Contacts of the strand formed by residues 988 - 994 (chain B) 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 GLY 988 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483A ASP* 3.9 7.7 + - - +
837B ASP 3.2 18.4 - - - -
838B SER* 4.7 1.1 - - - -
839B MET* 4.3 8.5 - - - -
979B LYS* 3.8 1.9 - - - +
980B PHE* 2.7 40.0 + - - +
986B GLN 3.5 1.5 + - - -
987B LYS* 1.3 75.2 - - - +
989B THR* 1.3 65.7 + - - +
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Residues in contact with THR 989 (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* 4.6 3.8 - - + +
353A ILE 4.6 4.7 + - - -
354A SER* 4.9 1.2 - - - -
482A PHE* 2.9 28.4 + - - +
483A ASP 3.7 1.1 - - - -
484A GLY* 3.2 22.7 - - - +
837B ASP 3.5 5.5 + - - -
838B SER* 2.7 13.3 - - - -
839B MET* 2.6 32.0 + - - -
976B ILE 4.6 0.2 + - - -
977B GLY* 3.7 12.9 + - - +
978B ASP 3.0 17.3 - - - +
979B LYS* 4.0 10.8 - - + +
980B PHE 4.5 0.2 - - - +
988B GLY* 1.3 78.0 - - - +
990B ILE* 1.3 65.0 + - - +
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Residues in contact with ILE 990 (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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354A SER* 4.2 8.1 - - - -
838B SER* 4.2 0.7 - - - -
839B MET* 3.2 14.4 - - + +
841B MET* 3.8 26.0 - - + +
846B ILE* 5.1 1.6 - - + -
974B PRO* 4.7 1.6 - - + -
975B GLN 2.8 31.2 - - - +
976B ILE* 2.9 28.5 - - + +
978B ASP* 3.2 8.0 + - + +
980B PHE* 3.5 38.1 - - + -
989B THR* 1.3 88.4 + - - +
991B GLY* 1.3 70.3 + - - +
992B ILE 3.5 23.6 - - - +
993B THR* 4.5 2.0 - - + -
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Residues in contact with GLY 991 (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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354A SER* 4.5 7.2 - - - -
355A GLY 5.4 0.7 - - - -
469A ARG* 2.5 33.7 + - - -
833B TYR* 4.1 17.7 - - - -
838B SER* 4.8 2.5 - - - -
839B MET 2.9 8.2 + - - -
976B ILE* 3.3 15.9 - - - +
989B THR 3.8 0.2 + - - -
990B ILE* 1.3 75.3 - - - +
992B ILE* 1.3 65.1 + - - +
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Residues in contact with ILE 992 (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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833B TYR* 3.3 38.1 - - + -
839B MET 4.1 0.8 + - - -
840B ILE* 3.5 7.8 - - + +
841B MET 3.1 22.3 + - - -
976B ILE* 3.8 8.1 - - + -
990B ILE* 3.5 3.2 - - - +
991B GLY* 1.3 82.9 - - - +
993B THR* 1.3 74.2 + - - +
994B TYR* 3.7 26.5 - - + +
66K PRO* 3.5 41.3 - - + +
67K PHE* 4.1 17.9 - - + -
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Residues in contact with THR 993 (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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465A TYR* 4.9 9.5 + - - -
841B MET 3.0 13.9 - - - +
843B GLN* 3.4 32.5 + - - +
846B ILE* 3.9 16.8 - - + -
974B PRO 5.3 0.7 - - - +
975B GLN* 4.9 5.6 - - - +
976B ILE* 4.4 14.5 - - + +
990B ILE* 4.5 12.3 - - + -
992B ILE* 1.3 92.2 - - - +
994B TYR* 1.3 65.9 + - - +
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Residues in contact with TYR 994 (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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830B TYR* 4.8 4.9 - + - -
831B SER* 2.7 41.2 - - - -
833B TYR* 4.2 2.4 - - - -
840B ILE* 3.3 31.0 - - + -
841B MET 3.1 6.5 + - - -
842B ASN* 3.3 6.1 - - - +
843B GLN* 2.4 34.5 + - - +
992B ILE* 3.7 28.5 - - + +
993B THR* 1.3 77.3 - - - +
995B ARG* 1.3 63.0 + - - +
998B ASP* 3.7 31.0 - - + -
999B MET* 3.6 27.1 - - + -
1076B HIS* 5.0 9.3 + + - -
66K PRO* 4.2 14.1 - - + +
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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