Contacts of the strand formed by residues 775 - 780 (chain A) in PDB entry 1QWN
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 GLU 775 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530A ARG* 3.0 31.8 + - - +
766A GLN 3.7 0.5 - - - +
767A THR* 3.5 2.9 - - - -
768A ILE* 2.7 46.1 + - + +
770A ARG* 4.1 19.1 + - - -
773A ALA 3.7 0.6 + - - -
774A PRO* 1.3 74.5 - - - +
776A ILE* 1.3 67.3 + - - +
777A ARG* 2.7 42.1 + - + +
891A ILE* 4.4 2.9 - - - +
892A TYR 3.3 18.2 - - - +
893A ARG* 3.7 13.9 - - - +
925A LEU* 4.9 0.7 - - + -
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Residues in contact with ILE 776 (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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694A LEU* 5.9 0.2 - - + -
710A PHE* 3.7 33.4 - - + -
765A HIS* 3.6 26.2 - - + +
766A GLN 3.2 7.9 - - - +
767A THR* 3.8 26.9 - - + +
774A PRO* 4.3 11.4 - - + -
775A GLU* 1.3 82.1 - - - +
777A ARG* 1.3 64.8 + - - +
778A ASN* 4.1 6.3 - - - +
792A MET* 4.6 3.1 - - - -
846A LEU* 5.2 0.4 - - + -
891A ILE* 3.4 3.1 - - - -
892A TYR* 2.9 55.1 + - + +
894A LEU* 4.4 14.4 - - + -
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Residues in contact with ARG 777 (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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529A SER* 4.4 15.2 + - - -
530A ARG* 3.4 24.8 - - - +
534A SER* 6.3 0.8 - - - -
570A ASP* 5.8 0.8 + - - -
617A ARG* 5.9 3.0 - - - +
764A VAL 3.5 3.1 - - - +
766A GLN* 2.8 57.2 + - + +
768A ILE* 3.5 23.3 - - + +
770A ARG* 3.7 19.2 - - - +
775A GLU* 2.7 37.6 + - - +
776A ILE* 1.3 78.0 - - - +
778A ASN* 1.3 62.8 + - - +
889A LEU* 4.0 22.2 - - + +
890A HIS 3.2 6.7 - - - +
891A ILE* 4.1 8.1 - - + -
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Residues in contact with ASN 778 (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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712A PHE* 3.8 5.4 - - - -
763A VAL* 3.8 10.3 - - + -
764A VAL 3.4 2.7 - - - -
765A HIS* 2.8 32.3 + - - -
776A ILE* 4.1 1.4 - - - +
777A ARG* 1.3 75.8 - - - +
779A LEU* 1.3 59.0 + - - +
780A VAL* 3.4 18.1 + - + +
792A MET* 3.3 25.2 - - - -
866A GLN* 3.0 25.0 + - - +
888A VAL 3.2 3.8 - - - +
889A LEU* 3.4 3.8 - - - -
890A HIS* 2.9 39.7 + - + +
892A TYR* 3.9 8.0 - - - -
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Residues in contact with LEU 779 (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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534A SER 3.6 8.7 - - - +
535A GLY* 3.6 30.3 - - - +
536A VAL* 3.1 36.1 - - + -
598A TRP* 5.7 5.8 - - + +
762A SER 3.7 0.5 - - - +
763A VAL* 3.3 4.0 - - - -
764A VAL* 2.9 54.2 + - + +
766A GLN* 4.0 4.4 - - - +
778A ASN* 1.3 68.6 - - - +
780A VAL* 1.3 60.2 + - - +
781A ASP* 3.8 3.8 + - + +
887A PRO* 4.5 6.5 - - + -
888A VAL 3.5 10.5 - - - +
889A LEU* 3.9 11.7 - - + +
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Residues in contact with VAL 780 (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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762A SER 3.5 8.5 - - - +
763A VAL* 4.5 11.0 - - + -
778A ASN* 3.7 29.8 - - + +
779A LEU* 1.3 71.7 - - - +
781A ASP* 1.3 62.6 + - - +
782A ILE 4.2 6.0 + - - +
790A ILE* 4.7 7.0 - - + -
866A GLN* 4.0 17.9 - - + +
867A ASP* 4.0 27.7 - - + +
886A LYS 4.0 1.7 - - - +
887A PRO* 3.3 5.2 - - - +
888A VAL* 2.8 41.4 + - + +
890A HIS* 4.0 17.3 - - + -
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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