Contacts of the helix formed by residues 574 - 583 (chain D) in PDB entry 5MS0
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 VAL 574 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561D GLY 4.8 8.1 - - - +
562D GLU* 5.0 10.2 - - + +
565D ALA* 4.4 20.9 - - + -
570D LYS* 6.3 0.4 - - + -
571D ASP 4.4 9.9 - - - +
572D THR* 3.2 5.9 - - - +
573D THR* 1.3 76.9 - - - +
575D GLY* 1.3 57.7 + - - +
576D ARG 3.3 0.9 - - - -
577D ALA* 3.4 7.2 - - - +
578D ILE* 2.6 38.2 + - - +
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Residues in contact with GLY 575 (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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513D MET* 4.0 25.8 + - - +
514D THR* 5.4 0.4 - - - -
571D ASP 5.4 1.0 + - - -
572D THR* 5.8 0.2 - - - +
573D THR 4.8 0.6 - - - +
574D VAL* 1.3 80.5 - - - +
576D ARG* 1.3 55.6 + - - +
578D ILE* 4.3 3.6 - - - -
579D LEU* 2.9 33.2 + - - +
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Residues in contact with ARG 576 (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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513D MET 4.2 5.0 + - - -
514D THR* 5.0 16.8 - - - -
525D MET 5.3 6.3 - - - +
573D THR* 4.2 18.7 - - - +
574D VAL 3.3 1.4 - - - +
575D GLY* 1.3 76.8 - - - +
577D ALA* 1.3 58.4 + - - +
579D LEU* 4.2 4.3 - - - +
580D TRP* 3.5 20.7 + - - +
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Residues in contact with ALA 577 (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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557D LYS 5.7 0.2 - - - +
558D ASP* 3.9 37.6 - - + +
561D GLY* 6.6 0.4 - - - -
573D THR 3.4 19.8 + - - +
574D VAL* 3.0 10.3 + - - +
576D ARG* 1.3 80.2 - - - +
578D ILE* 1.3 60.6 + - - +
579D LEU 3.5 0.2 - - - -
580D TRP* 3.9 11.9 + - - +
581D MET* 4.1 7.3 + - - +
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Residues in contact with ILE 578 (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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558D ASP* 5.9 0.4 - - - -
562D GLU* 6.2 4.0 - - + -
574D VAL 2.6 19.5 + - - +
575D GLY* 4.6 3.6 - - - +
577D ALA* 1.3 71.5 - - - +
579D LEU* 1.3 59.6 + - - +
580D TRP 3.2 1.6 - - - -
581D MET* 3.3 3.5 + - - +
582D ILE* 2.9 33.4 + - - +
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Residues in contact with LEU 579 (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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513D MET* 5.6 7.2 - - + -
514D THR* 6.2 2.5 - - - -
575D GLY 2.9 21.4 + - - +
576D ARG* 4.5 5.6 - - - +
578D ILE* 1.3 78.3 - - - +
580D TRP* 1.3 57.8 + - - +
581D MET 3.2 1.7 + - - -
582D ILE* 4.1 8.6 + - - +
583D VAL* 4.1 14.9 + - - +
584D PRO 5.2 0.3 - - - -
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Residues in contact with TRP 580 (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 ARG 3.5 18.2 + - - +
577D ALA* 4.0 8.3 - - - +
578D ILE 3.2 0.6 - - - -
579D LEU* 1.3 76.5 - - - +
581D MET* 1.3 59.6 + - - +
584D PRO* 4.6 13.5 - - - +
590D SER* 5.6 2.6 - - - -
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Residues in contact with MET 581 (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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558D ASP* 5.7 6.1 - - + -
577D ALA 4.4 8.5 - - - +
578D ILE* 3.3 6.2 + - - +
579D LEU 3.2 0.4 - - - -
580D TRP* 1.3 81.7 - - - +
582D ILE* 1.3 65.9 + - - +
583D VAL 3.6 1.3 - - - -
584D PRO* 4.3 5.6 - - - -
585D LYS* 3.2 24.9 + - - +
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Residues in contact with ILE 582 (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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578D ILE* 2.9 18.6 + - + +
579D LEU* 4.1 3.3 + - - -
581D MET* 1.3 80.3 - - - +
583D VAL* 1.3 63.6 + - - +
585D LYS* 3.5 10.9 + - - +
586D GLY 4.3 2.4 + - - -
623D GLN* 4.9 5.0 - - - +
627D THR* 5.3 13.5 - - - -
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Residues in contact with VAL 583 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579D LEU 4.1 13.2 + - - +
582D ILE* 1.3 80.6 - - - +
584D PRO* 1.3 57.8 - - - +
585D LYS 3.2 4.2 + - - -
586D GLY* 3.9 7.1 + - - -
587D LEU* 4.1 9.5 + - - +
593D ASN* 6.1 3.6 - - + -
620D PHE* 6.0 2.9 - - - +
623D GLN* 4.4 22.8 - - + +
624D ILE* 5.4 8.7 - - + +
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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