -
1106A LYS* 1.3 83.5 - - + +
1108A HIS* 1.3 63.4 + - - +
1109A SER* 4.7 0.3 - - - -
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Residues in contact with HIS1108 (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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1104A TYR* 4.0 8.8 + - + +
1105A ARG* 3.5 6.5 + - - +
1106A LYS 3.4 0.2 - - - -
1107A LYS* 1.3 80.7 - - - +
1109A SER* 1.3 67.4 + - - +
1110A LYS* 2.6 62.8 + - - +
1111A GLU* 2.5 61.2 + - + +
1116A GLN* 3.8 32.6 - - + +
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Residues in contact with SER1109 (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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1105A ARG 3.2 9.2 + - - -
1106A LYS* 2.7 34.2 + - - -
1107A LYS 4.6 0.7 - - - -
1108A HIS* 1.3 79.0 - - - +
1110A LYS* 1.3 57.3 + - - +
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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