Contacts of the strand formed by residues 919 - 922 (chain A) in PDB entry 1KQG
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 PHE 919 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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897A LEU* 3.7 29.8 - - + -
915A GLN* 3.8 22.2 - - - -
917A GLU 3.7 11.7 - - - -
918A GLN* 1.3 79.2 + - - +
920A VAL* 1.3 71.3 + - - +
921A GLU* 4.0 12.3 - - + -
949A ALA* 4.2 2.2 - - - -
950A VAL 3.2 16.4 - - - +
952A VAL* 3.7 25.4 - - + -
972A ILE* 5.6 0.2 - - - +
973A PRO* 3.1 35.5 - - + +
976A TRP* 4.2 5.1 - + - -
62B CYS* 3.9 20.6 - - + -
65B VAL 5.5 2.2 - - - -
66B TYR* 3.8 34.5 - + - -
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Residues in contact with VAL 920 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A GLN* 5.8 0.4 - - + -
919A PHE* 1.3 78.8 - - - +
921A GLU* 1.3 62.3 + - - +
922A ILE* 4.1 3.5 + - + +
938A VAL* 3.8 28.5 - - + -
940A VAL* 4.1 14.1 - - + -
947A ILE* 4.1 18.4 - - + -
949A ALA* 4.2 6.7 - - + -
950A VAL 2.9 9.8 + - - +
951A ALA* 3.8 3.1 - - - -
952A VAL* 2.9 26.3 + - - +
970A VAL* 4.6 5.8 - - + -
971A GLY 3.2 14.4 - - - +
972A ILE* 3.9 22.0 - - + -
973A PRO* 4.2 1.3 - - - -
1012A ILE* 4.7 6.3 - - + -
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Residues in contact with GLU 921 (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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261A ARG* 2.8 21.8 + - - -
895A TYR* 2.5 29.9 + - - +
919A PHE* 4.0 17.0 - - + -
920A VAL* 1.3 75.8 - - - +
922A ILE* 1.3 64.3 + - - +
952A VAL* 3.4 14.4 - - + +
954A THR* 4.8 0.4 - - + -
956A ARG* 2.9 26.5 + - - +
957A LEU* 3.2 22.7 - - + +
970A VAL* 3.6 0.7 - - - +
971A GLY 2.8 36.0 + - - -
973A PRO* 5.6 0.2 - - + -
66B TYR* 2.7 26.6 + - - -
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Residues in contact with ILE 922 (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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920A VAL* 5.0 4.0 - - + +
921A GLU* 1.3 79.5 - - - +
923A SER* 1.3 63.7 + - - +
926A LEU* 4.0 22.4 - - + -
927A ALA* 3.7 27.1 - - + +
932A ILE* 4.0 28.0 - - + -
951A ALA* 4.9 6.3 - - + -
952A VAL 3.0 8.3 + - - +
953A VAL* 3.3 13.8 - - + -
954A THR* 3.0 25.5 + - - +
957A LEU* 4.1 9.0 - - - -
969A THR 4.3 2.0 - - - -
970A VAL* 4.0 12.6 - - + -
1012A ILE* 3.8 24.9 - - + -
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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