Contacts of the strand formed by residues 490 - 499 (chain A) in PDB entry 5NER
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 490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488A PRO* 3.5 12.3 - - + +
489A ARG* 1.3 101.6 - - + +
491A LEU* 1.3 73.0 + - - +
492A ASN* 4.2 0.8 - - - +
526A THR* 5.1 15.5 + - + +
527A ILE 3.8 4.5 - - - +
528A SER* 4.3 18.0 - - - -
568A ALA* 6.0 0.3 - - - -
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Residues in contact with LEU 491 (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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441A ILE* 3.8 42.4 - - + -
481A ALA* 4.2 14.4 - - + -
487A LEU* 5.6 2.2 - - + -
488A PRO* 4.5 21.1 - - + +
490A LYS* 1.3 83.6 - - - +
492A ASN* 1.3 58.4 + - - +
493A PHE* 3.3 21.3 - - + -
526A THR* 4.1 2.4 - - - +
527A ILE* 2.6 45.7 + - + +
529A ARG* 4.4 21.8 - - + +
563A LEU* 4.4 9.9 - - + -
568A ALA* 4.8 13.0 - - + -
576A PRO* 5.7 0.2 - - + -
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Residues in contact with ASN 492 (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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490A LYS 4.2 0.7 - - - +
491A LEU* 1.3 73.6 - - - +
493A PHE* 1.3 62.0 + - - +
525A MET 3.3 4.3 - - - +
526A THR* 3.4 27.5 - - + +
563A LEU* 3.3 16.0 - - - +
564A ASP* 3.5 20.3 + - - +
567A THR* 3.3 34.8 + - - +
568A ALA* 5.9 0.3 - - - +
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Residues in contact with PHE 493 (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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441A ILE* 5.0 2.9 - - + -
443A VAL* 4.9 7.0 - - + -
479A LEU* 5.1 8.5 - - + -
481A ALA* 4.2 12.8 - - + -
491A LEU* 3.3 38.8 - - + -
492A ASN* 1.3 70.3 - - - +
494A GLN* 1.3 62.4 + - - +
495A VAL* 4.0 13.0 - - + -
524A ASN* 3.8 4.7 - - - +
525A MET* 2.4 48.1 + - + +
527A ILE* 3.5 30.5 - - + -
561A TYR* 4.2 27.8 - + + -
562A ARG 3.4 6.1 - - - +
563A LEU* 3.7 34.1 - - + -
578A LEU* 4.6 11.4 - - + -
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Residues in contact with GLN 494 (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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493A PHE* 1.3 72.3 - - - +
495A VAL* 1.3 62.2 + - - +
496A GLU* 3.9 8.9 + - - +
522A SER* 4.3 10.5 - - - -
523A LYS 3.5 5.2 + - - -
524A ASN* 2.8 43.4 + - - +
560A GLU 3.7 1.2 - - - +
561A TYR* 3.2 3.4 - - - -
562A ARG* 2.7 46.2 + - + +
611A NAG 3.3 46.6 + - - +
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Residues in contact with VAL 495 (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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477A PHE* 3.6 35.7 - - + -
479A LEU* 4.0 15.0 - - + -
493A PHE* 4.7 2.7 - - + -
494A GLN* 1.3 78.2 + - - +
496A GLU* 1.3 63.8 + - - +
497A LEU* 3.7 15.2 - - + +
521A HIS 4.2 0.3 - - - +
522A SER* 3.4 7.3 - - - -
523A LYS* 3.0 43.5 + - + +
525A MET* 3.9 20.0 - - + -
559A MET* 3.8 12.8 - - + -
560A GLU 3.3 9.2 - - - +
561A TYR* 4.3 6.3 - - + +
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Residues in contact with GLU 496 (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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494A GLN* 4.5 8.5 + - - +
495A VAL* 1.3 74.0 - - - +
497A LEU* 1.3 74.1 + - - +
498A LEU* 4.4 12.1 - - + +
520A SER* 4.5 8.5 - - - -
521A HIS 3.9 15.7 + - - +
522A SER* 3.3 23.6 - - - -
558A PHE* 3.6 1.4 - - - +
559A MET* 3.3 5.2 - - - -
560A GLU* 2.5 59.7 + - + +
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Residues in contact with LEU 497 (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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447A LEU* 5.3 2.0 - - + -
475A VAL* 4.1 21.1 - - + -
477A PHE* 3.7 31.9 - - + -
495A VAL* 3.7 14.4 - - + -
496A GLU* 1.3 85.2 - - - +
498A LEU* 1.3 69.9 + - - +
513A PHE* 4.0 24.9 - - + -
519A PRO 3.6 1.6 - - - +
520A SER* 3.5 1.2 - - - -
521A HIS* 2.9 41.8 + - + +
523A LYS* 6.4 0.4 - - + -
538A LEU* 4.3 7.6 - - + -
557A ILE* 5.5 2.9 - - + -
558A PHE 3.3 7.4 - - - +
559A MET* 3.7 22.4 - - + -
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Residues in contact with LEU 498 (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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496A GLU* 4.5 15.0 - - + +
497A LEU* 1.3 83.3 - - - +
499A LEU* 1.3 66.3 + - - +
501A LYS* 3.3 45.9 + - + +
509A ARG* 6.6 0.4 - - - -
519A PRO* 3.6 3.8 - - + +
520A SER* 3.7 25.6 - - - +
556A THR 3.6 1.7 - - - +
557A ILE* 3.6 4.0 - - - +
558A PHE* 2.9 40.8 + - + +
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Residues in contact with LEU 499 (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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473A PHE* 5.1 3.4 - - + -
475A VAL* 4.4 7.6 - - + -
498A LEU* 1.3 72.9 - - - +
500A ASP* 1.3 73.9 + - - +
501A LYS* 4.5 0.5 - - - -
509A ARG* 3.9 16.3 - - - +
511A ALA* 3.4 19.5 - - + +
512A LEU* 3.5 37.9 - - - +
513A PHE* 3.6 35.0 - - + +
519A PRO* 3.1 10.8 + - - +
540A ALA* 3.6 16.6 - - + -
555A ILE* 5.1 0.4 - - + -
556A THR 4.1 0.9 - - - -
557A ILE* 3.6 34.3 - - + -
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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