Contacts of the strand formed by residues 510 - 514 (chain A) in PDB entry 1NHX
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 LYS 510 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429A GLU 3.1 13.3 + - - +
430A GLY* 3.3 2.8 - - - -
431A ILE 2.8 26.2 + - - +
446A GLU* 2.8 33.5 + - - +
508A LEU 3.6 2.2 + - - -
509A PRO* 1.3 72.4 - - - +
511A ILE* 1.3 62.3 + - - +
512A PHE* 3.6 32.4 - - + -
543A ARG* 3.4 36.7 - - - +
544A ILE* 4.0 15.7 - - + +
705A EDO 3.6 14.9 + - - +
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Residues in contact with ILE 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ILE* 3.3 16.8 - - + +
433A PHE* 3.9 28.7 - - + -
446A GLU* 3.5 7.1 - - - +
447A ALA* 2.8 40.6 + - + -
450A TRP* 3.5 37.2 - - + -
453A GLY* 3.8 36.3 - - - +
454A VAL* 4.4 2.0 - - - +
456A VAL* 4.9 4.0 - - + -
497A TRP* 4.7 6.1 - - + -
509A PRO 4.0 4.9 - - - +
510A LYS* 1.3 78.1 - - - +
512A PHE* 1.3 62.9 + - - +
705A EDO 2.9 11.3 + - - +
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Residues in contact with PHE 512 (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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280A LEU* 5.9 0.7 - - + -
430A GLY* 4.9 2.0 - - - -
431A ILE 2.9 13.8 + - - +
432A ILE* 3.6 5.6 - - + -
433A PHE* 2.8 28.1 + - - +
444A VAL* 4.6 0.9 - - + -
445A TYR 3.3 9.9 - - - +
446A GLU* 3.6 37.5 - - + +
447A ALA 4.7 0.7 - - - +
456A VAL* 5.2 0.4 - - - -
510A LYS* 3.6 43.7 - - + -
511A ILE* 1.3 80.4 - - - +
513A HIS* 1.3 63.2 + - - +
539A TRP* 3.8 14.1 - + - -
540A MET* 3.6 70.2 - - + -
543A ARG* 4.2 1.3 - - + -
544A ILE* 4.4 7.6 - - + -
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Residues in contact with HIS 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A PHE* 3.1 19.5 - - + -
434A GLY* 4.1 9.5 + - - -
435A GLY* 4.1 8.9 - - - -
437A ARG* 5.6 4.3 - - + -
441A VAL* 4.1 18.4 - - + +
442A PRO 5.1 0.4 + - - +
444A VAL* 3.2 4.7 - - - +
445A TYR* 2.8 72.2 + - + +
456A VAL* 3.7 24.2 - - + -
460A MET* 4.2 16.3 - - + +
461A ARG 5.6 2.7 + - - -
512A PHE* 1.3 75.2 - - - +
514A VAL* 1.3 78.9 + - - +
515A ASN* 5.1 1.1 - - + -
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Residues in contact with VAL 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 3.5 32.3 - - + -
432A ILE* 3.7 4.9 - - + -
433A PHE 2.8 11.5 + - - +
434A GLY* 3.2 16.4 - - - -
435A GLY 3.2 6.2 + - - -
442A PRO 4.7 0.4 - - - -
443A LEU 3.2 11.2 - - - +
444A VAL* 4.2 1.6 - - + -
513A HIS* 1.3 82.5 + - - +
515A ASN* 1.3 61.5 + - - +
516A TRP* 3.8 38.8 - - + -
536A VAL* 4.1 4.3 - - + -
540A MET* 3.4 33.7 - - + -
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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