Contacts of the helix formed by residues 584 - 596 (chain A) in PDB entry 1NYR
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 584 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582A ASN* 5.5 8.0 - - - +
583A GLU* 1.3 84.2 + - - +
585A MET* 1.3 71.9 + - - +
586A GLY 4.8 1.3 - - - +
587A TYR* 3.0 24.4 + - + +
588A LYS* 3.2 4.0 + - - +
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Residues in contact with MET 585 (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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551A ILE* 4.1 17.7 - - - -
552A PRO 5.3 0.2 - - - +
553A VAL* 4.0 32.3 - - + +
583A GLU 3.6 2.3 + - - -
584A LYS* 1.3 69.9 - - - +
586A GLY* 1.3 53.4 + - - +
588A LYS* 2.6 34.4 + - - +
589A ILE* 2.8 38.7 + - + +
602A VAL* 3.7 29.6 - - + -
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Residues in contact with GLY 586 (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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584A LYS* 3.5 2.4 - - - +
585A MET* 1.3 76.8 - - - +
587A TYR* 1.3 66.4 + - - +
589A ILE* 3.6 11.1 - - - +
590A ARG* 2.8 27.4 + - - +
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Residues in contact with TYR 587 (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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581A ARG* 3.9 22.3 + - - -
583A GLU* 3.1 54.1 + - + +
584A LYS* 3.0 20.2 + - + +
585A MET 2.9 0.4 + - - -
586A GLY* 1.3 77.3 - - - +
588A LYS* 1.3 59.0 + - - +
590A ARG* 3.6 10.4 - - + +
591A GLU* 2.8 43.3 + - + +
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Residues in contact with LYS 588 (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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549A GLN* 5.7 0.5 - - - +
551A ILE* 3.4 32.2 - - + +
552A PRO 4.7 4.8 + - - -
555A VAL* 4.2 11.9 - - - +
579A ASP* 2.7 59.4 + - - +
580A ASP 4.1 1.4 - - - -
581A ARG* 2.8 39.6 + - - +
583A GLU* 3.8 23.9 + - + +
584A LYS 3.2 5.1 + - - +
585A MET* 2.6 16.3 + - - +
587A TYR* 1.3 72.5 - - - +
589A ILE* 1.3 62.1 + - - -
591A GLU* 3.5 2.6 + - - +
592A ALA* 3.1 22.2 + - - +
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Residues in contact with ILE 589 (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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551A ILE* 3.7 12.8 - - + -
585A MET* 2.8 53.4 + - + +
586A GLY* 3.8 9.4 - - - +
588A LYS* 1.3 69.5 - - - +
590A ARG* 1.3 63.9 + - + +
592A ALA* 2.7 23.7 + - - +
593A GLN* 2.8 25.0 + - + +
600A GLN* 3.3 33.9 - - - +
602A VAL* 4.7 6.1 - - + -
616A ARG* 5.8 1.8 - - - +
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Residues in contact with ARG 590 (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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586A GLY 2.8 22.2 + - - +
587A TYR* 3.6 10.4 - - - +
589A ILE* 1.3 79.1 - - + +
591A GLU* 1.3 62.4 + - - +
593A GLN* 3.8 6.1 - - - +
594A MET* 3.0 50.8 + - + +
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Residues in contact with GLU 591 (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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549A GLN* 5.9 1.0 + - - -
579A ASP* 5.0 0.2 - - - +
581A ARG* 3.1 42.8 + - - +
587A TYR* 2.8 32.5 + - + +
588A LYS 3.8 5.2 - - - +
589A ILE 3.1 0.2 - - - -
590A ARG* 1.3 80.4 - - - +
592A ALA* 1.3 61.6 + - - +
594A MET* 4.0 4.9 - - - +
595A GLN* 3.2 46.5 + - - +
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Residues in contact with ALA 592 (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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549A GLN* 4.6 23.6 - - + +
551A ILE* 5.0 1.1 - - + -
588A LYS 3.1 13.0 + - - +
589A ILE 2.7 14.5 + - - +
591A GLU* 1.3 73.1 - - - +
593A GLN* 1.3 62.5 + - - +
595A GLN* 3.3 2.3 + - - -
596A LYS 3.1 15.8 + - - -
597A ILE* 3.4 27.8 + - + +
600A GLN* 4.2 20.4 - - + +
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Residues in contact with GLN 593 (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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589A ILE* 2.8 31.5 + - + +
590A ARG* 3.8 6.3 - - - +
592A ALA* 1.3 78.1 - - - +
594A MET* 1.3 74.9 + - + +
596A LYS* 3.1 17.4 + - - +
600A GLN* 2.7 25.7 + - - +
616A ARG* 2.8 46.2 + - - +
618A TYR* 3.7 31.5 + - + +
619A GLY* 4.1 0.6 - - - +
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Residues in contact with MET 594 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A GLU* 5.9 0.3 - - - +
250A LEU* 3.8 11.4 - - - +
590A ARG* 3.0 50.6 + - + +
591A GLU* 4.1 5.4 - - - +
593A GLN* 1.3 88.3 - - + +
595A GLN* 1.3 60.2 + - + +
596A LYS* 3.2 11.8 + - - +
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Residues in contact with GLN 595 (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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249A GLU 5.7 3.1 - - - +
250A LEU* 4.2 18.5 - - + +
537A GLY 5.0 0.3 - - - +
546A LYS* 4.4 11.6 - - - -
549A GLN* 4.9 4.7 + - - -
591A GLU* 3.2 49.4 + - - +
592A ALA* 5.1 0.3 - - - -
593A GLN 3.2 0.8 - - - -
594A MET* 1.3 74.8 - - + +
596A LYS* 1.3 72.0 + - - +
597A ILE* 3.2 27.9 + - + +
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Residues in contact with LYS 596 (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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246A ILE* 5.0 7.7 - - - +
249A GLU* 5.3 3.8 + - - -
250A LEU* 4.5 13.3 - - + +
536A LYS* 2.7 30.4 + - - +
537A GLY* 3.7 26.5 - - - +
538A ALA* 4.3 6.3 - - + +
539A PHE 5.6 0.5 + - - -
544A ALA* 5.7 0.2 - - - +
592A ALA 3.1 1.6 + - - -
593A GLN 3.1 13.9 + - - +
594A MET* 3.8 10.5 + - - +
595A GLN* 1.3 82.0 - - - +
597A ILE* 1.3 66.3 + - - +
598A PRO* 3.3 8.0 - - - +
618A TYR* 3.1 48.8 - - + +
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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