Contacts of the strand formed by residues 413 - 421 (chain A) in PDB entry 2VWR
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 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A GLN* 5.5 1.4 + - - -
341A ALA* 3.9 15.5 - - + +
342A LEU 3.6 4.7 - - - +
343A HIS* 3.6 22.2 + - + +
391A ASN* 3.3 21.2 + - - +
411A GLY* 3.3 6.1 + - - +
412A GLU* 1.3 95.0 - - - +
414A VAL* 1.3 67.5 + - - +
415A ASN* 3.6 37.4 + - - +
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Residues in contact with VAL 414 (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 VAL 3.5 2.8 - - - +
341A ALA* 3.4 1.8 - - - -
342A LEU* 2.8 40.8 + - + +
344A LYS* 4.2 10.8 - - + -
351A LEU* 3.9 40.8 - - + -
390A ILE* 3.7 25.8 - - + -
391A ASN* 3.5 3.4 - - - +
407A ILE* 4.5 5.6 - - + -
410A SER* 3.5 26.9 - - - +
411A GLY 4.1 2.9 - - - +
412A GLU 4.3 0.4 - - - +
413A ARG* 1.3 77.6 - - - +
415A ASN* 1.3 58.6 + - - +
416A LEU* 3.7 9.9 - - + +
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Residues in contact with ASN 415 (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 GLN* 3.1 37.1 + - - +
340A VAL 3.4 17.3 - - - +
341A ALA* 3.8 4.1 - - - +
389A ALA 4.0 0.3 - - - +
390A ILE* 3.2 5.4 - - - +
391A ASN* 2.8 48.7 + - - +
392A GLY 5.7 1.4 - - - +
413A ARG* 3.6 37.6 + - - +
414A VAL* 1.3 73.6 - - - +
416A LEU* 1.3 61.1 + - - +
417A THR* 4.0 10.3 + - - -
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Residues in contact with LEU 416 (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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338A LEU 3.8 0.7 - - - +
339A GLN* 3.3 3.3 - - - -
340A VAL* 2.8 47.1 + - + +
342A LEU* 4.1 23.6 - - + -
351A LEU* 4.7 4.9 - - + -
353A ILE* 4.2 20.2 - - + -
355A LEU* 6.1 1.6 - - + -
366A ILE* 5.5 0.9 - - + -
381A LEU* 4.4 10.1 - - + -
387A VAL* 4.4 16.6 - - + -
389A ALA 3.5 6.1 - - - +
390A ILE* 4.2 24.7 - - + -
407A ILE* 5.6 0.7 - - + -
414A VAL* 3.7 22.0 - - + +
415A ASN* 1.3 75.9 - - - +
417A THR* 1.3 61.4 + - - +
418A ILE* 3.8 16.5 + - + +
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Residues in contact with THR 417 (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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337A ILE* 4.1 22.7 - - + -
338A LEU 3.5 5.2 - - - +
339A GLN* 3.9 25.3 + - + +
387A VAL* 3.6 2.8 - - - -
388A LEU* 2.7 44.8 + - + -
389A ALA* 2.9 28.8 + - + +
415A ASN* 4.0 6.8 + - - -
416A LEU* 1.3 72.4 - - - +
418A ILE* 1.3 56.3 + - - +
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Residues in contact with ILE 418 (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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336A GLU 3.6 0.5 - - - +
337A ILE* 3.2 9.0 - - - +
338A LEU* 2.8 49.4 + - + +
340A VAL* 4.7 4.3 - - + -
366A ILE* 4.8 0.2 - - + -
381A LEU* 3.5 31.0 - - + -
385A ASP* 3.4 37.9 - - + +
386A ARG 3.3 9.0 - - - +
387A VAL* 4.1 17.9 - - + -
388A LEU* 4.3 4.3 - - - -
416A LEU* 4.0 20.4 - - + +
417A THR* 1.3 81.8 - - - +
419A ALA* 1.3 66.7 + - - +
420A ARG* 4.8 0.2 - - - +
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Residues in contact with ALA 419 (chain A).
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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0A MET* 4.0 16.2 - - + -
336A GLU 3.3 4.9 - - - -
337A ILE* 3.7 18.6 - - + -
385A ASP* 3.6 1.0 - - - -
386A ARG* 2.8 48.3 + - + +
388A LEU* 3.9 18.0 - - + +
418A ILE* 1.3 74.5 - - - +
420A ARG* 1.3 59.7 + - - +
421A PRO* 3.3 9.7 - - + +
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Residues in contact with ARG 420 (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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0A MET* 3.3 1.5 - - - -
336A GLU* 2.7 59.2 + - + +
338A LEU* 4.3 28.3 - - + +
380A ARG* 2.7 31.0 + - - +
381A LEU* 4.0 1.0 - - - +
382A SER* 3.9 11.5 - - - -
384A ASN 6.2 0.2 - - - -
385A ASP* 2.8 40.4 + - - +
418A ILE* 4.1 0.8 - - - +
419A ALA* 1.3 72.5 - - - +
421A PRO* 1.3 68.8 - - + +
422A GLY 4.6 3.0 - - - +
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Residues in contact with PRO 421 (chain A).
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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-1A SER 3.6 9.6 - - - +
0A MET* 3.8 14.1 - - + -
365A PHE* 5.9 3.4 - - + -
384A ASN* 3.9 19.3 - - + +
386A ARG* 4.9 5.4 - - + +
419A ALA* 3.3 15.9 - - + +
420A ARG* 1.3 92.7 - - + +
422A GLY* 1.3 65.9 + - - +
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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