Contacts of the strand formed by residues 512 - 516 (chain D) in PDB entry 1Y9D
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 GLN 512 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510D HIS 4.3 0.4 + - - -
511D MET* 1.3 75.8 - - - +
513D ALA* 1.3 59.3 + - - +
514D PHE* 4.4 9.6 - - + -
528D GLN* 5.5 1.8 - - - +
532D ILE* 3.5 50.2 - - + +
536D GLU* 5.9 0.7 - - - +
537D PRO 4.1 3.7 + - - +
538D VAL* 3.3 7.6 - - + +
539D LEU 3.1 19.9 + - - -
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Residues in contact with ALA 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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503D SER* 3.6 24.7 - - - +
506D ALA* 3.6 26.7 - - + -
511D MET 3.6 1.7 + - - +
512D GLN* 1.3 75.2 - - - +
514D PHE* 1.3 75.3 + - - +
539D LEU* 3.0 19.1 - - + +
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Residues in contact with PHE 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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503D SER* 3.9 5.5 - - - -
512D GLN* 4.4 8.3 - - - -
513D ALA* 1.3 86.3 - - - +
515D ARG* 1.3 55.1 + - - +
516D VAL* 4.2 0.4 - - + -
525D VAL* 3.5 39.0 - - + -
528D GLN* 3.3 44.4 - - + -
529D ALA 4.7 2.7 - - - -
532D ILE* 3.6 30.3 - - + -
538D VAL* 3.7 14.1 - - + -
539D LEU 3.0 9.4 + - - +
540D ILE* 4.4 5.4 - - + -
541D ASP* 2.7 33.8 + - - +
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Residues in contact with ARG 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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510B HIS* 5.5 1.0 - - - -
473D THR* 4.1 2.4 - - - +
499D ASP* 3.0 39.6 + - - -
500D ILE 3.5 9.7 + - - -
501D ASP* 3.3 29.7 + - - +
503D SER* 3.6 13.8 - - - +
514D PHE* 1.3 74.0 - - - +
516D VAL* 1.3 66.4 + - - +
517D ASN* 6.2 0.4 - - + -
521D GLN* 4.9 3.8 + - - -
541D ASP* 2.9 41.0 + - - +
543D VAL* 3.4 29.4 - - + +
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Residues in contact with VAL 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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371D LEU* 3.6 19.4 - - + +
515D ARG* 1.3 80.8 - - - +
517D ASN* 1.3 60.6 + - - +
518D LYS 4.8 0.7 - - - +
521D GLN* 3.2 31.2 - - + +
522D LEU* 4.2 12.8 - - + -
525D VAL* 3.6 37.9 - - + -
540D ILE* 4.1 13.2 - - + -
541D ASP 2.9 9.3 + - - +
542D ALA* 4.0 5.6 - - + -
543D VAL* 2.8 27.7 + - - +
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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