Contacts of the helix formed by residues 584 - 591 (chain D) in PDB entry 2FGJ
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 ALA 584 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579D ALA* 2.7 20.9 + - + +
582D ALA* 3.3 0.9 - - + -
583D GLY* 1.3 73.1 - - - +
585D HIS* 1.3 62.9 + - - +
586D ASP 3.1 4.3 + - - -
587D PHE* 3.3 30.6 - - + -
588D ILE* 3.1 27.3 + - + +
613D ARG* 3.9 17.5 - - + +
614D ILE* 3.7 17.9 - - + -
617D ALA* 5.1 0.4 - - + -
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Residues in contact with HIS 585 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576D ILE* 4.0 20.7 - - + +
579D ALA* 3.3 4.6 + - - +
580D LYS* 3.8 44.9 - - + +
583D GLY 3.6 0.8 - - - -
584D ALA* 1.3 76.6 - - - +
586D ASP* 1.3 70.1 + - - +
588D ILE* 3.5 3.8 + - - +
589D SER* 2.9 54.7 + - - -
595D TYR* 2.9 37.2 + + - +
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Residues in contact with ASP 586 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583D GLY 4.9 5.9 + - - +
584D ALA 3.2 1.0 - - - -
585D HIS* 1.3 88.5 - - - +
587D PHE* 1.3 58.2 + - + +
589D SER* 3.2 8.3 + - - -
590D GLU* 3.1 35.0 + - + +
613D ARG* 6.0 1.3 - - - +
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Residues in contact with PHE 587 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559D ILE* 5.7 0.2 - - + -
584D ALA* 3.3 41.4 + - + -
586D ASP* 1.3 74.7 - - - +
588D ILE* 1.3 78.6 + - + +
590D GLU* 3.4 26.4 + - - +
591D LEU* 3.4 25.0 + - + +
606D LEU* 4.8 8.7 - - + -
610D GLN* 3.7 57.7 - - + +
613D ARG* 3.2 42.8 - - - +
614D ILE* 3.7 8.7 - - + -
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Residues in contact with ILE 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559D ILE* 3.9 13.9 - - + -
563D ILE* 4.3 0.9 - - + -
579D ALA* 4.3 3.6 - - + -
584D ALA* 3.1 25.7 + - + +
585D HIS 3.7 5.8 - - - +
587D PHE* 1.3 89.9 - - + +
589D SER* 1.3 60.0 + - - +
591D LEU* 3.2 18.3 + - - +
594D GLY* 3.3 38.2 - - - +
595D TYR* 3.7 44.6 - - + +
614D ILE* 3.6 24.0 - - + -
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Residues in contact with SER 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585D HIS* 2.9 46.9 + - - -
586D ASP* 3.5 6.7 - - - -
588D ILE* 1.3 76.6 - - - +
590D GLU* 1.3 61.2 + - - +
591D LEU 3.3 7.3 + - - +
594D GLY* 5.0 3.8 - - - -
595D TYR* 4.9 3.5 - - - -
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Residues in contact with GLU 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678C LYS* 5.2 10.4 + - - +
586D ASP* 3.1 18.9 + - - +
587D PHE* 3.5 27.5 + - - +
588D ILE 3.2 0.4 - - - -
589D SER* 1.3 77.2 - - - +
591D LEU* 1.3 61.0 + - - +
592D ARG* 3.7 2.6 + - - +
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Residues in contact with LEU 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C PRO* 5.9 8.1 - - + -
802C ATP 5.8 1.8 - - - +
559D ILE* 3.7 29.8 - - + -
587D PHE* 3.4 20.6 + - + +
588D ILE* 3.2 16.1 + - - +
589D SER 3.6 5.4 - - - +
590D GLU* 1.3 79.3 - - - +
592D ARG* 1.3 67.1 + - - +
593D GLU 3.2 0.2 - - - -
594D GLY* 3.0 14.8 + - - +
597D THR* 3.6 25.4 - - + +
606D LEU* 4.4 20.0 - - + -
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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