Contacts of the helix formed by residues 495 - 503 (chain I) in PDB entry 5G04
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 ASN 495 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491I ASN* 4.8 0.4 - - - +
493I GLU* 3.3 0.6 - - - -
494I GLY* 1.3 74.0 - - - +
496I GLN* 1.3 54.3 + - - +
497I TRP 3.3 0.9 - - - -
498I TYR* 2.8 31.7 + - + +
499I ASP* 2.8 35.1 + - - +
448O MET 3.8 1.6 - - - +
449O ASN* 3.6 21.5 + - - +
459O GLN* 3.7 2.9 - - - +
460O GLN* 3.2 30.7 - - - +
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Residues in contact with GLN 496 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494I GLY 3.5 4.2 + - - +
495I ASN* 1.3 71.1 - - - +
497I TRP* 1.3 57.6 + - - +
499I ASP* 3.2 20.0 - - + +
500I PHE* 3.1 27.0 + - - +
228O THR* 6.0 0.6 + - - -
459O GLN* 5.7 4.5 - - + +
460O GLN* 3.4 24.5 - - + +
462O ASN* 5.3 4.2 + - - +
492O HIS* 3.1 23.6 - - - -
495O GLU* 2.6 37.2 + - - +
496O ARG* 3.2 21.6 + - - +
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Residues in contact with TRP 497 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495I ASN 3.3 0.4 - - - -
496I GLN* 1.3 77.8 - - - +
498I TYR* 1.3 53.4 + + - +
500I PHE* 3.7 4.4 - + - -
501I LEU* 2.8 59.7 + - + +
507I LEU* 3.9 33.7 - - + -
513I LEU* 4.1 16.4 - - + -
516I TYR* 2.8 22.9 + + - -
443O GLN* 4.7 1.2 + - - -
446O LEU* 2.7 41.0 + - + +
460O GLN* 3.3 23.9 - - + +
470O LEU* 3.9 11.2 - - + -
473O LEU* 3.7 20.9 - - + -
489O VAL* 5.3 1.6 - - + -
492O HIS* 3.0 48.6 + + + +
496O ARG* 4.5 2.7 - - - +
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Residues in contact with TYR 498 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493I GLU* 3.8 22.2 - - + +
495I ASN* 2.8 33.9 + - + +
497I TRP* 1.3 75.0 - - - +
499I ASP* 1.3 61.1 + - - +
501I LEU* 4.6 2.9 - - + +
502I GLN* 3.0 29.3 + - + +
516I TYR* 3.0 60.3 - + + +
518I PRO* 5.1 10.7 - - + +
446O LEU 4.7 1.8 - - - -
447O SER* 3.3 28.6 + - - -
449O ASN* 4.6 5.2 - - - -
460O GLN* 3.9 4.6 - - - +
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Residues in contact with ASP 499 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493I GLU* 2.8 36.8 - - - +
494I GLY 3.9 5.9 - - - +
495I ASN 2.8 19.8 + - - +
496I GLN* 3.2 27.6 + - + +
498I TYR* 1.3 73.6 - - - +
500I PHE* 1.3 56.8 + - - +
502I GLN* 3.7 4.5 - - - +
503I ASN* 3.3 36.8 + - - +
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Residues in contact with PHE 500 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496I GLN 3.1 15.5 + - - +
497I TRP* 3.3 7.1 + + - +
499I ASP* 1.3 75.4 - - - +
501I LEU* 1.3 63.9 + - - +
502I GLN 3.3 0.4 - - - -
503I ASN* 3.4 23.6 + - + +
504I SER 4.5 6.6 + - - +
505I SER* 3.7 13.5 + - - -
507I LEU* 3.6 23.1 - - + -
488O GLU* 3.5 30.5 - - - -
491O LYS* 3.4 37.5 - - + -
492O HIS* 3.9 32.8 - + + +
495O GLU* 4.1 20.6 - - - +
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Residues in contact with LEU 501 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497I TRP* 2.8 49.9 + - + +
498I TYR* 4.9 2.5 - - + +
500I PHE* 1.3 72.9 - - - +
502I GLN* 1.3 63.8 + - - +
503I ASN 3.5 2.9 + - - +
505I SER* 4.2 5.7 + - - +
507I LEU* 3.8 17.7 - - + -
508I LYS* 3.7 50.8 + - + +
513I LEU* 4.1 11.2 - - + -
514I PHE 5.4 4.0 - - - +
516I TYR* 3.5 33.9 - - + +
443O GLN* 6.0 0.4 - - - +
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Residues in contact with GLN 502 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493I GLU* 3.3 32.7 + - - +
498I TYR* 3.0 22.8 + - + +
499I ASP 3.7 4.7 - - - +
501I LEU* 1.3 76.4 - - - +
503I ASN* 1.3 69.2 + - - +
508I LYS* 3.5 23.3 + - - +
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Residues in contact with ASN 503 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499I ASP* 3.3 22.2 + - - +
500I PHE* 3.4 18.4 + - + +
501I LEU 3.3 6.3 - - - +
502I GLN* 1.3 90.5 - - - +
504I SER* 1.3 65.8 + - - +
505I SER* 3.9 2.3 + - - -
508I LYS* 5.0 6.2 - - - +
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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