Contacts of the helix formed by residues 530 - 533 (chain A) in PDB entry 1FGR
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 PRO 530 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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526A LYS 3.3 13.9 - - - +
527A LEU 3.7 4.3 - - - +
528A LEU 3.3 5.2 - - - -
529A THR* 1.3 94.3 - - - +
531A HIS* 1.3 63.2 + - + +
532A TYR 3.2 3.7 + - - -
533A ARG* 3.6 17.7 + - + +
762A VAL* 6.2 0.2 - - + -
766A GLN 5.4 0.2 - - - +
767A ARG* 3.6 39.7 - - + +
835A ASN* 3.4 31.5 + - - +
836A SER* 3.9 0.3 - - - -
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Residues in contact with HIS 531 (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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507A MET* 5.0 1.7 - - - +
527A LEU 3.5 24.9 + - - -
528A LEU* 2.9 9.7 + - - +
530A PRO* 1.3 81.8 - - + +
532A TYR* 1.3 64.1 + - + +
535A ASN* 5.1 0.7 - - - +
624A TRP* 5.2 4.9 + - - -
682A ILE* 5.3 1.6 - - + +
683A ILE* 3.7 40.9 + - + +
686A ALA* 3.3 24.7 - - + +
687A SER* 4.5 1.0 - - - -
764A LEU* 3.7 20.4 - - + +
767A ARG* 4.9 5.3 + - - -
785A PHE* 5.9 2.4 - + - -
835A ASN* 2.7 49.6 + - - +
836A SER* 3.2 14.9 - - - -
837A ILE 4.3 0.7 + - - -
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Residues in contact with TYR 532 (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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244A GLU* 4.5 8.1 - - - +
507A MET* 3.9 23.1 - - + -
510A PHE* 3.6 13.8 + - - +
511A VAL* 3.6 41.0 - - + +
514A THR* 2.8 43.5 + - + -
515A HIS* 4.7 4.7 - - - +
528A LEU* 3.6 30.0 - - + +
529A THR* 3.0 29.8 + - + +
531A HIS* 1.3 87.8 - - + +
533A ARG* 1.3 67.1 + - - +
534A ASN 3.2 1.2 + - - -
535A ASN* 3.0 22.5 + - - +
536A MET 4.6 0.5 + - - -
648A TRP* 4.9 0.3 - - - -
682A ILE* 4.1 11.0 - - + +
836A SER* 3.9 1.6 - - - -
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Residues in contact with ARG 533 (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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244A GLU* 5.6 0.9 - - - -
246A LEU* 2.9 40.2 - - + +
248A HIS* 4.9 9.9 - - - -
529A THR 3.8 3.9 + - - +
530A PRO* 3.6 13.3 + - + +
532A TYR* 1.3 75.6 - - - +
534A ASN* 1.3 69.1 + - - +
535A ASN 3.2 4.9 + - - -
758A ALA* 5.8 2.8 - - - +
760A ASP* 4.6 15.9 + - - -
761A GLU* 2.8 44.8 + - - +
762A VAL* 4.4 21.2 + - - +
768A ASP* 6.0 2.7 - - - -
835A ASN* 5.9 0.6 - - + +
836A SER* 2.7 30.1 + - - +
837A ILE 3.7 3.3 - - - +
838A SER* 3.6 16.8 + - - -
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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