Contacts of the strand formed by residues 609 - 614 (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 CYS 609 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496B MET* 3.4 6.9 - - - +
518B THR* 3.4 8.7 - - - +
519B HIS 3.1 35.3 + - - +
521B THR* 2.6 37.2 - - + -
587B PHE* 3.1 25.8 - - - -
608B ILE* 1.3 73.9 - - - +
610B ARG* 1.3 63.9 + - - +
648B TYR* 3.8 19.7 - - + -
649B LEU 3.3 18.4 - - - +
650B ASP* 4.7 0.4 - - - -
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Residues in contact with ARG 610 (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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494B PHE* 2.9 43.4 + - - -
495B GLY* 3.3 18.5 + - - -
496B MET* 3.4 29.2 - - + -
517B MET* 4.1 10.4 + - - +
519B HIS 4.9 0.2 - - - +
609B CYS* 1.3 79.3 - - - +
611B PRO* 1.3 82.4 + - + +
612B LEU* 4.5 16.1 - - + +
648B TYR* 3.2 7.7 - - - -
649B LEU* 3.1 30.6 + - + -
654B GLU* 3.8 17.2 + - - +
659B ILE* 6.1 1.0 - - - +
674B GLU* 4.9 11.9 + - - +
679B THR* 3.6 28.5 - - - +
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Residues in contact with PRO 611 (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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51B PHE* 3.5 24.9 - - + -
517B MET* 3.5 40.5 - - + +
518B THR* 4.6 2.9 - - - +
610B ARG* 1.3 99.3 + - + +
612B LEU* 1.3 71.9 + - - +
637B PHE* 4.8 7.6 - - + -
646B VAL* 5.7 2.7 - - + -
647B GLU 4.0 1.8 - - - +
648B TYR* 3.5 28.9 - - + -
675B ILE* 5.0 8.9 + - + +
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Residues in contact with LEU 612 (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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610B ARG* 4.5 21.1 - - - +
611B PRO* 1.3 79.8 - - - +
613B ILE* 1.3 58.3 + - - +
614B ILE 4.0 0.3 + - - -
646B VAL* 3.2 26.4 - - - +
647B GLU* 3.5 9.7 + - - +
649B LEU* 3.5 34.1 - - + -
659B ILE* 3.9 19.7 - - + -
672B HIS* 3.4 39.7 - - + -
673B LEU 3.7 9.9 - - - +
674B GLU* 4.2 13.2 - - + -
675B ILE* 3.8 12.1 - - - -
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Residues in contact with ILE 613 (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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44B LYS* 4.0 13.5 - - + -
47B LEU* 4.0 13.2 - - + -
612B LEU* 1.3 74.9 - - - +
614B ILE* 1.3 74.8 + - - +
620B SER* 3.9 18.4 - - - -
621B ARG* 4.3 3.1 - - + +
622B VAL* 3.8 25.4 - - + -
645B LEU* 4.7 3.1 - - + +
646B VAL* 3.4 23.8 - - + -
672B HIS* 3.1 8.8 - - - +
673B LEU* 3.0 53.0 + - + +
675B ILE* 3.5 20.6 - - + -
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Residues in contact with ILE 614 (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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576B ARG* 6.1 3.6 - - + -
580B ARG* 3.5 55.2 - - + +
612B LEU 4.0 0.2 + - - -
613B ILE* 1.3 79.3 - - - +
615B VAL* 1.3 73.2 + - - +
616B SER* 4.0 5.2 - - - +
621B ARG* 3.1 26.3 + - + +
644B GLY 5.2 0.4 - - - +
645B LEU 3.3 16.2 + - - +
647B GLU* 3.1 40.8 - - - +
671B THR 3.5 7.2 - - - +
672B HIS* 3.4 11.2 - - + +
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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
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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