Contacts of the strand formed by residues 1056 - 1059 (chain A) in PDB entry 3QCF
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 VAL1056 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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920A ALA 3.1 6.0 + - - +
921A TYR* 3.2 15.6 - - + +
922A ILE 3.0 19.3 + - - -
944A THR* 4.8 0.2 - - - -
946A ILE* 3.7 31.9 - - + +
948A VAL* 3.9 27.4 - - + -
1045A SER 5.5 2.7 - - - +
1049A ARG* 3.1 49.1 - - + +
1054A GLY 3.6 2.6 + - - +
1055A PRO* 1.3 68.9 - - - +
1057A LEU* 1.3 64.6 + - - +
1058A VAL* 3.6 6.2 + - + -
1070A TYR* 5.3 2.2 - - - +
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Residues in contact with LEU1057 (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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922A ILE* 3.5 17.5 - - + +
924A THR* 3.8 20.4 - - + -
935A PHE* 3.8 19.1 - - + -
938A MET* 3.5 31.4 - - + -
939A ILE* 3.9 19.5 - - + -
944A THR* 4.1 11.4 - - + +
946A ILE 3.1 12.7 + - - +
947A ILE* 3.5 9.5 - - + -
948A VAL* 2.7 32.2 + - - +
1055A PRO 3.5 2.8 + - - +
1056A VAL* 1.3 72.4 - - - +
1058A VAL* 1.3 59.2 + - - +
1059A HIS* 3.9 22.7 - - + -
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Residues in contact with VAL1058 (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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921A TYR* 3.8 29.6 - - + -
922A ILE 2.8 12.4 + - - +
923A ALA* 3.4 3.5 - - - -
924A THR 3.2 22.5 + - - -
948A VAL* 3.5 11.4 - - + +
950A ILE* 4.1 11.4 - - + -
1056A VAL* 4.0 4.7 - - + +
1057A LEU* 1.3 79.9 - - - +
1059A HIS* 1.3 63.3 + - - +
1067A THR* 3.6 35.0 - - + +
1070A TYR* 4.0 30.1 - - + -
1071A ILE* 4.6 3.8 - - + -
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Residues in contact with HIS1059 (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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924A THR* 2.9 33.2 - - + +
925A GLN 3.9 5.4 - - - +
926A GLY* 3.7 5.5 - - - -
927A PRO* 4.7 0.9 - - + -
935A PHE* 4.8 4.3 - + - -
947A ILE* 4.3 1.8 - - + -
948A VAL 2.9 20.2 + - - +
949A MET* 3.4 28.8 - - + +
950A ILE* 3.0 25.6 + - - +
951A THR* 4.3 0.2 - - + -
961A CYS* 3.8 24.9 - - - -
964A TYR* 3.0 30.6 + + - -
1057A LEU* 3.9 14.8 - - + -
1058A VAL* 1.3 73.6 - - - +
1060A CYS* 1.3 77.5 + - - +
1067A THR* 3.3 8.3 - - - -
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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