Contacts of the strand formed by residues 316 - 321 (chain A) in PDB entry 2QY0
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 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A GLN* 5.8 0.2 - - - +
311A TYR* 3.5 15.1 - - - -
314A ARG 4.8 0.4 - - - -
315A ASP* 1.3 81.0 - - - +
317A PHE* 1.3 75.8 + - - +
318A ILE* 3.9 15.9 - - + -
338A THR* 4.0 17.9 - - + -
339A ALA 3.3 13.5 - - - +
340A VAL* 4.3 4.5 - - + -
347A TRP* 4.4 1.8 - - - -
465D ASN* 2.8 29.6 + - - +
501D ASP* 2.8 32.0 + - - +
503D PHE* 3.7 17.2 - + - -
513D MET* 3.5 41.5 - - + -
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Residues in contact with PHE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A PRO* 4.3 15.3 - - + -
304A ILE* 4.0 17.3 - - + -
305A GLN 5.2 3.6 - - - +
306A ASN 5.7 0.2 - - - +
311A TYR* 3.7 19.1 - - + +
316A TYR* 1.3 78.8 - - - +
318A ILE* 1.3 74.3 + - - +
319A ALA* 4.5 4.0 - - + -
337A PHE* 3.8 14.0 - + - +
338A THR* 3.4 4.9 - - - +
339A ALA* 3.0 57.3 + - + -
347A TRP* 3.6 39.0 - + - -
349A ARG 5.7 1.1 - - - -
351A MET* 4.1 39.0 - - + -
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Residues in contact with ILE 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ILE* 3.6 5.4 - - - +
305A GLN* 3.2 52.6 + - + +
316A TYR* 3.9 15.5 - - + -
317A PHE* 1.3 81.9 - - - +
319A ALA* 1.3 73.6 + - - +
320A THR* 4.2 2.4 + - - +
337A PHE 3.2 9.4 - - - +
338A THR* 4.0 10.1 - - - +
500D LEU 5.5 0.7 - - - +
501D ASP* 3.3 35.7 - - + +
503D PHE* 4.7 0.2 - - + -
517D ASN* 3.7 37.5 - - + +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A THR* 4.4 13.9 - - + -
303A ILE 3.3 7.9 - - - +
304A ILE* 4.8 1.1 - - + +
317A PHE* 4.5 4.7 - - + -
318A ILE* 1.3 80.0 - - - +
320A THR* 1.3 62.0 + - - +
327A LEU* 3.6 28.1 - - + +
336A SER* 5.0 0.3 - - - -
337A PHE* 3.0 35.7 + - + -
351A MET* 4.5 11.4 - - + -
352A PRO* 4.6 1.3 - - + -
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Residues in contact with THR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A THR* 3.6 5.2 - - - +
303A ILE* 2.7 59.8 + - + +
305A GLN* 4.1 26.5 - - + +
318A ILE* 4.2 2.2 - - - -
319A ALA* 1.3 74.0 - - - +
321A CYS* 1.3 77.0 + - - +
327A LEU* 4.4 4.0 - - - -
354A CYS* 3.7 2.6 - - - -
806A GOL 3.3 17.8 + - - -
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Residues in contact with CYS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A PHE 3.2 7.6 - - - +
303A ILE* 3.7 11.0 - - - +
320A THR* 1.3 88.8 + - - +
322A LYS* 1.3 64.9 + - - +
323A GLN* 4.0 5.5 + - - -
325A TYR* 3.3 25.8 - - + +
326A GLN* 3.6 2.7 - - - -
327A LEU* 3.5 34.5 - - - -
354A CYS* 2.0 44.4 - - + -
806A GOL 4.1 6.1 - - - -
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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