Contacts of the strand formed by residues 512 - 516 (chain D) in PDB entry 4OMD
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 ARG 512 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422D HIS* 3.9 12.5 - - - -
464D ARG* 5.1 0.4 - - - +
504D HIS* 3.5 30.6 + - + +
505D LEU 3.6 3.4 - - - -
506D VAL* 3.8 19.8 - - + +
510D GLY 3.4 6.5 + - - +
511D THR* 1.3 76.1 - - - +
513D SER* 1.3 60.6 + - - +
514D THR* 3.8 4.4 + - - +
537D HIS* 4.9 1.6 + - - -
550D GLU* 2.4 47.1 + - - -
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Residues in contact with SER 513 (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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334D SER* 4.1 5.8 - - - -
422D HIS* 4.0 4.5 - - - -
504D HIS* 3.3 2.5 - - - -
505D LEU* 2.7 45.5 + - - +
511D THR* 3.7 4.6 + - - +
512D ARG* 1.3 73.1 - - - +
514D THR* 1.3 59.8 + - - +
515D LEU* 3.3 9.2 + - - -
535D THR* 2.6 42.0 + - - +
537D HIS* 3.5 15.7 - - - +
538D SER* 4.9 2.8 + - - -
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Residues in contact with THR 514 (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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304D ASN* 4.0 0.2 + - - -
333D CYS* 4.6 2.6 - - - -
334D SER* 3.7 11.3 + - - -
422D HIS* 2.8 38.4 + - + -
503D ILE 3.6 3.8 - - - +
504D HIS* 2.8 35.5 + - + +
512D ARG* 3.8 4.2 + - - +
513D SER* 1.3 70.9 - - - +
515D LEU* 1.3 62.1 + - - +
516D LEU 3.7 23.3 - - - +
517D ALA* 4.0 13.2 - - + +
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Residues in contact with LEU 515 (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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302D SER* 4.3 1.0 + - - -
304D ASN* 2.8 34.7 + - - +
334D SER* 3.9 13.5 - - - +
489D ALA* 3.6 30.1 - - + -
491D LEU* 4.8 0.4 - - + -
503D ILE* 2.9 28.7 + - + +
505D LEU* 3.9 35.2 - - + +
513D SER* 4.0 10.3 - - - +
514D THR* 1.3 73.0 - - - +
516D LEU* 1.3 61.5 + - - +
533D PHE* 3.4 33.5 - - + +
534D MET 4.9 1.1 - - - +
535D THR* 4.4 6.5 - - + -
549D LEU* 4.2 3.6 - - + -
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Residues in contact with LEU 516 (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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302D SER* 4.2 12.1 - - - +
305D CYS* 3.7 29.8 - - - -
498D ARG* 4.8 4.7 - - + +
501D LEU* 4.3 19.3 - - + +
502D ALA* 3.1 5.2 - - - +
503D ILE* 2.7 51.6 + - + +
514D THR* 3.3 6.8 - - - +
515D LEU* 1.3 81.3 - - - +
517D ALA* 1.3 75.2 + - - +
519D ARG* 4.6 7.4 - - + +
528D PHE* 3.6 31.6 - - + -
533D PHE* 3.9 11.4 - - + -
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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