Contacts of the strand formed by residues 493 - 499 (chain A) in PDB entry 4P3N
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 SER 493 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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491A GLY 4.0 2.2 + - - -
492A PHE* 1.3 75.2 - - - +
494A PHE* 1.3 66.9 + - - +
548A ILE* 3.6 2.1 - - - -
549A LYS* 3.0 49.6 + - - +
555A TYR* 5.0 1.7 + - - -
678C GLU* 4.5 3.4 - - - -
681C LYS* 6.2 0.2 - - - -
682C ILE* 3.4 39.6 - - - +
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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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480A LEU* 6.1 0.4 - - + -
483A LEU* 4.5 4.7 - - + -
484A ARG* 4.0 36.1 - - + -
487A TYR* 3.8 17.5 - + + -
492A PHE 3.8 15.7 - - - -
493A SER* 1.3 78.8 + - - +
495A LYS* 1.3 63.3 + - - +
496A LEU* 4.3 16.7 - - + +
526A PHE* 4.1 28.3 - + - -
528A GLU* 5.0 15.4 - - + +
546A ILE* 3.3 24.5 - - + -
547A GLN 3.2 15.3 - - - +
548A ILE* 4.2 5.6 - - + -
549A LYS 4.7 0.9 - - - +
555A TYR* 5.1 1.8 - - - -
678C GLU* 5.0 7.4 + - - +
682C ILE* 5.6 0.2 - - - +
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Residues in contact with LYS 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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494A PHE* 1.3 76.1 - - - +
496A LEU* 1.3 63.9 + - - +
497A ASN* 5.1 1.1 - - - +
529A LYS 5.5 1.6 - - - -
531A GLU* 6.0 0.2 + - - -
546A ILE* 3.2 10.2 - - - +
547A GLN* 2.9 57.0 + - + +
555A TYR* 3.6 49.4 - - + +
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Residues in contact with LEU 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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480A LEU* 4.0 20.2 - - + -
483A LEU* 4.8 2.0 - - + -
494A PHE* 4.3 12.6 - - + +
495A LYS* 1.3 78.4 - - - +
497A ASN* 1.3 61.4 + - - +
523A LEU* 4.4 16.2 - - + +
526A PHE* 3.9 32.3 - - + -
528A GLU* 4.2 16.4 - - + +
529A LYS 4.4 8.8 + - - +
530A TRP* 3.4 15.1 - - + -
531A GLU* 3.0 23.4 + - - +
544A ILE* 4.3 7.6 - - + -
545A ASP 3.6 1.8 - - - -
546A ILE* 3.8 31.6 - - + -
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Residues in contact with ASN 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 LYS 5.1 0.7 - - - +
496A LEU* 1.3 76.0 - - - +
498A LEU* 1.3 58.3 + - - +
499A SER* 3.8 11.0 + - - -
523A LEU* 5.4 0.9 - - - -
530A TRP* 5.0 0.4 - - - -
531A GLU* 3.3 17.3 - - + +
533A ASN* 3.1 29.9 - - - +
544A ILE* 3.4 7.4 - - - +
545A ASP* 2.8 76.0 + - - +
546A ILE* 4.7 1.0 - - - -
547A GLN* 5.0 10.0 - - - +
557A GLN* 5.1 0.2 - - - +
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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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497A ASN* 1.3 70.4 - - - +
499A SER* 1.3 76.1 + - - +
500A THR* 3.7 19.7 - - + -
516A GLU* 4.8 2.7 - - + +
519A LEU* 4.3 20.4 - - + -
520A GLU* 3.8 34.8 - - + +
523A LEU* 3.7 29.1 - - + +
530A TRP* 3.9 17.4 - - + -
531A GLU 2.9 9.3 + - - -
532A LEU* 3.6 7.9 - - + +
533A ASN* 2.9 31.5 + - - +
542A PRO* 5.0 0.7 - - + -
543A LYS 3.6 9.9 - - - +
544A ILE* 4.6 4.9 - - + +
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Residues in contact with SER 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 ASN* 3.8 15.8 + - - -
498A LEU* 1.3 76.7 + - - +
500A THR* 1.3 61.2 + - - +
533A ASN* 3.4 7.6 + - - +
536A ASP* 3.6 19.1 + - - +
537A GLY* 3.6 22.1 - - - -
542A PRO* 3.5 4.2 - - - +
543A LYS* 2.9 55.5 + - - +
545A ASP* 4.8 0.2 + - - -
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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