Contacts of the strand formed by residues 585 - 592 (chain A) in PDB entry 1N0U
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 ARG 585 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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576A LEU* 3.1 22.5 - - + +
577A SER 3.2 6.3 - - - +
578A LYS* 3.6 41.6 - - + +
582A LYS 5.3 5.0 + - - +
583A HIS 5.4 1.1 - - - -
584A ASN* 1.3 81.4 - - - +
586A ILE* 1.3 65.4 + - - +
587A TYR* 4.3 7.2 - - + -
691A VAL* 3.4 8.8 - - - +
692A THR* 2.9 43.3 + - - +
708A THR* 4.5 0.7 - - - -
840A ASP 2.9 23.8 + - - -
841A LYS 2.8 19.2 + - - -
842A LEU* 3.0 42.3 + - - +
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Residues in contact with ILE 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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575A ALA 3.5 3.6 - - - +
576A LEU* 3.5 4.0 - - - +
577A SER 3.0 28.0 + - - -
584A ASN* 6.4 0.2 - - + -
585A ARG* 1.3 79.7 - - - +
587A TYR* 1.3 68.8 + - - +
588A LEU* 4.1 26.0 - - + -
663A VAL* 4.8 7.2 - - + -
688A ILE* 4.6 10.8 - - + -
690A ASP 3.7 5.8 - - - +
691A VAL* 4.2 15.5 - - + -
693A LEU* 6.1 0.4 - - + -
705A ILE* 4.5 13.2 - - + +
708A THR* 3.5 26.0 - - + -
709A MET* 3.6 35.2 - - + +
712A ALA* 4.2 7.4 - - + +
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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
----------------------------------------------------------
574A THR* 3.9 20.2 - - + -
575A ALA 3.3 5.4 - - - -
576A LEU* 3.3 35.3 - - + +
585A ARG* 4.3 10.7 - - + -
586A ILE* 1.3 77.3 - - - +
588A LEU* 1.3 64.3 + - - +
688A ILE* 3.7 2.3 - - - -
689A LEU* 2.8 26.8 + - + -
690A ASP* 2.8 54.5 + - + +
692A THR* 4.2 19.3 - - + +
842A LEU* 3.6 30.2 - - + +
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Residues in contact with LEU 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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574A THR* 3.7 2.3 - - - +
575A ALA* 2.7 44.4 + - + +
586A ILE* 4.1 4.7 - - + -
587A TYR* 1.3 75.2 - - - +
589A LYS* 1.3 75.3 + - - +
590A ALA* 5.1 0.2 - - - -
686A VAL* 3.7 26.5 - - + -
687A ASN 3.2 20.0 - - - +
688A ILE* 4.1 3.1 - - + -
689A LEU* 4.1 4.7 - - - +
709A MET* 4.0 13.7 - - + -
712A ALA* 3.6 47.8 - - + +
713A THR* 3.8 11.7 - - - +
716A GLY* 4.0 11.0 - - - -
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Residues in contact with LYS 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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570A GLU* 3.7 34.5 + - + +
571A SER* 3.6 20.2 + - - +
572A SER 5.9 0.4 - - - -
573A GLN* 4.3 3.9 - - - +
574A THR* 3.3 36.6 - - - +
588A LEU* 1.3 85.9 - - - +
590A ALA* 1.3 62.8 + - - +
685A ARG 4.0 0.2 - - - +
686A VAL* 3.6 1.0 - - - -
687A ASN* 2.9 37.9 + - + +
689A LEU* 3.6 21.3 - - + +
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Residues in contact with ALA 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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567A VAL* 4.6 1.6 - - + -
569A SER 3.8 0.5 - - - +
570A GLU* 3.1 4.4 - - - +
571A SER* 2.8 31.5 + - - -
588A LEU* 4.3 1.2 - - + +
589A LYS* 1.3 75.2 - - - +
591A GLU* 1.3 60.6 + - - +
684A VAL* 4.5 9.0 - - + -
685A ARG 3.1 10.1 - - - +
686A VAL* 4.4 12.6 - - + +
716A GLY* 3.7 25.6 - - - +
717A PHE* 3.9 10.3 - - + +
720A ALA* 3.9 6.9 - - + +
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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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567A VAL* 3.5 7.8 - - - +
569A SER 3.8 3.4 - - - -
570A GLU* 4.0 21.6 - - + +
590A ALA* 1.3 77.1 - - - +
592A PRO* 1.3 78.5 - - + +
685A ARG* 2.8 71.1 + - + +
687A ASN* 2.8 24.6 - - - +
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Residues in contact with PRO 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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566A THR* 5.6 0.2 - - - +
567A VAL* 3.3 26.0 - - + +
568A GLU* 3.3 25.4 - - - +
569A SER* 3.4 14.1 - - - +
570A GLU 4.0 0.7 - - - +
591A GLU* 1.3 102.4 - - + +
593A ILE* 1.3 66.3 + - - +
594A ASP* 3.9 1.6 + - - -
683A SER* 3.6 7.4 - - - +
685A ARG* 4.7 1.6 - - - +
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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