Contacts of the strand formed by residues 821 - 827 (chain B) in PDB entry 2NVX
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 GLN 821 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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796B LEU* 3.9 14.6 - - + +
798B TYR* 3.7 27.9 + - - +
800B GLN* 3.1 16.8 - - - +
820B GLY* 1.4 77.0 - - - -
822B ASN* 1.3 59.7 + - - +
823B ALA* 2.8 9.7 + - - +
849B GLY 4.3 2.6 + - - -
850B LEU* 3.3 24.1 - - + +
851B PHE* 2.8 61.5 + - + +
852B ARG 4.0 3.8 - - - +
1091B TYR* 4.0 4.3 - - - -
1092B TYR 3.0 22.7 + - - +
8J PHE* 4.3 8.8 - - + -
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Residues in contact with ASN 822 (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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800B GLN* 2.7 16.0 + - - +
801B LYS 3.5 6.9 + - - -
802B PRO* 3.4 12.7 - - - +
803B LEU* 3.0 61.0 + - + +
821B GLN* 1.3 68.1 - - - +
823B ALA* 1.3 53.2 + - - +
850B LEU* 5.8 0.6 - - - +
1032B SER* 4.8 0.5 - - - -
1089B PRO* 4.5 1.7 - - + +
1090B THR* 4.2 6.2 + - - -
1091B TYR* 3.6 29.6 + - - +
8J PHE* 5.8 0.3 - - - -
48J ARG* 2.8 40.1 + - - -
52J THR* 3.7 7.2 - - + +
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Residues in contact with ALA 823 (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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821B GLN 2.8 12.7 + - - +
822B ASN* 1.3 72.6 - - - +
824B ILE* 1.3 63.0 + - - +
825B VAL* 3.2 2.6 + - - +
850B LEU* 4.6 6.1 - - + -
851B PHE* 4.2 18.2 - - + -
1009B ASP* 3.7 22.0 - - + +
1010B LEU* 4.6 16.4 - - + -
1089B PRO* 4.5 0.7 - - - -
1090B THR 3.2 31.0 + - - +
1092B TYR* 4.7 2.7 - - + -
48J ARG* 3.9 0.9 - - - -
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Residues in contact with ILE 824 (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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823B ALA* 1.3 68.6 - - - +
825B VAL* 1.3 60.0 + - - +
1006B ILE* 4.6 1.3 - - + -
1007B VAL 4.3 4.7 - - - +
1008B PRO 3.6 1.4 - - - -
1009B ASP* 2.8 41.5 + - - +
1010B LEU* 3.1 5.8 + - - -
1087B PHE* 3.6 36.6 - - + -
1088B GLY 3.7 10.8 - - - +
1089B PRO* 3.6 22.7 - - + -
9J SER* 3.6 12.3 - - - +
44J TYR* 3.4 29.8 - - + -
45J CYS* 4.0 12.3 - - + -
48J ARG* 3.1 19.9 - - + +
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Residues in contact with VAL 825 (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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823B ALA 3.2 6.7 + - - +
824B ILE* 1.3 74.8 - - - +
826B ALA* 1.3 61.7 + - - +
827B ILE* 5.1 5.8 - - + -
1010B LEU* 3.2 32.1 - - + +
1012B ILE* 3.9 18.4 - - + -
1025B HIS* 4.8 9.4 - - + -
1029B CYS* 4.7 5.6 - - - -
1086B PHE 4.2 0.5 - - - +
1087B PHE* 3.7 5.7 - - - -
1088B GLY 2.9 32.5 + - - +
1090B THR* 3.6 29.2 - - + +
1092B TYR* 3.6 25.8 - - + -
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Residues in contact with ALA 826 (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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825B VAL* 1.3 75.2 - - - +
827B ILE* 1.3 61.8 + - - +
828B ALA* 3.5 2.6 + - + +
1008B PRO* 3.8 16.2 - - + -
1010B LEU 2.5 14.1 + - - +
1011B ILE* 3.1 12.9 - - + -
1012B ILE* 2.9 28.5 + - - +
1072B MET* 4.4 10.8 - - + -
1085B ILE* 4.4 3.6 - - + -
1086B PHE 3.7 4.5 - - - -
1087B PHE* 3.6 20.2 - - + -
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Residues in contact with ILE 827 (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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663A SER* 2.9 26.3 + - - -
664A THR* 3.5 20.0 - - - +
825B VAL* 5.1 7.9 - - + -
826B ALA* 1.3 72.2 - - - +
828B ALA* 1.3 60.3 + - - +
1012B ILE* 3.5 31.6 - - + -
1014B PRO* 3.7 29.6 - - + -
1017B ILE* 4.1 6.7 - - + -
1025B HIS* 4.8 7.6 - - + +
1026B LEU* 3.8 17.3 - - + -
1085B ILE* 3.5 3.0 - - - +
1086B PHE* 3.0 43.3 + - + +
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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