Contacts of the helix formed by residues 531 - 537 (chain D) in PDB entry 6M04
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 531 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505D ILE* 3.3 27.8 - - + +
506D PRO 3.4 18.4 - - - +
507D ALA* 4.4 0.9 - - - +
509D ILE* 4.8 0.9 - - + -
510D SER* 5.0 1.6 - - - -
527D VAL 4.3 6.2 + - - +
528D GLU* 4.5 5.8 - - + -
529D GLN 4.0 1.6 - - - +
530D THR* 1.3 77.8 - - + +
532D PHE* 1.3 63.8 + - - +
533D SER 3.3 1.6 - - - -
534D PHE* 3.1 33.7 - - + -
535D LEU* 3.3 12.8 - - + +
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Residues in contact with PHE 532 (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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528D GLU* 3.3 48.9 - - + +
529D GLN* 4.0 8.5 - - - +
530D THR 3.4 0.8 - - - -
531D ALA* 1.3 79.3 - - - +
533D SER* 1.3 57.7 + - - +
535D LEU* 3.0 15.2 + - + +
536D ARG* 2.6 61.1 + - + +
555D TRP 3.5 20.0 - - - -
558D LEU* 3.4 39.9 - - + -
559D LEU* 3.5 25.6 - - + -
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Residues in contact with SER 533 (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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529D GLN 3.8 13.0 + - - -
530D THR* 4.3 9.0 + - - -
531D ALA* 3.3 1.4 - - - +
532D PHE* 1.3 81.1 - - - +
534D PHE* 1.3 61.1 + - - +
536D ARG* 4.0 21.4 + - - +
537D ASP* 3.2 30.1 + - - +
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Residues in contact with PHE 534 (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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509D ILE* 3.2 46.2 - - + -
510D SER* 3.5 33.0 - - - +
512D MET 3.2 29.8 - - - -
513D THR* 4.7 10.0 + - - -
515D LEU* 5.6 11.2 - - + -
530D THR 5.1 0.4 + - - -
531D ALA* 3.1 37.2 - - + -
532D PHE 3.3 0.2 - - - -
533D SER* 1.3 79.5 - - - +
535D LEU* 1.3 72.5 + - + +
537D ASP* 3.7 7.7 + - - +
538D HIS* 3.3 27.9 + - + +
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Residues in contact with LEU 535 (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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505D ILE* 4.6 8.1 - - + -
515D LEU 6.1 1.3 - - - +
518D LEU* 5.7 4.7 - - + -
528D GLU* 3.3 40.4 - - + +
531D ALA* 3.3 17.3 - - + +
532D PHE* 3.0 25.1 + - + +
534D PHE* 1.3 94.1 - - + +
536D ARG* 1.3 61.1 + - - +
537D ASP 3.1 1.8 - - - -
538D HIS* 3.0 2.6 + - - +
539D LEU* 2.6 51.6 + - + +
556D VAL* 4.7 1.6 - - + -
559D LEU* 3.3 18.6 - - + +
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Residues in contact with ARG 536 (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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532D PHE* 2.6 54.1 + - + +
533D SER* 4.0 20.2 + - - +
535D LEU* 1.3 72.9 - - - +
537D ASP* 1.3 74.0 + - - +
558D LEU 4.6 2.5 + - - +
559D LEU* 3.5 31.1 - - - +
560D LYS* 6.2 2.2 - - - +
561D ASN* 3.5 19.9 + - - +
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Residues in contact with ASP 537 (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 THR* 5.6 2.0 - - - +
533D SER 3.2 18.4 + - - +
534D PHE* 3.9 8.7 - - - +
535D LEU 3.1 0.6 - - - -
536D ARG* 1.3 90.2 + - - +
538D HIS* 1.3 61.1 + - + +
540D ARG* 5.5 1.7 + - - -
561D ASN* 2.7 20.7 + - - +
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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