Contacts of the strand formed by residues 519 - 523 (chain R) 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 LEU 519 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498R LEU* 3.6 37.2 - - + +
501R LEU* 3.6 23.8 - - + -
502R ALA* 3.6 27.8 - - + +
509R SER* 3.7 14.8 - - - +
510R SER 3.2 13.2 - - - +
511R TYR* 3.7 9.4 - - + -
516R PHE* 4.5 1.3 - - - -
518R GLY* 1.3 73.0 - - - -
520R ILE* 1.3 86.9 + - - +
521R TYR* 4.0 3.8 - - + +
530R LEU 3.5 1.6 - - - +
531R LEU* 3.7 1.9 - - - -
532R ILE* 2.9 46.2 + - + +
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Residues in contact with ILE 520 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162R LEU* 4.0 31.4 - - + -
509R SER* 3.1 1.4 - - - -
510R SER* 2.3 57.8 + - - +
512R GLU* 4.3 10.5 + - - +
516R PHE* 4.9 15.5 - - + -
518R GLY 5.3 0.2 - - - +
519R LEU* 1.3 77.1 - - - +
521R TYR* 1.3 58.9 + - - +
522R ARG* 3.9 30.7 - - + +
529R VAL* 4.1 11.7 - - + -
530R LEU 3.9 2.5 - - - -
531R LEU* 5.1 6.5 - - + +
13X A 4.5 7.0 - - - +
14X T 4.3 22.2 - - - +
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Residues in contact with TYR 521 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501R LEU* 5.4 3.6 - - + -
505R HIS* 4.8 8.5 - + + -
508R PHE* 3.2 43.1 - + + -
509R SER* 2.9 23.8 - - - +
519R LEU* 4.2 6.7 - - + -
520R ILE* 1.3 74.7 - - - +
522R ARG* 1.3 62.3 + - - +
523R MET* 3.3 48.8 - - + +
529R VAL* 3.2 11.6 - - - +
530R LEU* 2.9 64.7 + - + +
532R ILE* 4.6 4.0 - - + -
556R ILE* 3.7 22.4 - - + +
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Residues in contact with ARG 522 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162R LEU* 4.9 4.8 - - - +
166R LYS* 3.2 47.3 - - - +
507R THR 5.4 1.8 - - - +
508R PHE* 2.3 62.9 + - - +
509R SER* 5.3 2.9 - - - +
510R SER* 6.2 1.3 - - - -
520R ILE* 3.9 22.2 - - + +
521R TYR* 1.3 71.1 - - - -
523R MET* 1.3 60.3 + - - +
524R VAL* 4.1 5.9 + - + +
528R ILE 4.3 0.9 - - - -
529R VAL* 3.6 26.5 - - - +
14X T 4.5 11.3 + - - -
15X T 3.8 13.9 + - - -
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Residues in contact with MET 523 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508R PHE* 5.4 1.8 - - + -
521R TYR* 3.3 43.4 - - + +
522R ARG* 1.3 72.3 - - - +
524R VAL* 1.3 60.6 + - - +
525R LYS* 3.4 27.4 - - + +
526R PRO 2.9 10.2 - - - +
527R LYS* 3.0 4.2 - - - +
528R ILE 2.8 44.8 + - - +
530R LEU* 4.3 2.0 - - + -
552R ALA* 3.6 43.5 - - + +
555R ALA* 4.8 7.4 - - + -
556R ILE* 4.3 13.5 - - + +
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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