Contacts of the strand formed by residues 710 - 717 (chain B) in PDB entry 4QUN
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 LEU 710 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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704B GLU* 3.6 0.3 - - - +
705B ILE* 2.8 57.8 + - + +
706B PRO* 5.2 0.8 - - - +
708B ALA 3.1 9.6 - - - +
709B ASN* 1.3 77.5 - - - +
711B VAL* 1.3 74.2 + - - +
712B ASN* 4.0 17.5 - - - +
834B ASP* 4.4 17.3 - - - +
860B CYS* 4.3 13.2 - - + -
864B ARG* 3.6 39.0 - - - +
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Residues in contact with VAL 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702B ASN* 3.9 21.3 - - + -
703B MET 3.5 7.0 - - - +
704B GLU* 4.2 21.8 - - + +
709B ASN 4.5 1.1 + - - -
710B LEU* 1.3 82.4 - - - +
712B ASN* 1.3 66.3 + - - +
713B LYS* 3.6 28.4 + - + +
832B ARG* 5.3 0.2 + - - -
834B ASP* 4.4 12.6 + - - +
835B SER* 5.1 3.6 + - - -
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Residues in contact with ASN 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B ASN* 3.5 0.7 - - - -
703B MET* 2.7 45.6 + - + +
705B ILE* 5.0 4.6 - - - +
710B LEU* 4.0 17.9 - - - +
711B VAL* 1.3 74.7 - - - +
713B LYS* 1.3 62.0 + - - +
714B TYR* 3.6 16.3 + - + +
832B ARG* 3.8 33.0 - - - +
856B GLU* 4.1 14.3 + - - +
857B THR* 4.8 6.9 + - - +
860B CYS* 3.5 30.6 - - - +
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Residues in contact with LYS 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B ASN* 3.3 26.9 - - - +
711B VAL* 3.6 19.6 + - + +
712B ASN* 1.3 74.1 - - - +
714B TYR* 1.3 61.1 + - - +
832B ARG* 2.9 26.4 + - - +
835B SER* 3.1 46.3 + - - +
836B GLU 4.6 1.1 - - - +
837B PRO* 3.8 28.0 - - + -
838B VAL 3.1 12.0 + - - -
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Residues in contact with TYR 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700B TYR* 3.7 6.4 - - - +
701B VAL* 2.8 48.2 + - + +
702B ASN* 3.8 2.6 + - - +
703B MET* 3.9 7.9 - - + -
712B ASN* 3.6 19.9 - - + +
713B LYS* 1.3 74.9 - - - +
715B ILE* 1.3 70.1 + - - +
716B ALA* 4.7 2.0 - - + +
828B VAL* 6.2 0.2 - - + -
832B ARG* 3.1 23.8 - - - -
837B PRO* 4.1 4.6 - - - +
838B VAL* 3.2 11.2 - - + +
840B VAL* 3.8 22.2 - - + -
852B LEU* 4.3 10.8 - - + -
853B VAL* 3.8 44.4 + - + -
856B GLU* 2.5 38.7 + - - +
857B THR* 4.5 2.1 + - - -
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Residues in contact with ILE 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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687B VAL* 3.8 20.4 - - + -
698B ALA* 4.1 13.9 - - + -
699B SER 3.4 4.5 - - - +
700B TYR* 4.0 18.4 - - + -
714B TYR* 1.3 77.7 - - - +
716B ALA* 1.3 59.5 + - - +
717B THR* 4.7 0.7 - - - -
731B VAL* 4.0 11.7 - - + -
735B GLN* 3.7 31.4 - - - +
737B LEU* 3.8 23.6 - - + -
837B PRO* 4.2 9.8 - - + +
838B VAL 2.9 7.5 + - - -
839B LEU* 3.4 21.6 - - + +
840B VAL 2.8 32.6 + - - +
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Residues in contact with ALA 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698B ALA* 3.3 1.4 - - - -
699B SER 2.8 35.0 + - - +
701B VAL* 4.0 18.2 - - + -
714B TYR* 4.0 3.7 - - + -
715B ILE* 1.3 71.6 - - - +
717B THR* 1.3 61.8 + - - +
840B VAL* 3.3 6.1 - - + +
845B GLY 4.2 0.7 - - - +
849B THR* 4.0 22.4 - - + -
881B ARG* 3.8 27.0 + - - -
884B MET* 4.5 3.6 - - + -
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Residues in contact with THR 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696B ILE* 4.6 8.2 - - + +
697B ASN 2.5 23.4 + - - -
698B ALA* 3.4 15.1 - - - +
715B ILE* 4.7 1.3 - - - +
716B ALA* 1.3 76.5 - - - +
718B GLN* 1.3 69.2 + - - +
728B PHE* 4.1 12.9 - - + -
839B LEU* 3.7 26.0 - - + -
840B VAL 3.1 4.4 + - - -
841B HIS* 3.1 34.7 - - + +
845B GLY* 3.1 20.2 - - - -
881B ARG* 4.1 2.9 - - - +
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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