Contacts of the strand formed by residues 753 - 759 (chain B) in PDB entry 6CNB
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 753 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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728B MET* 3.2 25.3 - - + +
730B TYR* 2.6 43.4 + - - +
732B GLN* 4.2 6.5 - - - +
752B GLY* 1.3 74.0 - - - -
754B ASN* 1.3 58.9 + - - +
755B ALA* 3.8 1.1 + - - -
781B GLY 4.7 0.6 + - - -
782B PHE* 3.7 21.1 - - + -
783B GLY* 3.4 35.3 - - - +
784B ARG 5.1 0.6 - - - +
1023B TYR* 3.2 8.3 - - - -
1024B TYR* 3.1 34.6 + - - +
1026B LYS* 6.4 0.2 - - + -
8J PHE* 3.1 24.1 - - + -
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Residues in contact with ASN 754 (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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732B GLN* 3.1 25.4 + - + +
733B GLN 3.7 9.0 + - - +
735B MET* 3.2 55.2 - - - +
753B GLN* 1.3 74.1 - - - +
755B ALA* 1.3 49.8 + - - +
782B PHE* 5.1 0.7 - - - -
1021B PRO* 3.8 8.1 - - - +
1022B ILE 2.9 27.3 + - - +
1023B TYR* 4.1 8.3 - - + -
8J PHE* 5.2 3.0 - - - -
48J ARG* 2.2 38.0 + - - +
52J THR* 4.2 2.5 + - + -
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Residues in contact with ALA 755 (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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753B GLN 3.8 0.8 + - - +
754B ASN* 1.3 71.4 - - - +
756B THR* 1.3 62.1 + - - +
757B VAL* 3.3 7.6 - - - +
782B PHE* 3.5 30.1 - - + -
941B ASP* 4.0 5.6 - - - +
942B ILE* 3.7 25.4 - - + -
1021B PRO* 4.7 0.2 - - - -
1022B ILE 2.8 31.5 + - - +
1024B TYR* 4.1 9.6 - - + -
48J ARG* 3.2 5.6 - - - +
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Residues in contact with THR 756 (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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755B ALA* 1.3 69.8 - - - +
757B VAL* 1.3 55.6 + - - +
938B ILE* 4.7 5.5 - - + +
939B VAL 4.2 2.0 - - - +
940B PRO* 3.3 2.5 - - - +
941B ASP* 2.4 47.2 + - + +
1019B PHE* 4.5 3.8 - - - -
1020B GLY 4.0 6.1 + - - -
1021B PRO* 4.5 3.8 - - - -
9J SER* 3.9 24.0 - - - +
44J TYR* 3.5 28.6 + - - -
45J CYS* 4.1 8.2 - - + +
48J ARG* 2.8 34.9 - - - +
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Residues in contact with VAL 757 (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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755B ALA 3.3 15.7 - - - +
756B THR* 1.3 75.0 + - - +
758B ALA* 1.3 75.7 + - - +
759B VAL* 5.3 0.4 - - + -
940B PRO* 4.4 0.2 - - - -
942B ILE* 3.0 30.3 - - + +
944B MET* 4.3 3.8 - - + -
961B LEU* 4.1 3.1 - - - +
1019B PHE* 3.0 20.8 - - - +
1020B GLY 3.3 15.5 + - - +
1022B ILE* 3.5 30.1 - - + -
1024B TYR* 3.6 25.6 - - + +
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Residues in contact with ALA 758 (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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757B VAL* 1.3 90.5 - - - +
759B VAL* 1.3 66.3 + - - +
760B MET* 4.8 0.2 - - + -
932B PRO* 4.7 2.5 - - + -
940B PRO* 3.5 27.4 - - + +
942B ILE 3.3 7.1 + - - -
943B ILE* 3.4 22.0 - - + -
944B MET* 3.7 7.6 + - - +
1004B LEU* 4.6 5.6 - - + -
1017B ILE* 4.4 11.4 - - + -
1018B PHE 3.9 0.2 - - - -
1019B PHE* 3.3 15.9 - - + -
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Residues in contact with VAL 759 (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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711A SER* 3.2 22.2 - - - -
712A ILE* 4.8 11.0 - - + +
757B VAL* 5.3 1.1 - - + -
758B ALA* 1.3 81.4 - - - +
760B MET* 1.3 62.4 + - - +
944B MET* 3.7 15.3 - - + +
945B ASN 4.7 0.7 - - - +
946B PRO* 3.9 29.6 - - + -
949B PHE* 4.3 26.5 - - + -
961B LEU* 4.7 8.7 - - + -
1017B ILE* 3.2 8.9 - - - +
1018B PHE* 3.3 31.2 + - + +
1022B ILE* 5.6 2.5 - - + -
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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