Contacts of the helix formed by residues 1098 - 1102 (chain B) in PDB entry 2R92
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A VAL* 5.8 0.2 - - - -
778B MET* 5.4 7.0 - - - +
794B ASN* 5.4 6.7 - - - +
853B SER* 5.5 0.2 - - - -
972B LYS* 3.8 30.5 - - + +
978B ASP* 2.9 34.5 - - + +
979B LYS 5.4 1.1 - - - +
1094B ARG* 3.6 20.0 - - - +
1095B LEU 5.0 4.5 - - - +
1096B ARG* 3.8 15.5 - - + -
1097B HIS* 1.3 97.3 - - - +
1099B VAL* 1.3 65.9 + - - +
1100B ASP* 3.5 2.9 - - + +
1101B ASP* 3.1 36.4 + - - +
1102B LYS* 3.9 7.5 - - - +
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Residues in contact with VAL1099 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A VAL* 3.7 26.7 - - + +
466A SER* 3.3 33.0 - - - +
975B GLN* 3.8 16.4 - - - +
977B GLY* 3.5 33.5 + - - +
978B ASP* 3.7 9.5 + - - +
1098B MET* 1.3 71.8 - - - +
1100B ASP* 1.3 82.0 + - - +
1101B ASP 2.6 13.5 + - - -
1102B LYS* 2.6 16.9 + - - +
1103B ILE* 3.1 18.0 + - + +
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Residues in contact with ASP1100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A SER* 2.7 29.1 + - - -
944B THR* 5.0 2.6 - - - +
975B GLN* 2.9 25.5 + - - +
1098B MET* 3.4 3.7 + - + +
1099B VAL* 1.3 77.5 - - - +
1101B ASP* 1.3 60.2 + - - +
1102B LYS 3.3 2.5 - - - -
1103B ILE* 4.5 7.5 - - - +
1122B ARG* 3.3 15.5 + - - -
1K MET* 3.0 39.1 + - - +
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Residues in contact with ASP1101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945B GLU* 5.3 7.8 - - - +
972B LYS* 2.9 32.8 + - - -
1097B HIS* 5.7 0.7 - - - -
1098B MET* 3.4 36.8 - - - +
1099B VAL 2.6 4.4 + - - -
1100B ASP* 1.3 80.2 - - - +
1102B LYS* 1.3 66.1 + - + +
1122B ARG* 3.2 26.8 + - - +
10T U 4.7 10.9 + - - +
11T G 5.3 0.5 + - - -
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Residues in contact with LYS1102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A ARG* 3.6 6.3 - - - +
351A THR* 4.9 3.1 - - - -
352A VAL* 4.3 17.6 - - + +
484A GLY* 4.9 8.7 + - - -
486A GLU* 3.7 38.5 + - + +
979B LYS* 6.3 0.2 - - - +
1097B HIS* 3.9 45.1 + - - +
1098B MET 3.9 10.3 - - - +
1099B VAL* 2.6 7.4 + - - +
1101B ASP* 1.3 90.1 - - + +
1103B ILE* 1.3 68.5 + - - +
1104B HIS* 2.9 13.9 + - - +
1122B ARG* 3.1 6.6 + - - +
15P G 4.5 12.9 + - - -
10T U 5.7 16.2 - - - +
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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