Contacts of the strand formed by residues 497 - 502 (chain A) in PDB entry 5ES4
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 HIS 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A THR 2.7 4.4 + - - -
469A ARG* 3.2 1.0 - - - -
470A GLY 2.7 27.0 + - - -
494A GLU* 3.4 42.2 + - + +
495A GLN* 3.4 3.9 + - - +
496A GLY* 1.3 87.0 + - - +
498A PRO* 1.3 58.7 - - - +
499A TRP 3.1 4.0 + - - +
500A GLY* 3.4 9.1 + - - -
526A GLY 5.7 0.2 - - - +
527A GLU* 3.9 26.2 - - + +
528A GLU* 3.1 50.8 + - + +
552A ARG* 4.3 0.8 + - - -
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Residues in contact with PRO 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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463A HIS* 5.7 0.3 - - - -
464A TYR 4.2 4.2 - - - +
465A TYR* 4.6 9.2 - - + +
466A GLU 4.3 4.7 - - - +
467A GLN 3.7 22.7 - - - +
468A THR* 3.4 4.0 - - - +
469A ARG* 3.8 7.6 - - - +
470A GLY* 3.0 21.2 - - - +
496A GLY 3.8 5.6 - - - +
497A HIS* 1.3 86.2 - - - +
499A TRP* 1.3 97.5 + - + +
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Residues in contact with TRP 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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462A PRO 5.6 2.2 - - - -
463A HIS* 5.4 16.6 - + + +
465A TYR* 3.6 33.7 - + - -
470A GLY* 4.4 1.6 - - - -
497A HIS* 3.1 1.3 - - - -
498A PRO* 1.3 110.6 + - + +
500A GLY* 1.3 59.5 + - - +
501A ARG* 3.3 10.5 + - + +
526A GLY* 3.3 17.8 - - - +
530A ASN* 5.2 2.4 + - - +
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Residues in contact with GLY 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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470A GLY 4.0 4.8 + - - -
497A HIS* 3.4 12.8 + - - -
498A PRO 3.7 0.2 - - - -
499A TRP* 1.3 75.8 - - - +
501A ARG* 1.3 60.9 + - - +
502A PHE 3.4 2.0 - - - -
524A ALA* 3.0 14.9 - - - +
526A GLY 2.7 35.9 + - - -
527A GLU* 3.2 20.3 + - - -
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Residues in contact with ARG 501 (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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462A PRO* 3.3 25.2 + - + +
463A HIS* 4.8 16.2 + - + +
470A GLY 3.7 3.0 + - - -
499A TRP* 3.3 9.1 - - + +
500A GLY* 1.3 81.0 - - - +
502A PHE* 1.3 59.8 + - - +
504A ALA* 3.2 20.5 - - + +
523A GLY 2.9 15.4 - - - +
524A ALA* 3.2 3.7 - - - -
525A PRO* 3.6 23.9 - - + +
526A GLY* 3.6 16.6 - - - +
530A ASN* 3.3 6.5 + - - -
564A TYR* 3.1 41.4 - - - -
567A GLN* 5.0 7.7 - - - +
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Residues in contact with PHE 502 (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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462A PRO* 3.6 5.0 - - - +
470A GLY 3.2 17.1 + - - +
471A GLY* 3.0 7.2 - - - -
472A GLN* 2.9 35.7 + - - -
473A VAL* 3.8 17.3 - - + -
491A LEU* 3.7 11.0 - - + -
492A TYR* 3.2 42.0 - - - -
493A GLY* 3.6 20.0 - - - +
500A GLY 3.4 0.8 - - - -
501A ARG* 1.3 74.8 - - - +
503A GLY* 1.3 58.7 + - - +
522A ILE* 3.5 34.1 - - + -
523A GLY 3.5 4.0 - - - -
524A ALA* 3.8 7.4 - - + -
527A GLU* 4.8 2.2 - - - +
535A TYR* 3.8 30.1 - + - -
537A PHE* 4.1 4.5 - + - -
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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