Contacts of the helix formed by residues 992 - 997 (chain A) in PDB entry 4X7J
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 SER 992 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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990A TYR 3.8 2.0 + - - -
991A MET* 1.3 77.1 - - - +
993A PRO* 1.3 72.1 - - - +
994A GLU* 3.3 30.7 - - - -
995A GLN* 2.7 29.3 + - - +
996A ILE* 3.2 17.7 + - - +
1005A VAL* 3.3 11.5 + - - +
1008A PHE* 3.8 22.9 - - - +
1065A ARG* 4.1 1.6 - - - -
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Residues in contact with PRO 993 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
992A SER* 1.3 86.4 - - - +
994A GLU* 1.3 61.1 + - - +
996A ILE* 3.2 5.9 + - + +
997A HIS* 2.7 51.4 + - + +
1008A PHE* 3.5 32.5 - - + -
1035A ARG* 4.1 11.6 - - - +
1060A PRO* 5.0 14.1 - - + +
1065A ARG* 3.9 4.0 - - - +
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Residues in contact with GLU 994 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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992A SER* 3.3 17.1 - - - +
993A PRO* 1.3 80.2 - - - +
995A GLN* 1.3 60.9 + - - +
997A HIS* 3.9 0.6 + - - -
998A GLY 3.4 1.6 + - - -
999A ASN* 2.9 47.0 + - + +
1000A SER 4.2 10.8 - - - +
1001A TYR* 3.8 21.9 - - + +
1002A SER 5.2 0.9 + - - -
1004A LYS* 5.0 0.2 - - - +
1005A VAL* 3.4 12.1 + - - +
1060A PRO 4.5 1.7 - - - +
1062A PRO* 3.5 20.7 - - + +
1065A ARG* 2.8 43.1 + - - -
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Residues in contact with GLN 995 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936A ARG* 2.9 42.6 + - - +
937A ASN* 5.3 0.2 + - - -
991A MET* 3.7 27.8 - - - +
992A SER* 2.7 38.7 + - - +
994A GLU* 1.3 76.1 - - - +
996A ILE* 1.3 65.2 + - - +
998A GLY* 3.1 13.6 + - - -
999A ASN 4.9 3.1 - - - -
1001A TYR* 4.1 26.1 - - + -
1005A VAL* 3.4 20.1 - - + +
1009A SER* 5.5 0.7 + - - -
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Residues in contact with ILE 996 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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988A LYS 4.2 15.0 - - - +
991A MET* 3.7 23.6 - - + +
992A SER 3.2 9.3 + - - +
993A PRO* 3.7 8.1 - - + +
995A GLN* 1.3 76.4 - - - +
997A HIS* 1.3 70.9 + - + +
998A GLY* 3.3 1.2 + - - -
1035A ARG* 3.4 32.8 - - - +
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Residues in contact with HIS 997 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993A PRO* 2.7 37.5 + - + +
994A GLU* 3.9 0.6 + - - +
996A ILE* 1.3 84.0 - - + +
998A GLY* 1.3 62.1 + - - +
999A ASN* 3.4 27.3 + - - +
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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