Contacts of the strand formed by residues 345 - 351 (chain D) in PDB entry 4QY2
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 TYR 345 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C GLY 3.4 5.2 - - - +
7C HIS* 4.1 1.6 - - + -
313C MET* 3.8 19.1 - - + -
329D ILE* 4.1 3.6 - - + -
340D MET* 3.7 4.7 - - - -
344D TRP* 1.3 86.0 - + + +
346D GLY* 1.3 59.3 + - - +
359D ALA* 3.5 8.3 - - - +
360D ASP* 2.8 23.6 + - - +
363D SER* 3.4 43.7 - - - +
364D THR* 3.1 12.1 + - - -
367D ALA* 3.8 13.5 - - + +
434D ALA* 2.7 46.6 + - - +
437D GLU* 3.6 14.7 - - + +
438D MET* 3.7 33.0 - - + -
441D LEU* 3.9 10.8 - - + -
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Residues in contact with GLY 346 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C LEU* 3.6 11.9 - - - +
6C GLY 2.9 31.4 + - - -
337D TRP* 3.7 6.2 - - - -
340D MET* 3.8 7.7 - - - +
345D TYR* 1.3 76.4 - - - +
347D PHE* 1.3 68.2 + - - -
358D ALA 3.5 10.3 - - - -
360D ASP* 3.7 8.1 - - - -
441D LEU* 4.3 2.7 - - - +
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Residues in contact with PHE 347 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C ILE* 3.7 27.6 - - + -
4C CYS 3.4 4.0 - - - +
5C LEU* 3.5 24.2 - - + -
337D TRP* 4.0 2.1 - - - -
340D MET* 4.8 0.2 - - - -
346D GLY* 1.3 76.6 - - - -
348D ARG* 1.3 66.3 + - - +
349D HIS* 4.3 1.8 - - + +
356D GLY 4.6 0.2 - - - -
357D GLN* 3.3 7.8 - - - +
358D ALA 2.7 38.6 + - - +
359D ALA 4.9 0.7 - - - -
360D ASP* 3.8 30.3 - - + -
441D LEU* 3.9 21.1 - - + -
444D ARG* 4.5 2.7 - - - -
445D VAL* 3.8 17.7 - - + -
475D ILE* 4.8 1.8 - - + -
476D ARG* 3.6 53.8 - - + +
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Residues in contact with ARG 348 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C ILE* 3.5 1.3 - - - -
4C CYS* 2.6 48.4 + - + +
337D TRP* 3.2 70.4 - - + +
339D GLY* 4.5 11.7 - - - +
347D PHE* 1.3 78.1 - - - +
349D HIS* 1.3 58.7 + - - +
350D GLN* 5.8 0.2 - - - -
356D GLY 3.4 6.1 - - - +
357D GLN* 3.1 35.9 + - + +
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Residues in contact with HIS 349 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C LYS 3.3 4.7 - - - +
3C ILE* 4.1 8.5 - - + -
4C CYS* 5.8 0.2 - - - -
347D PHE* 5.8 1.1 - - + -
348D ARG* 1.3 77.0 - - - +
350D GLN* 1.3 67.3 + - - +
351D ASN* 3.9 16.9 + - - -
354D GLY 4.1 0.4 + - - -
355D THR* 3.3 33.4 - - - -
356D GLY* 3.2 40.1 + - - +
358D ALA 6.2 0.2 - - - -
469D ASP* 3.8 22.4 + - - -
472D MET* 3.6 35.4 - - + +
476D ARG* 3.4 30.0 + - - -
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Residues in contact with GLN 350 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C ASP* 3.5 6.0 - - - +
2C LYS* 2.8 67.1 + - + +
4C CYS* 5.9 2.2 - - - -
348D ARG 5.7 0.4 - - - +
349D HIS* 1.3 79.0 - - - +
351D ASN* 1.3 63.5 + - - +
354D GLY 3.4 5.2 - - - +
355D THR* 4.4 14.5 - - + +
472D MET* 3.6 2.9 - - - +
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Residues in contact with ASN 351 (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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1C ASP* 3.1 14.6 - - - +
349D HIS* 3.9 12.2 + - - -
350D GLN* 1.3 76.4 - - - +
352D ALA* 1.3 71.4 + - + +
353D GLN* 3.3 18.8 + - - +
354D GLY* 2.8 41.8 + - - +
467D CYS 3.2 27.8 + - - +
468D ASP* 3.4 1.6 - - - +
469D ASP* 3.2 27.5 + - - +
472D MET* 4.3 4.5 - - + +
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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