Contacts of the strand formed by residues 385 - 391 (chain A) in PDB entry 1QAS
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 VAL 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A LEU* 4.7 4.0 - - + -
338A ARG* 3.0 32.3 - - - +
340A LEU* 4.5 9.9 - - + -
373A ILE* 4.8 3.1 - - + -
377A ALA* 3.8 16.8 - - + +
378A PHE* 3.6 27.6 - - + -
384A PRO* 1.3 75.0 - - - +
386A ILE* 1.3 63.0 + - - +
387A LEU* 3.8 24.9 - - + -
434A LYS 3.3 2.8 + - - -
435A ILE* 3.3 20.4 - - + +
436A LEU* 3.0 24.3 + - - +
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Residues in contact with ILE 386 (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 LEU* 5.0 8.5 - - + -
307A VAL* 5.2 2.9 - - + -
338A ARG 2.8 6.2 + - - +
339A CYS* 3.4 29.0 - - + -
340A LEU 2.9 26.5 + - - +
384A PRO* 5.1 1.1 - - + +
385A VAL* 1.3 76.5 - - - +
387A LEU* 1.3 66.4 + - - +
388A SER* 4.4 3.4 - - - +
436A LEU* 3.3 21.8 - - + +
438A LYS* 3.9 26.5 - - + -
499A CYS* 4.4 18.8 - - - -
520A MET* 6.0 0.7 - - - -
547A LEU* 4.7 8.3 - - + -
574A ILE* 4.1 16.4 - - + -
601A TYR* 4.5 13.9 - - + +
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Residues in contact with LEU 387 (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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340A LEU* 3.6 33.2 - - + -
342A LEU* 4.1 11.7 - - + -
370A LEU* 3.9 26.9 - - + -
373A ILE* 3.9 19.7 - - + -
385A VAL* 3.8 9.6 - - + -
386A ILE* 1.3 78.7 - - - +
388A SER* 1.3 62.2 + - - +
389A LEU* 3.4 9.2 + - + +
405A LEU* 4.7 0.9 - - + -
409A LEU* 4.4 5.2 - - + -
435A ILE* 3.7 22.7 - - + -
436A LEU 2.8 9.3 + - - -
437A LEU* 3.5 20.9 - - + -
438A LYS 2.9 22.3 + - - +
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Residues in contact with SER 388 (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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339A CYS* 5.0 4.2 - - - +
340A LEU 2.7 19.8 + - - -
341A GLU* 3.2 21.9 - - - +
342A LEU* 2.9 29.8 + - - +
386A ILE* 3.8 4.7 + - - +
387A LEU* 1.3 71.3 - - - +
389A LEU* 1.3 59.8 + - - +
390A GLU 3.9 0.3 + - - -
438A LYS* 3.6 34.9 - - - +
520A MET* 5.9 0.2 - - - -
549A ARG* 4.8 10.2 + - - -
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Residues in contact with LEU 389 (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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342A LEU* 3.6 32.1 - - + +
344A CYS* 4.4 5.4 - - - -
366A PHE* 4.3 15.0 - - + -
387A LEU* 3.9 16.2 - - + +
388A SER* 1.3 75.2 - - - +
390A GLU* 1.3 58.9 + - - +
391A ASN* 3.6 7.0 + - + +
401A MET* 4.5 11.0 - - + -
405A LEU* 4.4 12.3 - - + -
437A LEU* 4.2 31.0 - - + -
438A LYS* 2.8 21.9 + - - +
439A GLY* 3.9 12.1 - - - -
440A LYS 5.2 0.3 + - - -
492A LEU* 4.7 10.3 - - + -
496A ILE* 4.8 6.3 - - + -
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Residues in contact with GLU 390 (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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312A ASN* 5.8 0.3 + - - -
342A LEU 3.0 8.5 + - - -
343A ASP* 3.4 34.6 - - - +
344A CYS* 3.0 22.9 + - - -
345A TRP* 4.9 2.1 - - - -
356A HIS* 6.0 0.7 - - - -
388A SER 3.9 0.8 + - - +
389A LEU* 1.3 70.8 - - - +
391A ASN* 1.3 57.2 + - - +
392A HIS* 2.9 35.8 + - + +
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Residues in contact with ASN 391 (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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344A CYS* 3.8 4.5 - - + +
389A LEU* 3.6 7.2 + - + +
390A GLU* 1.3 72.2 - - - +
392A HIS* 1.3 65.9 + - - +
393A CYS* 3.2 23.0 - - - +
398A GLN* 3.0 36.4 + - - +
401A MET* 3.2 33.3 - - + -
487A LYS* 5.6 1.6 + - - -
488A LEU* 4.4 8.0 - - + +
492A LEU* 3.9 11.1 - - + +
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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