Contacts of the strand formed by residues 461 - 464 (chain A) 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 VAL 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A PRO* 4.3 17.7 - - + -
406A GLU 3.3 9.6 - - - +
407A LYS* 3.7 30.7 - - + -
433A LEU* 3.6 3.6 - - - +
434A LEU* 2.7 64.5 + - + +
456A LEU* 6.1 0.2 - - - -
459A GLY 4.2 5.8 - - - +
460A ASP* 1.3 77.4 - - - +
462A VAL* 1.3 69.9 + - - +
463A GLU* 4.9 5.6 - - + +
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Residues in contact with VAL 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A PRO* 3.5 2.9 - - - +
406A GLU* 2.8 42.9 + - + +
408A VAL* 5.1 1.5 - - + +
416A LEU* 3.4 39.0 - - + -
419A LEU* 5.4 0.4 - - + -
420A ILE* 3.5 21.3 - - + -
430A ALA* 3.4 26.2 - - + -
432A TYR 3.8 7.2 - - - +
433A LEU* 4.5 6.7 - - + +
456A LEU* 5.4 7.6 - - + -
460A ASP 4.2 0.4 - - - -
461A VAL* 1.3 75.8 - - - +
463A GLU* 1.3 65.9 + - - +
464A ARG* 4.6 6.7 - - + -
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Residues in contact with GLU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A PHE* 5.3 1.9 - - - -
403A THR* 3.5 23.9 + - - +
404A TYR 3.6 3.8 - - - +
405A PRO* 4.2 17.7 - - + +
430A ALA* 3.1 18.6 - - - +
431A ASN* 3.2 21.1 + - - +
432A TYR* 3.1 42.2 + - + +
441A ARG* 3.4 17.4 + - - -
461A VAL* 4.9 6.3 - - + +
462A VAL* 1.3 82.9 - - - +
464A ARG* 1.3 64.7 + - - +
523A GLN* 5.6 1.3 + - - -
1040B ARG* 3.5 15.4 + - - -
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Residues in contact with ARG 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403A THR* 3.2 10.6 - - - -
404A TYR* 2.9 64.2 + - + +
406A GLU* 2.8 49.7 + - + +
415A LYS* 4.2 18.6 - - - +
416A LEU* 4.9 6.7 - - + +
419A LEU* 3.7 16.8 - - + -
429A GLY 3.9 4.7 - - - -
430A ALA* 4.3 2.2 - - - -
431A ASN 5.4 0.2 - - - -
462A VAL* 3.9 5.1 - - + -
463A GLU* 1.3 73.4 - - - +
465A HIS* 1.3 64.2 + - - +
467A GLU* 3.1 34.6 + - - +
470A ASP* 4.2 15.0 + - - -
525A GLU* 5.0 0.4 + - - -
528A ARG* 5.3 4.6 - - - +
116F ASP* 4.2 17.2 + - - +
117F PRO* 5.4 0.6 - - - +
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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