Contacts of the helix formed by residues 587 - 593 (chain D) in PDB entry 5DO7
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 587 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402C PHE* 3.8 25.8 - - + +
403C PHE* 3.8 32.3 - - + +
405C LEU* 5.2 0.2 - - + -
583D LEU* 3.7 18.2 - - + -
585D THR 3.5 1.6 - - - -
586D VAL* 1.3 98.0 - - + +
588D ALA* 1.3 57.2 - - - +
589D TRP* 2.2 25.1 + - - +
590D ILE* 2.3 38.1 + - + +
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Residues in contact with ALA 588 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580D LEU* 5.3 1.6 - - + +
581D SER* 5.4 2.2 - - - +
583D LEU* 3.1 50.7 - - + +
584D TRP 4.4 1.6 - - - +
585D THR* 3.5 12.7 + - - -
587D PRO* 1.3 78.0 - - - +
589D TRP* 1.3 57.3 - - - +
590D ILE* 3.1 4.7 - - - -
591D SER* 2.8 32.1 + - - +
592D LYS 4.0 0.2 + - - -
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Residues in contact with TRP 589 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585D THR* 4.0 19.3 + - - +
587D PRO 2.2 13.0 + - - +
588D ALA* 1.3 72.7 - - - +
590D ILE* 1.3 51.0 + - - +
592D LYS* 2.8 66.1 + - + +
593D VAL* 4.0 1.6 + - - +
638D TYR* 5.4 5.2 - - - -
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Residues in contact with ILE 590 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403C PHE* 4.2 12.1 - - + -
569D SER* 3.7 29.4 - - - +
570D PHE* 4.2 15.5 - - + -
573D ALA* 3.8 13.0 - - + -
587D PRO* 2.3 51.3 + - + +
588D ALA* 4.1 2.5 - - - +
589D TRP* 1.3 66.3 - - - +
591D SER* 1.3 57.6 + - - +
593D VAL* 2.6 54.0 + - + +
594D SER 3.3 2.3 + - - -
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Residues in contact with SER 591 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573D ALA* 3.4 39.5 - - - -
580D LEU* 3.4 18.3 - - - +
583D LEU* 5.5 0.7 - - - -
588D ALA* 2.8 22.6 + - - -
590D ILE* 1.3 74.5 - - - +
592D LYS* 1.3 60.6 + - - +
594D SER* 2.8 19.0 + - - +
597D ARG* 3.3 32.8 + - - -
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Residues in contact with LYS 592 (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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588D ALA 4.0 0.2 + - - -
589D TRP* 2.8 47.2 + - + +
591D SER* 1.3 79.7 + - - +
593D VAL* 1.3 53.8 + - + +
597D ARG* 3.6 12.6 - - - +
598D TRP* 2.5 35.4 + - + -
638D TYR* 3.7 38.0 + - + +
646D ILE* 4.1 10.1 - - + +
650D LEU* 5.0 0.3 - - - +
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Residues in contact with VAL 593 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D PHE* 3.0 27.8 - - + -
589D TRP 5.0 0.9 - - - +
590D ILE* 2.6 50.1 + - + +
592D LYS* 1.3 74.1 - - + +
594D SER* 1.3 57.1 + - - -
595D PHE* 3.5 2.3 + - - -
650D LEU* 3.2 33.2 - - + +
654D PHE* 6.0 1.6 - - + -
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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