Contacts of the helix formed by residues 1131 - 1142 (chain N) 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 GLY1131 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205 C 3.8 16.2 - - - -
342M GLY* 4.2 7.0 - - - -
1129N ARG* 3.4 14.8 + - - +
1130N PHE* 1.3 79.4 - - - +
1132N GLU* 1.3 67.9 + - - +
1134N GLU* 2.7 22.8 + - - +
1135N ARG* 3.0 18.4 + - - +
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Residues in contact with GLU1132 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185 TT 4.0 15.8 + - - -
205 C 4.5 3.8 + - - +
332M LYS* 5.4 0.3 - - - +
337M ARG* 2.7 50.8 + - + +
341M MET* 4.2 23.4 + - + +
342M GLY* 4.5 1.4 - - - -
839M ARG* 2.5 34.8 + - + -
843M LYS* 4.3 12.1 - - - -
1401M SER 4.8 0.3 - - - +
1129N ARG* 5.3 1.9 - - - +
1131N GLY* 1.3 70.4 - - - -
1133N MET* 1.3 62.0 + - + +
1135N ARG* 2.9 22.9 + - - +
1136N ASP* 2.9 23.7 - - - +
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Residues in contact with MET1133 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185 TT 3.7 58.9 - - - +
448M PRO* 4.3 10.1 - - - -
449M SER* 3.2 34.6 - - - +
450M LEU* 5.1 5.2 - - + -
835M GLY 5.3 2.5 - - - +
838M GLN* 3.3 35.2 - - + +
839M ARG* 5.3 6.1 - - + +
1131N GLY 3.4 0.6 - - - -
1132N GLU* 1.3 74.4 - - + +
1134N GLU* 1.3 76.0 + - - +
1136N ASP* 3.3 15.1 + - - +
1137N CYS* 3.0 26.5 + - - -
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Residues in contact with GLU1134 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185 TT 5.0 1.4 + - - +
205 C 4.4 7.7 + - - +
445M ASN* 4.3 4.7 - - - +
447M GLN* 3.8 22.4 + - - +
449M SER* 3.0 22.7 + - - +
455M MET* 3.5 35.3 - - + +
490M HIS* 5.4 1.1 - - - +
1129N ARG 4.3 7.6 - - - +
1130N PHE* 3.3 29.1 - - + -
1131N GLY* 2.7 44.1 + - - +
1132N GLU 3.8 0.2 + - - -
1133N MET* 1.3 84.4 + - - +
1135N ARG* 1.3 63.0 + - - +
1137N CYS* 3.4 4.3 - - - +
1138N MET* 3.3 11.8 + - - +
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Residues in contact with ARG1135 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341M MET* 2.9 48.9 - - - +
842M VAL* 4.6 2.8 - - - +
843M LYS* 3.7 15.0 - - - +
846M GLU* 3.0 32.2 + - - +
1066M VAL* 6.2 0.6 - - - +
1424M VAL* 4.7 0.2 - - - +
1425M SER* 3.4 9.1 + - - +
1428M VAL* 4.2 13.4 - - + +
1130N PHE* 3.5 14.9 - - + -
1131N GLY 3.0 9.8 + - - +
1132N GLU* 2.9 14.8 + - - +
1134N GLU* 1.3 72.8 - - - +
1136N ASP* 1.3 83.7 + - - +
1137N CYS 2.5 4.9 + - - -
1138N MET* 2.5 32.7 + - - +
1139N ILE* 3.0 34.2 + - + +
1147N LEU* 3.9 18.2 - - + -
1151N LEU* 5.7 1.8 - - + -
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Residues in contact with ASP1136 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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838M GLN* 5.3 3.0 + - - +
839M ARG* 5.7 3.6 - - - +
842M VAL* 3.3 31.2 - - + +
1066M VAL* 3.2 18.6 - - + +
1070M GLN* 4.2 12.8 - - - +
1132N GLU* 2.9 17.1 - - - +
1133N MET* 3.3 16.2 - - - +
1135N ARG* 1.3 107.4 + - - +
1137N CYS* 1.3 57.7 + - - +
1139N ILE* 3.4 9.3 + - - +
1140N ALA 3.0 21.7 + - - -
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Residues in contact with CYS1137 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449M SER* 3.8 27.1 - - - -
451M HIS 2.8 30.1 - - - +
452M LYS* 4.4 3.8 - - - +
455M MET* 4.0 19.1 - - + -
1070M GLN* 4.1 5.2 - - - +
1133N MET 3.0 16.1 + - - -
1134N GLU 3.4 10.5 - - - +
1135N ARG 2.5 5.1 + - - -
1136N ASP* 1.3 70.5 - - - +
1138N MET* 1.3 69.0 + - - +
1140N ALA* 2.9 18.0 + - - +
1141N HIS* 2.9 16.9 + - - -
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Residues in contact with MET1138 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443M LEU* 4.1 6.3 - - + -
455M MET* 3.8 23.6 - - - +
505M CYS* 3.9 10.3 - - - -
1130N PHE* 3.4 28.7 - - + -
1134N GLU 3.5 0.4 - - - +
1135N ARG 2.5 10.4 + - - +
1137N CYS* 1.3 77.1 - - - +
1139N ILE* 1.3 62.1 + - - +
1141N HIS* 3.0 22.7 + - + +
1142N GLY 2.9 18.9 + - - -
1143N ALA* 3.0 39.6 + - + -
1146N PHE* 3.8 26.7 - - + -
1147N LEU* 4.3 20.0 - - + -
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Residues in contact with ILE1139 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846M GLU* 5.2 1.8 - - + +
1063M MET* 3.0 35.7 - - + +
1066M VAL* 3.8 22.2 - - + -
1424M VAL* 3.2 27.6 - - + -
1436M ILE* 3.7 24.0 - - + +
1135N ARG* 3.0 45.8 + - + +
1136N ASP* 3.5 10.8 - - - +
1138N MET* 1.3 76.4 - - - +
1140N ALA* 1.3 62.3 + - - +
1142N GLY* 3.2 6.6 + - - -
1143N ALA 6.0 0.4 - - - -
1147N LEU* 3.5 21.5 - - + -
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Residues in contact with ALA1140 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452M LYS* 3.6 29.4 - - + +
1062M GLU* 4.9 3.6 - - - +
1063M MET* 4.3 16.9 + - - +
1066M VAL* 3.7 20.4 - - + +
1067M LEU* 4.8 9.3 - - + +
1070M GLN* 4.2 8.1 - - - +
1136N ASP 3.0 12.0 + - - +
1137N CYS* 2.9 11.8 + - - +
1139N ILE* 1.3 78.7 - - - +
1141N HIS* 1.3 60.6 - - - +
1142N GLY* 3.2 1.6 + - - -
88R TYR* 4.7 4.2 + - - -
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Residues in contact with HIS1141 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452M LYS* 3.1 49.4 + - + +
455M MET 3.1 15.7 + - - -
504M LEU* 3.5 29.3 + - - +
505M CYS* 3.7 19.1 - - - -
510M GLN* 3.4 30.5 - - + -
1137N CYS* 2.9 19.1 + - + -
1138N MET* 3.0 30.7 + - + +
1140N ALA* 1.3 76.1 - - - +
1142N GLY* 1.3 59.6 + - - +
1143N ALA* 3.0 8.9 + - + +
88R TYR* 3.6 13.8 + - - -
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Residues in contact with GLY1142 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504M LEU* 4.7 1.3 - - - -
1063M MET* 4.8 2.0 - - - -
1436M ILE* 3.8 12.7 - - - +
1437M GLY* 4.3 0.7 - - - -
1438M THR* 3.2 26.1 + - - -
1138N MET 2.9 4.7 + - - -
1139N ILE 3.2 10.5 + - - -
1140N ALA 3.1 4.7 - - - -
1141N HIS* 1.3 79.7 - - - +
1143N ALA* 1.3 51.3 + - - +
1144N ALA* 2.6 20.0 + - - +
88R TYR* 3.6 18.6 - - - -
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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