Contacts of the strand formed by residues 337 - 344 (chain A) in PDB entry 1QFM
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 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A ASN* 3.4 15.5 - - - +
311A TYR* 4.0 16.2 - - + -
335A LYS 4.2 2.5 - - - +
336A ASP* 1.3 73.4 - - - +
338A LEU* 1.3 71.4 + - - +
339A GLU* 3.2 14.5 + - + +
353A TYR* 3.2 3.9 - - - -
354A LEU* 2.8 43.0 + - + +
508A GLY 3.8 8.7 - - - +
509A GLU 3.8 14.6 - - - +
510A TYR 3.9 2.0 - - - -
511A GLY* 3.2 34.1 - - - +
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Residues in contact with LEU 338 (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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303A LYS* 3.7 11.8 + - + +
310A ASN 3.0 9.7 + - - +
311A TYR* 3.5 29.3 - - + +
312A ARG* 4.1 20.6 - - - +
313A LEU* 4.0 18.4 - - + +
330A VAL* 5.2 2.0 - - + -
336A ASP 3.7 2.0 + - - -
337A VAL* 1.3 72.5 - - - +
339A GLU* 1.3 60.6 + - - +
340A TRP 3.9 3.6 - - - +
341A VAL* 3.7 32.8 - - + -
351A LEU* 3.9 24.0 - - + -
352A CYS 3.7 12.6 - - - +
353A TYR* 3.7 26.0 - - + +
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Residues in contact with GLU 339 (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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303A LYS* 3.4 17.2 + - - -
337A VAL* 3.9 10.7 - - + +
338A LEU* 1.3 72.1 - - - +
340A TRP* 1.3 73.9 + - + +
352A CYS* 2.8 21.1 + - - +
354A LEU* 3.5 40.0 - - + +
359A ASN* 2.8 31.4 + - - +
382A VAL 5.6 0.3 - - - +
479A SER* 4.3 10.4 + - - -
481A THR* 4.8 2.5 - - - +
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Residues in contact with TRP 340 (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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303A LYS* 4.0 9.4 - - - +
338A LEU* 3.6 1.3 - - - +
339A GLU* 1.3 94.0 + - + +
341A VAL* 1.3 77.0 + - - +
342A ALA* 4.2 6.1 - - + -
350A VAL* 4.0 19.3 - - + -
352A CYS* 3.0 54.6 + - + +
361A LEU* 4.0 14.4 - - + -
382A VAL* 4.0 25.5 + - + -
384A GLY 5.7 0.2 - - - -
385A TYR* 3.5 44.9 - + + -
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Residues in contact with VAL 341 (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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292A TYR 5.3 0.9 - - - +
293A VAL* 3.8 41.0 - - + +
303A LYS* 4.3 8.2 - - + +
313A LEU* 3.8 29.4 - - + -
338A LEU* 3.7 25.8 - - + -
340A TRP* 1.3 87.6 - - - +
342A ALA* 1.3 66.6 + - - +
349A LEU* 4.2 3.4 - - + -
350A VAL 3.2 12.3 - - - +
351A LEU* 3.8 17.0 - - + -
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Residues in contact with ALA 342 (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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293A VAL* 4.3 5.2 - - - -
340A TRP* 4.2 9.0 - - + -
341A VAL* 1.3 75.8 - - - +
343A CYS* 1.3 60.6 + - - +
349A LEU* 3.2 6.8 - - - +
350A VAL* 2.8 32.7 + - + +
385A TYR* 3.4 41.1 - - + +
387A GLY 4.2 3.1 - - - +
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Residues in contact with CYS 343 (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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242A ASP* 4.5 2.9 - - - +
293A VAL* 3.9 11.0 + - + +
294A THR* 3.6 30.5 - - - +
342A ALA* 1.3 72.1 - - - +
344A VAL* 1.3 63.4 + - - +
346A SER 3.4 25.6 - - - -
348A PHE 3.3 10.8 - - - -
349A LEU* 4.0 9.2 - - + -
366A LEU* 4.5 2.2 - - - -
387A GLY 3.5 4.7 - - - +
388A GLN* 3.1 4.9 - - - -
389A LYS* 3.0 42.3 + - - -
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Residues in contact with VAL 344 (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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343A CYS* 1.3 75.1 - - - +
345A ARG* 1.3 69.9 + - - +
346A SER 3.2 3.3 + - - -
348A PHE* 3.0 41.4 + - + +
350A VAL* 3.8 25.1 - - + -
363A LEU* 4.8 0.2 - - + -
385A TYR* 3.8 1.6 - - - +
387A GLY* 3.7 19.7 - - - +
388A GLN 3.4 15.0 - - - +
389A LYS* 4.1 0.2 - - - +
391A ASP 3.6 9.2 - - - +
393A GLU 3.8 17.5 - - - +
394A ILE* 4.0 4.3 - - + -
412A LEU* 3.6 26.5 - - + -
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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