Contacts of the helix formed by residues 1097 - 1107 (chain M) in PDB entry 2JA7
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 GLY1097 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1079M MET* 4.6 7.4 - - - -
1081M LEU* 4.6 12.8 - - - +
1096M SER* 1.3 76.9 - - - +
1098M VAL* 1.3 54.1 + - - -
1099M PRO* 3.2 4.6 - - - +
1100M ARG* 2.4 34.1 + - - +
1101M LEU 3.0 5.9 + - - -
1355M VAL* 3.8 22.4 - - - -
1358M SER* 4.8 5.4 + - - -
1359M ASP* 5.5 0.4 - - - -
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Residues in contact with VAL1098 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830M LYS* 4.0 31.9 - - + +
833M GLU* 4.3 23.8 - - + +
834M THR* 4.5 11.4 - - - +
837M ILE* 4.4 10.6 - - + +
1076M ALA 4.3 7.0 - - - +
1079M MET* 3.9 41.7 - - + +
1081M LEU* 5.4 4.3 - - + +
1097M GLY* 1.3 67.1 - - - +
1099M PRO* 1.3 72.2 - - + +
1101M LEU* 3.2 9.7 + - - +
1102M LYS* 3.0 21.3 + - - +
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Residues in contact with PRO1099 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830M LYS* 4.5 17.7 - - - +
833M GLU* 5.0 7.9 - - - +
1081M LEU* 6.2 1.6 - - + -
1095M THR* 3.9 22.9 - - + +
1096M SER* 4.2 6.1 - - - -
1097M GLY 3.1 6.1 - - - +
1098M VAL* 1.3 98.7 - - + +
1100M ARG* 1.3 56.9 + - - +
1102M LYS* 3.2 11.6 - - + +
1103M GLU* 3.0 25.3 + - - +
1112M LYS* 4.9 14.8 - - - +
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Residues in contact with ARG1100 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1094M VAL* 6.1 4.0 - - + +
1095M THR* 4.3 20.3 + - + -
1096M SER 2.8 31.2 - - - +
1097M GLY 2.4 13.5 + - - -
1099M PRO* 1.3 71.4 - - - +
1101M LEU* 1.3 58.7 + - - +
1102M LYS 3.0 1.3 - - - -
1103M GLU* 2.7 51.3 + - - +
1104M ILE* 2.8 23.5 + - + +
1111M MET* 3.7 27.5 - - - +
1113M THR 5.0 1.0 + - - -
1330M ASN* 3.4 17.3 + - - +
1332M PHE* 4.7 5.8 - - - -
1351M GLU* 2.8 46.5 + - - +
1355M VAL* 3.8 16.6 - - + -
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Residues in contact with LEU1101 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837M ILE* 4.2 20.9 - - + -
841M LEU* 5.7 0.2 - - + -
1072M ILE* 4.9 16.4 - - + -
1076M ALA* 4.4 9.9 - - + -
1079M MET* 4.2 21.8 - - + -
1097M GLY 3.0 5.4 + - - +
1098M VAL* 3.6 10.5 - - - +
1100M ARG* 1.3 76.9 - - - +
1102M LYS* 1.3 62.8 + - - +
1104M ILE* 2.9 12.8 + - + +
1105M LEU* 2.9 50.6 + - + +
1352M VAL* 5.1 14.8 - - + -
1355M VAL* 3.8 21.7 - - + +
1356M ILE* 6.2 2.2 - - + -
1371M LEU* 6.1 0.7 - - + -
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Residues in contact with LYS1102 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24 A 5.4 10.5 - - - -
34 G 5.4 8.9 - - - -
833M GLU* 3.0 40.6 + - + +
836M TYR* 6.3 1.8 - - - -
837M ILE* 4.0 20.8 - - + +
840M ARG* 4.4 11.0 - - - +
1098M VAL 3.0 12.6 + - - +
1099M PRO* 3.2 13.9 - - + +
1101M LEU* 1.3 76.4 - - - +
1103M GLU* 1.3 60.5 + - - +
1105M LEU* 3.4 3.8 + - - +
1106M ASN* 2.4 49.4 + - - +
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Residues in contact with GLU1103 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095M THR* 3.7 23.4 + - - +
1099M PRO 3.0 13.4 + - - +
1100M ARG* 2.7 29.3 + - - +
1102M LYS* 1.3 77.7 - - - +
1104M ILE* 1.3 57.3 + - - -
1106M ASN* 3.8 5.1 + - - +
1107M VAL* 3.3 14.4 + - - -
1108M ALA* 3.5 27.1 + - + +
1110M ASN 4.7 1.6 - - - +
1111M MET* 3.4 32.9 - - + +
1112M LYS* 3.6 28.3 + - - +
1332M PHE* 5.0 2.1 - - - -
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Residues in contact with ILE1104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1100M ARG* 2.8 39.2 + - - +
1101M LEU* 2.9 9.8 + - + +
1103M GLU* 1.3 71.3 - - - +
1105M LEU* 1.3 71.1 + - + +
1106M ASN 3.1 1.8 - - - -
1107M VAL* 3.0 22.2 + - - +
1332M PHE* 4.0 12.4 - - + -
1348M LEU* 3.5 30.3 - - + -
1351M GLU* 3.9 17.0 - - + -
1352M VAL* 3.8 36.3 - - + +
1355M VAL* 3.9 17.0 - - + -
1375M MET* 4.2 3.0 - - + +
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Residues in contact with LEU1105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837M ILE* 3.5 31.6 - - + +
840M ARG* 4.0 15.9 - - + +
841M LEU* 4.0 22.9 - - + -
1101M LEU* 2.9 41.9 + - + +
1102M LYS* 4.1 2.0 - - - +
1104M ILE* 1.3 80.1 - - + +
1106M ASN* 1.3 60.9 + - - +
1107M VAL* 3.6 0.7 + - - +
1352M VAL* 5.8 0.9 - - + -
1371M LEU* 4.3 14.4 - - + -
1375M MET* 4.5 6.5 - - - -
1383M SER* 3.8 2.8 - - - -
1384M VAL* 3.0 54.4 + - + +
1385M THR* 4.0 1.2 + - - -
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Residues in contact with ASN1106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34 G 5.9 7.2 - - - +
44 T 6.1 2.0 - - - +
840M ARG* 2.6 23.9 + - - +
1102M LYS* 2.4 50.7 + - - +
1103M GLU* 4.1 5.6 - - - +
1105M LEU* 1.3 76.5 - - - +
1107M VAL* 1.3 75.2 - - - +
1108M ALA* 4.4 10.3 - - + +
1383M SER* 3.7 9.0 - - - -
1385M THR* 3.9 12.9 + - - +
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Residues in contact with VAL1107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44 T 5.2 0.9 + - - -
1103M GLU 3.3 3.1 + - - -
1104M ILE 3.0 21.5 + - - +
1106M ASN* 1.3 83.2 - - - +
1108M ALA* 1.3 62.6 + - - +
1109M LYS 3.9 1.0 + - - -
1332M PHE* 4.5 15.3 - - + -
1333M ILE* 4.2 22.2 - - + +
1375M MET* 4.0 21.3 - - + -
1381M LEU* 4.2 28.7 - - + +
1383M SER* 4.1 17.9 - - - +
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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