Contacts of the strand formed by residues 679 - 686 (chain B) in PDB entry 5NC5
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 GLY 679 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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676B THR* 2.9 26.6 + - - +
677B ALA 3.2 3.4 - - - +
678B THR* 1.4 79.8 - - - +
680B PHE* 1.3 62.8 + - - +
829B GLY 3.3 13.0 - - - -
830B GLN* 4.0 4.0 - - - -
837B THR* 4.3 9.1 - - - +
841B MET* 4.8 2.6 - - - +
862B MET* 3.9 15.2 - - - +
863B SER* 4.3 1.9 + - - -
866B GLU* 5.8 2.3 - - - +
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Residues in contact with PHE 680 (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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678B THR 5.2 0.7 - - - -
679B GLY* 1.3 77.6 - - - +
681B ASP* 1.3 63.0 + - - +
682B PHE* 4.3 11.9 - - + -
713B LEU* 4.2 10.5 - - + -
716B VAL* 4.3 7.4 - - + -
827B ILE* 4.4 2.9 - - + -
828B LEU* 3.9 9.4 - - - +
829B GLY* 2.9 55.8 + - - +
830B GLN* 3.7 14.8 - - - -
831B ALA 4.8 0.4 - - - -
837B THR* 5.5 1.8 - - - -
840B ALA* 4.2 13.2 - - + -
841B MET* 4.2 14.6 - - + -
844B MET* 3.6 41.1 - - + -
859B TRP* 3.7 19.5 - + + -
862B MET* 3.3 12.3 - - - +
863B SER* 3.1 13.9 - - - +
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Residues in contact with ASP 681 (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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680B PHE* 1.3 76.3 - - - +
682B PHE* 1.3 57.8 + - - +
826B GLU* 2.5 35.2 - - - +
827B ILE 3.9 1.1 - - - -
828B LEU* 3.3 13.2 - - - +
859B TRP* 3.4 7.5 - - - -
860B THR* 3.1 52.3 + - - +
861B GLY* 4.0 8.8 - - - -
862B MET* 4.0 17.9 + - + +
863B SER* 2.9 7.5 + - - -
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Residues in contact with PHE 682 (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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680B PHE* 4.2 7.6 - - + -
681B ASP* 1.3 73.2 + - - +
683B GLU* 1.3 63.4 + - - +
684B LEU* 3.6 24.5 - - + -
702B LEU* 3.7 12.6 - - + -
826B GLU* 3.5 4.9 - - - +
827B ILE* 2.7 64.5 + - + +
844B MET* 4.2 15.3 - - + -
848B ALA* 3.8 18.4 - - + -
857B TYR* 3.2 44.6 - + + -
858B ASP 3.9 1.8 - - - -
859B TRP* 3.4 39.5 - + + -
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Residues in contact with GLU 683 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B PHE* 1.3 74.5 - - - +
684B LEU* 1.3 59.5 + - - +
685B ILE* 3.8 5.4 - - + +
817B GLU* 4.1 1.3 - - - +
818B ARG 5.7 0.4 - - - +
819B TYR* 3.8 38.0 - - + -
824B SER* 3.0 24.0 + - - -
825B MET 3.5 1.0 - - - -
826B GLU* 3.4 44.0 + - - +
857B TYR* 3.0 7.6 - - - +
858B ASP 2.8 44.0 + - - +
860B THR* 3.8 23.3 - - + +
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Residues in contact with LEU 684 (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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682B PHE* 3.6 25.9 - - + -
683B GLU* 1.3 73.2 - - - +
685B ILE* 1.3 60.3 + - - +
695B LEU* 3.7 21.4 - - + +
698B ALA* 4.0 4.7 - - + +
699B ARG* 3.5 42.0 - - + +
702B LEU* 4.0 3.6 - - + -
824B SER* 3.1 7.8 - - - -
825B MET* 3.0 39.9 + - + +
827B ILE* 4.4 7.0 - - + -
851B LEU* 3.7 24.7 - - + -
855B VAL* 3.8 9.9 - - + -
856B GLY 3.6 11.4 - - - +
857B TYR* 4.6 0.7 - - + -
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Residues in contact with ILE 685 (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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683B GLU* 3.8 9.6 - - + +
684B LEU* 1.3 81.5 - - - +
686B ASP* 1.3 61.9 + - - +
687B GLN* 3.3 36.8 + - + +
695B LEU* 4.5 4.7 - - - -
819B TYR* 3.8 34.3 - - + +
820B ASN* 5.8 0.4 - - + +
822B LEU* 3.7 27.1 - - + -
823B PRO 3.6 3.1 - - - +
824B SER* 4.3 8.1 - - - -
855B VAL* 3.5 6.1 - - - +
856B GLY 2.8 40.5 + - - +
857B TYR 4.6 1.1 - - - -
858B ASP* 4.2 18.2 - - + +
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Residues in contact with ASP 686 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B ILE* 1.3 70.8 - - - +
687B GLN* 1.3 56.6 + - - +
688B ALA 3.4 2.3 + - - -
689B GLY* 3.0 12.7 + - - -
690B LEU* 2.7 39.1 + - - +
691B GLY* 2.9 29.5 + - - +
695B LEU* 4.0 16.8 - - + +
822B LEU* 3.7 19.8 - - - +
823B PRO* 2.9 42.6 + - + +
854B GLY 4.3 2.2 - - - -
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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