Contacts of the strand formed by residues 515 - 520 (chain B) in PDB entry 1NA8
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 515 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513B LEU 4.3 2.0 - - - +
514B PRO* 1.3 79.4 - - - +
516B THR* 1.3 74.4 + - - +
517B VAL* 3.4 12.9 + - + -
526B LEU* 3.3 4.7 - - - -
527B PHE* 2.7 47.4 + - + +
529B PHE* 4.1 11.0 - - + -
627B VAL* 4.4 14.8 - - + -
629B GLN* 3.8 48.7 - - + +
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Residues in contact with THR 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B PRO 4.2 1.0 + - - -
515B VAL* 1.3 77.9 - - - +
517B VAL* 1.3 60.3 + - - +
518B TYR 3.7 17.9 - - - +
519B ASP* 4.0 17.5 - - + +
524B ARG* 5.1 9.3 + - - +
526B LEU* 2.7 30.4 - - + +
629B GLN* 5.8 0.7 + - - -
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Residues in contact with VAL 517 (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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515B VAL* 4.0 8.7 - - + +
516B THR* 1.3 76.3 - - - +
518B TYR* 1.3 62.2 + - + +
525B ILE* 2.8 16.6 + - + +
527B PHE* 3.8 31.9 - - + -
560B PHE* 4.6 10.5 - - + -
610B TYR* 3.3 47.9 + - + -
626B ASP 5.5 1.2 - - - +
627B VAL* 3.4 25.5 - - + +
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Residues in contact with TYR 518 (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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516B THR* 3.7 4.8 - - - +
517B VAL* 1.3 80.2 - - + +
519B ASP* 1.3 66.6 + - - +
520B GLN* 3.4 40.0 - - + +
521B HIS* 3.4 19.4 - - - -
523B PHE* 3.4 18.2 - + - -
524B ARG* 3.3 1.6 - - - -
525B ILE* 2.8 40.7 + - + +
610B TYR* 3.5 21.5 - - + +
612B LEU* 3.7 26.0 - - + -
614B PHE* 3.5 14.1 - + - -
623B GLU* 2.5 46.6 + - + -
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Residues in contact with ASP 519 (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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524A ARG* 5.0 1.2 + - - -
516B THR* 4.0 14.2 - - + +
518B TYR* 1.3 81.7 - - - +
520B GLN* 1.3 71.4 + - - +
522B GLY* 5.0 4.2 + - - -
523B PHE 3.3 8.0 + - - +
524B ARG* 3.1 42.1 + - - +
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Residues in contact with GLN 520 (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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518B TYR* 3.4 38.5 - - + +
519B ASP* 1.3 82.3 + - - +
521B HIS* 1.3 81.7 + - + +
522B GLY 3.1 3.1 - - - +
523B PHE* 2.8 31.6 + - - +
623B GLU* 3.7 11.1 + - - -
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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