Contacts of the helix formed by residues 501 - 505 (chain A) in PDB entry 5FZ9
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 GLU 501 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ARG* 4.5 6.4 + - - +
499A HIS* 3.0 4.2 + - - -
500A ILE* 1.3 78.8 - - - +
502A ASP* 1.3 65.9 + - - +
503A HIS 3.4 0.3 + - - -
504A TRP* 3.0 21.4 + - - +
505A SER* 3.4 37.0 + - - +
507A SER* 3.8 15.7 + - - +
581A THR* 4.4 4.5 - - - +
582A PHE 6.1 0.2 - - - +
584A ARG 5.9 1.2 - - - +
587A HIS* 2.8 14.4 - - + -
601A ASN* 3.2 22.7 + - - +
618A TYR* 4.4 1.4 + - - -
1756A DMS 3.9 12.1 - - - +
1759A MN 2.1 37.2 + - - -
1760A EPE 5.5 0.7 + - - -
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Residues in contact with ASP 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ARG* 4.0 21.4 + - - +
482A MET* 3.5 17.3 - - - +
500A ILE 3.9 0.8 + - - -
501A GLU* 1.3 73.5 + - - +
503A HIS* 1.3 69.4 + - + +
504A TRP 3.1 1.4 + - - -
505A SER* 3.2 16.5 + - - -
548A LEU* 5.6 0.8 - - - +
551A GLN* 4.2 4.6 + - - +
601A ASN* 5.2 3.2 - - - +
618A TYR* 3.8 3.6 - - - +
623A ARG* 3.2 26.6 + - - -
626A VAL* 3.7 31.2 - - + +
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Residues in contact with HIS 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A MET* 4.3 4.3 - - + -
502A ASP* 1.3 73.5 - - + +
504A TRP* 1.3 66.7 + - - +
505A SER* 3.1 0.7 - - - +
607A TRP* 3.0 30.5 + - + -
611A GLY* 4.4 2.6 + - - -
614A CYS* 3.5 22.6 - - + +
615A VAL* 4.1 23.6 - - + +
618A TYR* 2.9 22.9 + + - -
625A CYS* 4.0 9.1 - - + -
626A VAL* 3.0 39.2 + - + -
627A PHE* 3.3 58.4 + + + -
629A HIS* 5.4 1.2 + - - +
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Residues in contact with TRP 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A ILE* 3.8 21.2 - - + +
501A GLU* 3.0 16.4 + - - +
503A HIS* 1.3 77.2 - - - +
505A SER* 1.3 64.5 + - - +
583A PRO* 3.2 23.1 - - + +
584A ARG* 3.2 69.1 - - + +
607A TRP* 3.3 8.5 - - + +
610A LEU* 3.7 25.8 - - + +
613A GLN* 4.2 13.7 - - + -
614A CYS* 3.4 35.7 - - + -
617A HIS* 4.0 26.9 - + + -
618A TYR* 4.8 2.0 - - - -
1760A EPE 3.3 19.0 + - - -
1764A EDO 4.4 9.9 - - - -
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Residues in contact with SER 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A MET* 3.9 6.8 - - - +
501A GLU* 3.4 16.5 + - - +
502A ASP 3.2 15.0 + - - -
503A HIS 3.1 2.2 - - - -
504A TRP* 1.3 82.8 - - - +
506A TYR* 1.3 62.9 + - - +
581A THR* 4.8 0.3 + - - +
582A PHE 4.3 3.3 - - - +
583A PRO* 4.1 8.2 - - - +
584A ARG 4.8 0.9 + - - -
601A ASN* 3.2 28.1 + - - +
602A PHE 3.6 13.9 - - - -
603A CYS* 3.6 16.6 - - - -
607A TRP* 3.9 9.4 - - - +
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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