Contacts of the helix formed by residues 1098 - 1102 (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 MET1098 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486N TYR* 5.0 0.7 - - - +
778N MET* 4.9 7.2 - - - +
794N ASN* 4.7 12.1 - - - +
853N SER* 5.1 0.7 - - - -
972N LYS* 3.8 29.4 - - + +
978N ASP* 2.9 32.3 - - + +
979N LYS 5.3 0.9 - - - +
1094N ARG* 3.5 25.8 - - - +
1095N LEU 5.0 4.5 - - - +
1096N ARG* 4.0 14.4 - - + -
1097N HIS* 1.3 92.5 - - - +
1099N VAL* 1.3 70.1 + - - +
1100N ASP* 3.5 2.9 - - + +
1101N ASP* 3.1 34.8 + - - +
1102N LYS* 3.9 6.9 - - - +
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Residues in contact with VAL1099 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352M VAL* 3.6 29.8 - - + -
466M SER* 3.4 17.7 - - - -
467M THR* 3.7 9.2 - - + -
975N GLN* 4.1 10.1 - - - +
977N GLY* 3.3 37.7 + - - +
978N ASP* 3.4 9.6 + - - +
1097N HIS 4.1 0.2 + - - -
1098N MET* 1.3 70.3 - - - +
1100N ASP* 1.3 82.7 + - - +
1101N ASP 2.4 15.8 + - - -
1102N LYS* 2.4 21.2 + - - -
1103N ILE* 3.2 19.2 + - + -
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Residues in contact with ASP1100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466M SER* 2.8 25.3 + - - -
944N THR* 5.3 2.6 - - - +
975N GLN* 3.3 24.3 + - - +
978N ASP* 4.7 0.6 + - - -
1098N MET* 3.4 3.1 + - + +
1099N VAL* 1.3 78.0 - - - +
1101N ASP* 1.3 63.3 + - - +
1102N LYS 3.3 2.5 - - - -
1103N ILE* 4.7 7.2 - - - +
1122N ARG* 3.6 13.2 + - - -
1W MET* 2.8 43.3 + - - +
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Residues in contact with ASP1101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225 BRU 4.6 5.2 + - - -
235 G 4.6 5.4 + - - -
855N PHE* 5.4 0.7 - - - -
945N GLU* 5.4 6.4 - - - +
972N LYS* 3.1 35.3 + - - -
1097N HIS* 5.9 0.9 - - - -
1098N MET* 3.1 39.5 + - - +
1099N VAL 2.4 10.9 + - - -
1100N ASP* 1.3 74.1 - - - +
1102N LYS* 1.3 60.8 + - + +
1122N ARG* 3.1 28.7 + - - +
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Residues in contact with LYS1102 (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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225 BRU 5.6 14.3 - - + +
96 G 4.4 12.9 + - - -
350M ARG 4.1 3.7 - - - +
351M THR* 5.1 2.2 - - - -
352M VAL* 4.3 19.4 - - + +
484M GLY* 4.6 9.9 + - - -
486M GLU* 4.0 37.3 + - - +
1097N HIS* 3.7 47.0 + - - +
1098N MET 3.9 8.7 - - - +
1099N VAL* 2.4 18.1 + - - +
1100N ASP 3.3 0.2 - - - -
1101N ASP* 1.3 80.9 - - + +
1103N ILE* 1.3 72.3 + - + +
1104N HIS* 3.1 11.4 + - - +
1122N ARG* 2.9 11.5 + - - +
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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