Contacts of the strand formed by residues 513 - 518 (chain C) in PDB entry 6NID
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 513 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C LEU* 4.1 34.5 - - - -
506C LYS 3.5 7.0 - - - -
507C MET* 3.8 13.1 - - + -
511C ASN 4.3 0.2 + - - -
512C HIS* 1.3 69.6 - - - +
514C ILE* 1.3 61.0 + - - +
535C GLU* 3.3 7.6 + - - +
536C ILE* 2.9 46.7 + - - +
544C VAL* 4.0 14.4 - - + +
549C VAL* 5.2 4.7 - - - -
552C LEU* 4.1 22.0 - - + -
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Residues in contact with ILE 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505C LEU* 3.4 7.6 - - - -
506C LYS* 2.7 39.5 + - + +
508C ASN* 3.5 35.2 - - + +
512C HIS* 3.6 9.0 - - + +
513C CYS* 1.3 82.7 - - - +
515C VAL* 1.3 75.5 + - - +
516C ALA* 3.1 7.0 + - - +
533C GLY* 3.6 20.9 - - - +
534C ASP 3.4 6.7 - - - +
535C GLU* 3.7 24.9 - - + -
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Residues in contact with VAL 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C ILE* 4.3 10.3 - - + -
504C THR 3.8 6.1 - - - +
505C LEU* 4.1 14.8 - - + -
514C ILE* 1.3 70.0 - - - +
516C ALA* 1.3 62.2 + - - +
517C ARG 3.9 16.8 - - - +
518C ILE* 4.0 17.7 - - + -
530C LEU* 4.3 16.6 - - + -
531C HIS 3.7 18.6 - - - +
532C VAL* 3.4 3.5 - - - +
533C GLY 2.9 27.5 + - - -
534C ASP* 2.9 29.0 + - + +
536C ILE* 4.2 14.8 - - + -
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Residues in contact with ALA 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C THR* 2.9 21.4 + - - +
506C LYS* 3.9 29.8 - - + -
514C ILE* 3.1 6.8 + - + +
515C VAL* 1.3 74.0 - - - +
517C ARG* 1.3 70.6 + - - +
532C VAL* 3.6 16.7 - - - +
1474F GLU* 4.1 13.9 - - - +
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Residues in contact with ARG 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A VAL* 3.6 28.6 + - - +
489A ARG* 5.4 0.4 - - - +
490A LEU* 4.2 35.0 - - + +
566A LYS* 3.2 20.3 - - - +
503C ILE* 3.3 8.0 - - - +
504C THR* 3.0 39.6 + - + +
515C VAL* 3.5 2.4 - - - +
516C ALA* 1.3 84.2 + - - +
518C ILE* 1.3 69.3 + - - +
519C MET 4.2 0.2 - - - -
532C VAL* 4.0 5.2 - - + -
1474F GLU* 2.4 36.4 + - - -
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Residues in contact with ILE 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490A LEU* 5.1 2.3 - - - +
502C GLY 3.7 6.7 - - - +
503C ILE* 3.9 9.4 - - + -
515C VAL* 4.0 6.1 - - + -
517C ARG* 1.3 85.8 - - - +
519C MET* 1.3 64.7 + - - +
520C HIS* 3.2 4.0 + - - +
524C ILE* 4.2 9.2 - - + -
525C HIS* 3.6 45.5 - - + +
530C LEU 3.5 27.1 - - - +
531C HIS* 4.0 2.5 - - + -
532C VAL* 3.8 31.7 - - + +
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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