Contacts of the strand formed by residues 1022 - 1026 (chain B) in PDB entry 6CNC
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 ILE1022 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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735B MET* 6.1 0.7 - - - -
754B ASN* 2.8 6.6 - - - +
755B ALA* 2.8 31.8 + - - +
757B VAL* 3.4 19.0 - - + +
759B VAL* 5.7 2.9 - - + -
914B SER* 3.7 10.3 - - - +
944B MET* 5.2 0.7 - - - -
957B LYS* 3.2 46.4 - - + +
960B GLU* 4.1 20.6 - - + +
961B LEU* 4.2 24.9 - - + +
1020B GLY 3.2 12.1 + - - +
1021B PRO* 1.3 73.7 - - - +
1023B TYR* 1.3 72.0 + - - +
1024B TYR* 3.8 17.2 + - + +
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Residues in contact with TYR1023 (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 3.2 24.9 + - - -
733B GLN 3.9 3.6 - - - -
734B PRO* 3.5 23.6 - - + -
735B MET* 4.7 1.6 - - + +
746B TYR* 2.7 24.2 + + - -
750B PRO* 3.8 0.5 - - - +
751B ALA 2.5 37.3 + - - -
752B GLY* 3.1 10.1 + - - -
753B GLN 3.1 25.8 - - - -
754B ASN* 4.1 5.2 - - + +
914B SER 3.7 7.6 - - - -
915B ARG* 3.2 60.6 - - + +
960B GLU* 4.1 2.5 + - - +
1022B ILE* 1.3 81.4 - - - +
1024B TYR* 1.3 59.8 + - - +
1025B GLN* 3.9 9.4 + - + -
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Residues in contact with TYR1024 (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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752B GLY* 4.4 0.2 - - - -
753B GLN* 2.8 35.4 + - - +
755B ALA* 4.0 14.4 - - + -
757B VAL* 3.5 27.6 - - + +
771B LEU* 4.1 20.4 - - + -
782B PHE* 4.8 4.2 - - + -
912B PHE* 4.7 7.7 - - + -
913B SER* 3.5 17.7 - - - +
914B SER* 3.8 17.9 - - - -
918B GLN* 5.9 0.9 - - + -
942B ILE* 3.4 31.6 - - + -
944B MET* 3.0 32.9 - - + +
957B LYS* 3.5 9.3 + - - -
1022B ILE* 3.8 21.9 + - + +
1023B TYR* 1.3 73.3 - - - +
1025B GLN* 1.3 60.6 + - - +
1026B LYS 3.8 2.6 + - - -
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Residues in contact with GLN1025 (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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464B ILE* 5.5 0.9 - - - +
687B LEU* 5.0 9.2 - - - +
702B GLN* 3.7 25.7 + - - +
706B GLY* 3.8 13.8 - - - +
709B ALA* 3.7 20.6 - - + +
710B ILE 5.2 0.2 - - - +
746B TYR* 3.9 7.3 + - - -
751B ALA* 3.2 28.9 - - - +
752B GLY* 3.6 7.6 - - - -
912B PHE* 4.9 0.4 - - - -
913B SER* 3.1 23.2 + - - +
915B ARG* 4.2 19.2 - - - +
1023B TYR* 3.9 8.0 + - + +
1024B TYR* 1.3 72.3 - - - +
1026B LYS* 1.3 65.7 + - - +
1027B LEU* 2.9 21.3 - - + +
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Residues in contact with LYS1026 (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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709B ALA* 3.8 0.3 - - - -
710B ILE* 3.2 29.2 + - + +
728B MET* 4.0 20.1 - - + +
753B GLN* 6.2 0.4 - - + -
783B GLY* 3.2 21.3 - - - +
785B CYS* 2.6 27.9 - - - -
904B ARG 5.0 0.4 + - - -
906B PRO* 3.5 26.9 - - + +
910B ASP* 3.8 7.9 - - + -
911B LYS 4.0 3.8 - - - +
912B PHE* 3.7 38.4 - - + -
1024B TYR 3.8 3.8 + - - -
1025B GLN* 1.3 73.7 - - - +
1027B LEU* 1.3 65.8 + - - +
1030B MET* 2.5 41.1 - - - +
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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