Contacts of the strand formed by residues 491 - 500 (chain A) in PDB entry 5FFO
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 491 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A PRO* 4.4 9.8 - - + +
490A ARG* 1.3 83.5 - - + +
492A LEU* 1.3 65.7 + - - +
493A ASN* 4.0 6.3 + - - +
527A THR* 4.1 23.3 - - + -
528A ILE 3.8 2.0 - - - -
529A SER* 3.5 27.2 + - - +
568A THR* 4.5 11.8 + - - +
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Residues in contact with LEU 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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442A ILE* 4.3 34.1 - - + -
482A ALA* 4.4 11.0 - - + -
483A ASP 5.2 0.4 - - - +
488A LEU* 4.6 11.4 - - + -
489A PRO* 4.2 17.5 - - + +
490A ARG 3.3 7.4 + - - +
491A LYS* 1.3 76.0 - - - +
493A ASN* 1.3 62.0 + - - +
494A PHE* 3.4 22.6 - - + -
528A ILE* 2.9 34.0 + - + +
530A ARG* 4.2 22.0 - - + +
564A LEU* 4.3 9.0 - - + -
569A ALA* 3.9 25.6 - - + -
577A PRO* 5.7 0.9 - - + -
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Residues in contact with ASN 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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491A LYS* 4.0 8.1 + - - +
492A LEU* 1.3 71.2 - - - +
494A PHE* 1.3 60.6 + - - +
495A GLN* 5.7 0.4 - - - -
526A MET 3.4 4.5 - - - +
527A THR* 2.7 34.6 + - - +
564A LEU* 3.1 6.9 - - - +
565A ASP* 3.1 32.8 + - + +
568A THR* 3.6 32.1 + - + +
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Residues in contact with PHE 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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442A ILE* 5.0 6.7 - - + -
444A VAL* 5.0 13.9 - - + -
480A LEU* 4.2 21.8 - - + -
482A ALA* 3.7 21.8 - - + -
492A LEU* 3.4 31.2 - - + -
493A ASN* 1.3 72.4 - - - +
495A GLN* 1.3 62.6 + - - +
496A VAL* 4.0 3.1 - - + -
525A ASN* 3.6 2.1 - - - +
526A MET* 2.4 63.3 + - + +
528A ILE* 3.4 31.0 - - + -
562A TYR* 5.1 8.1 - + + -
563A ARG 3.2 24.5 - - - +
564A LEU* 4.3 16.8 - - + -
579A LEU* 5.6 6.1 - - + -
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Residues in contact with GLN 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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493A ASN 4.3 0.6 + - - +
494A PHE* 1.3 74.6 - - - +
496A VAL* 1.3 61.6 + - - +
497A GLU* 4.2 17.1 + - - +
524A LYS 4.1 3.8 - - - -
525A ASN* 4.0 17.3 - - - +
562A TYR* 3.7 0.7 - - - -
563A ARG* 2.9 46.6 + - + +
564A LEU 5.3 4.9 - - - -
565A ASP* 3.8 25.8 - - + +
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Residues in contact with VAL 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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478A PHE* 4.7 12.3 - - + -
480A LEU* 4.0 27.8 - - + -
494A PHE* 4.4 8.7 - - + -
495A GLN* 1.3 75.7 - - - +
497A GLU* 1.3 65.9 + - - +
498A LEU* 3.6 22.6 - - + +
522A HIS 3.9 1.6 - - - +
523A SER* 3.8 1.4 - - - -
524A LYS* 3.2 38.7 + - + +
526A MET* 4.6 11.2 - - + -
560A MET* 4.5 13.5 - - + -
561A GLU 3.3 16.4 - - - +
562A TYR* 4.2 7.9 - - + -
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Residues in contact with GLU 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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495A GLN* 4.3 18.1 + - + +
496A VAL* 1.3 85.8 + - - +
498A LEU* 1.3 63.1 + - - +
499A LEU* 4.5 8.0 + - + -
521A SER* 6.5 0.2 - - - -
522A HIS 4.0 2.5 - - - +
523A SER* 3.4 30.3 + - - -
559A PHE* 5.3 0.2 - - - -
561A GLU* 2.8 62.9 + - + +
563A ARG* 6.2 3.8 - - + -
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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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448A LEU* 5.8 1.1 - - + -
476A VAL* 4.3 16.6 - - + -
478A PHE* 4.1 31.0 - - + -
496A VAL* 3.6 23.1 - - + -
497A GLU* 1.3 83.0 - - - +
499A LEU* 1.3 63.1 + - - +
500A LEU* 4.2 2.5 - - + -
514A PHE* 4.1 28.3 - - + -
520A PRO 4.0 0.6 - - - +
521A SER* 3.2 28.6 - - - -
522A HIS* 3.4 16.5 + - + +
558A ILE* 5.6 5.4 - - + -
559A PHE 3.5 10.1 - - - +
560A MET* 3.8 21.5 - - + -
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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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497A GLU* 4.5 7.6 + - + -
498A LEU* 1.3 76.4 - - - +
500A LEU* 1.3 64.6 + - - +
501A ASP 3.9 0.3 + - - -
502A LYS* 4.1 30.8 + - + +
520A PRO 4.0 2.2 - - - +
521A SER* 3.6 25.8 - - - -
557A THR 4.1 0.3 - - - +
558A ILE* 5.6 0.2 - - - -
559A PHE* 2.9 66.0 + - + +
561A GLU* 5.0 6.5 - - - +
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Residues in contact with LEU 500 (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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474A PHE* 4.8 5.4 - - + -
476A VAL* 5.0 5.4 - - + -
498A LEU* 6.2 1.6 - - + -
499A LEU* 1.3 74.7 - - - +
501A ASP* 1.3 71.6 + - - +
502A LYS* 3.3 0.9 + - - -
510A ARG* 3.8 13.2 + - - +
512A ALA* 3.6 20.9 - - + +
513A LEU* 3.6 28.5 - - - +
514A PHE* 3.7 30.1 - - + -
520A PRO* 3.3 17.8 + - - +
541A ALA* 3.8 24.0 - - + -
556A ILE* 5.5 0.7 - - + -
557A THR 4.3 1.3 - - - -
558A ILE* 3.8 33.4 - - + -
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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