Contacts of the strand formed by residues 516 - 521 (chain D) in PDB entry 1Y8Q
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 516 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449D GLU* 3.0 22.0 + - - +
482D ILE* 4.0 2.3 - - - +
483D GLU* 2.9 61.2 + - + +
512D ARG* 5.4 0.4 - - - +
514D GLY 3.9 8.5 - - - +
515D SER* 1.3 76.8 - - - +
517D LEU* 1.3 65.8 + - - +
529D LEU* 3.3 35.4 - - + +
530D ILE 3.5 5.6 - - - +
531D ASN* 2.7 41.4 + - - +
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Residues in contact with LEU 517 (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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464D LEU* 4.0 31.4 - - + -
480D VAL* 4.1 10.3 - - + -
481D GLN 3.5 3.8 - - - +
482D ILE* 3.6 39.0 - - + -
490D LEU* 3.7 10.3 - - + -
506D LEU* 5.8 1.3 - - + -
511D ILE* 4.3 16.2 - - + -
515D SER* 5.2 2.7 - - - +
516D ARG* 1.3 77.8 - - - +
518D GLN* 1.3 59.8 + - - +
519D ALA 3.8 0.4 + - - -
528D LEU 3.7 0.9 - - - +
529D LEU* 3.5 3.4 - - - +
530D ILE* 2.7 49.0 + - + +
532D ILE* 4.1 30.1 - - + -
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Residues in contact with GLN 518 (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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479D ASP 3.6 2.1 - - - +
480D VAL* 3.4 3.0 - - - -
481D GLN* 2.8 65.9 + - + +
483D GLU* 3.9 17.5 + - + +
516D ARG 4.1 1.0 + - - -
517D LEU* 1.3 73.0 - - - +
519D ALA* 1.3 59.6 + - - +
520D ASP* 3.1 19.1 - - - +
527D THR* 3.8 22.4 - - + +
528D LEU 3.8 2.0 - - - +
529D LEU* 3.6 28.2 - - + +
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Residues in contact with ALA 519 (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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469D VAL* 4.6 3.6 - - + -
475D MET* 3.8 20.1 - - + +
479D ASP 3.8 3.4 - - - -
480D VAL* 3.8 20.9 - - + -
517D LEU 3.8 0.8 + - - -
518D GLN* 1.3 71.9 - - - +
520D ASP* 1.3 62.4 + - - +
527D THR* 3.5 2.8 - - - +
528D LEU* 2.8 45.3 + - + +
530D ILE* 4.2 18.6 - - + -
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Residues in contact with ASP 520 (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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475D MET* 3.9 2.2 - - - -
478D PRO* 3.2 5.0 - - - +
479D ASP* 2.7 46.2 + - + +
481D GLN* 5.0 2.1 - - - +
518D GLN* 3.1 30.5 - - - +
519D ALA* 1.3 75.0 - - - +
521D ASP* 1.3 60.2 + - - +
522D PHE* 3.9 33.0 - - + -
526D TYR 3.7 3.1 - - - +
527D THR* 2.7 30.3 + - - +
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Residues in contact with ASP 521 (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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475D MET* 3.4 24.3 - - + +
476D VAL* 2.7 32.1 + - - -
477D ALA 3.0 20.0 + - - +
520D ASP* 1.3 73.9 - - - +
522D PHE* 1.3 58.1 + - - +
523D LEU* 3.2 14.7 + - - +
524D GLN* 3.1 32.6 + - + +
525D ASP 2.8 22.9 + - - -
526D TYR* 3.1 15.1 + - + +
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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