Contacts of the strand formed by residues 714 - 718 (chain B) in PDB entry 6WCZ
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 HIS 714 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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706B GLU 4.7 3.4 - - - -
707B GLU* 3.9 30.3 - - + +
708B VAL 4.2 5.4 - - - -
709B PRO* 5.0 2.7 - - + +
713B HIS* 1.3 73.7 - - - +
715B PHE* 1.3 59.6 + - - +
716B ASN* 3.7 11.9 - - - -
730B CYS* 3.1 44.0 + - - +
731B ARG* 4.1 12.8 - - - -
732B HIS* 4.7 1.8 + - + -
849B CYS* 3.3 15.6 - - - -
1002B ZN 2.1 35.6 - - - -
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Residues in contact with PHE 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B LEU* 4.9 5.4 - - + -
516B LEU* 3.6 28.9 - - + -
517B GLY* 3.6 22.0 - - - -
520B LEU* 4.0 11.4 - - + -
705B TRP* 5.1 5.9 - - + +
706B GLU* 2.9 31.4 + - - +
707B GLU* 4.9 0.6 - - - +
708B VAL 4.9 2.3 + - - +
710B PHE* 3.4 41.5 - + - -
711B CYS* 6.4 0.7 - - + -
713B HIS* 3.5 25.8 - + + -
714B HIS* 1.3 80.9 - - - +
716B ASN* 1.3 61.5 - - - +
727B VAL* 4.6 9.2 - - + -
728B VAL 3.5 5.4 - - - +
729B PRO* 3.5 30.3 - - + -
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Residues in contact with ASN 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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705B TRP* 5.9 0.9 - - - -
706B GLU* 3.6 18.2 - - - +
714B HIS* 3.7 6.0 + - - -
715B PHE* 1.3 79.4 - - - +
717B LYS* 1.3 57.5 + - - +
718B LEU* 4.2 10.3 - - + -
727B VAL* 3.3 4.5 - - - +
728B VAL* 2.4 54.9 + - + +
729B PRO 5.2 0.4 - - - -
730B CYS* 4.3 5.0 - - + +
841B LEU* 3.4 15.8 - - + +
845B GLU* 5.3 7.1 + - - +
1002B ZN 2.6 35.0 - - - -
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Residues in contact with LYS 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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521B GLU* 4.3 17.7 + - - -
705B TRP* 3.5 20.5 - - + -
706B GLU* 3.4 30.1 + - - +
716B ASN* 1.3 76.1 - - - +
718B LEU* 1.3 72.0 + - - +
719B TYR* 3.2 34.2 + - + +
725B SER* 3.3 25.0 + - - -
726B ILE 3.3 4.7 - - - +
727B VAL* 3.8 19.1 - - + +
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Residues in contact with LEU 718 (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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716B ASN* 4.2 10.5 - - + -
717B LYS* 1.3 87.1 - - - +
719B TYR* 1.3 76.9 + - - +
720B LEU* 5.3 1.3 - - + -
724B ARG 2.9 1.9 - - - +
726B ILE* 2.5 55.2 + - + +
728B VAL* 3.9 24.7 - - + -
769B PHE* 6.2 5.2 - - + -
770B HIS* 5.2 4.7 - - + -
840B TYR 3.8 23.8 - - - +
841B LEU* 4.4 21.1 - - + -
842B GLY 5.2 1.6 - - - +
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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
------------------------------------------------------------
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