Contacts of the helix formed by residues 985 - 992 (chain S) in PDB entry 1BKD
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 985 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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983S VAL* 3.8 14.5 + - - +
984S GLU* 1.3 74.8 + - - +
986S ASP* 1.3 59.3 + - - +
988S LYS* 3.6 12.2 - - - +
989S ARG* 3.1 50.9 + - - +
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Residues in contact with ASP 986 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763S TRP* 5.9 0.2 - - + -
769S GLY* 4.3 17.3 + - - -
771S ILE* 4.1 24.6 - - + +
774S PHE* 3.9 20.5 - - + -
984S GLU* 2.8 23.3 + - - +
985S SER* 1.3 71.9 - - - +
987S ILE* 1.3 63.4 + - - +
989S ARG* 3.1 27.2 + - - +
990S PHE* 3.1 21.1 + - - +
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Residues in contact with ILE 987 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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763S TRP* 3.9 24.7 - - + -
774S PHE* 3.8 20.6 - - + -
779S LEU* 3.7 19.5 - - + -
783S GLU* 3.7 31.9 - - + +
784S ILE* 5.2 0.4 - - - -
787S GLN* 3.7 17.7 - - + -
984S GLU* 2.9 25.7 + - + +
986S ASP* 1.3 75.9 - - - +
988S LYS* 1.3 62.1 + - - +
990S PHE* 3.3 11.4 + - - +
991S PHE* 3.2 40.7 + - + -
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Residues in contact with LYS 988 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787S GLN* 4.3 14.5 + - + +
790S LEU* 5.7 2.4 - - - +
791S LEU* 3.8 38.6 - - + +
794S ASP* 4.1 17.4 + - - +
983S VAL* 4.7 16.6 - - + +
984S GLU 3.0 17.6 + - - +
985S SER* 3.6 14.1 - - - +
987S ILE* 1.3 77.6 - - - +
989S ARG* 1.3 58.2 + - + +
991S PHE 3.6 0.9 + - - -
992S GLU* 3.1 48.1 + - - +
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Residues in contact with ARG 989 (chain S).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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771S ILE* 5.2 6.2 - - + +
985S SER* 3.1 46.0 + - - +
986S ASP* 3.1 32.4 + - - +
988S LYS* 1.3 76.3 - - - +
990S PHE* 1.3 59.8 + - - +
992S GLU* 3.6 14.1 + - - +
993S ASN* 2.9 54.3 + - - +
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Residues in contact with PHE 990 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771S ILE* 5.0 9.4 - - + -
774S PHE* 3.4 48.5 - + + -
775S ASP* 4.0 18.2 - - - -
779S LEU* 4.7 4.0 - - + -
834S TRP* 4.1 11.7 - + - -
986S ASP 3.1 11.5 + - - +
987S ILE* 3.3 10.8 - - - +
988S LYS 3.3 0.2 - - - -
989S ARG* 1.3 78.5 - - - +
991S PHE* 1.3 96.1 + + - +
993S ASN* 3.3 4.7 + - - +
994S LEU* 3.3 44.0 + - + +
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Residues in contact with PHE 991 (chain S).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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775S ASP 6.0 0.2 - - - -
779S LEU* 3.9 9.2 - - + -
784S ILE* 3.6 42.8 - - + -
787S GLN* 4.8 5.4 - - + -
788S LEU* 3.9 25.4 - - + -
791S LEU* 3.8 20.9 - - + -
827S HIS* 4.5 12.0 + - - -
830S ASN* 5.6 1.0 + - - -
831S LEU* 4.5 3.4 - - + +
834S TRP* 3.7 29.2 - + - -
987S ILE* 3.2 44.7 + - + +
988S LYS* 5.1 0.4 - - - -
990S PHE* 1.3 89.9 - + - +
992S GLU* 1.3 62.7 + - - +
993S ASN 3.3 0.2 - - - -
994S LEU* 3.6 33.6 + - + +
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Residues in contact with GLU 992 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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791S LEU* 3.5 27.5 - - + +
827S HIS* 5.7 1.8 - - - -
988S LYS* 3.1 36.2 + - - +
989S ARG* 3.6 15.5 - - - +
991S PHE* 1.3 78.8 - - - +
993S ASN* 1.3 67.3 + - - +
994S LEU 3.5 2.8 + - - +
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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