Contacts of the strand formed by residues 408 - 413 (chain A) in PDB entry 2VZE
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 GLY 408 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A ILE* 3.2 11.8 - - - +
395A ILE 3.9 7.4 - - - -
402A LEU* 4.2 2.5 - - - -
407A GLU* 1.3 75.5 - - - +
409A ASP* 1.3 59.3 + - - -
447A ARG* 3.2 28.0 - - - +
448A GLY 2.8 38.1 + - - -
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Residues in contact with ASP 409 (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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394A ILE* 3.5 1.7 - - - -
395A ILE* 2.8 39.1 + - + +
396A ASP 4.8 1.2 - - - -
397A ASP* 5.1 1.0 + - - -
408A GLY* 1.3 71.8 - - - -
410A ILE* 1.3 64.4 + - - +
411A GLY 3.5 0.5 + - - -
438A ARG* 2.9 38.3 + - - +
443A LEU* 4.1 14.4 - - + -
445A GLY* 5.9 3.4 - - - +
446A ASP 3.8 5.0 - - - +
447A ARG* 3.1 31.3 + - - -
462A ALA* 4.1 13.0 - - - +
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Residues in contact with ILE 410 (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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361A TYR* 3.9 30.1 - - + +
383A MET* 3.7 29.2 - - + -
392A VAL* 4.0 23.6 - - + -
393A GLN 3.5 6.5 - - - +
394A ILE* 3.7 18.2 - - + -
395A ILE* 5.2 0.4 - - - -
409A ASP* 1.3 72.3 - - - +
411A GLY* 1.3 60.1 + - - +
443A LEU* 4.0 4.7 - - - +
444A LEU* 3.2 28.1 + - + +
445A GLY 4.5 0.9 + - - -
446A ASP* 3.0 21.6 + - + +
447A ARG 3.6 18.2 - - - +
448A GLY* 3.8 9.0 - - - +
456A PHE* 4.7 7.6 - - + -
458A PHE* 5.1 0.7 - - + -
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Residues in contact with GLY 411 (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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391A ASP 3.8 0.2 - - - +
392A VAL* 3.2 8.5 - - - +
393A GLN 2.9 33.8 + - - -
395A ILE* 5.2 3.4 - - - -
409A ASP 3.5 2.2 + - - -
410A ILE* 1.3 75.3 - - - +
412A ILE* 1.3 63.9 + - - -
441A PHE* 3.9 14.8 - - - -
442A TRP 3.1 14.4 - - - -
443A LEU* 4.6 1.1 - - - -
444A LEU* 3.9 3.8 - - - -
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Residues in contact with ILE 412 (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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366A THR* 3.7 16.8 - - + -
369A THR* 3.6 24.5 - - + -
390A TYR* 3.6 41.3 - - + -
391A ASP 3.4 7.4 - - - +
392A VAL* 4.1 4.7 - - + -
411A GLY* 1.3 78.1 - - - +
413A ARG* 1.3 75.6 + - - +
414A VAL* 3.4 4.4 + - + +
419A PRO* 4.1 12.1 - - + -
422A ILE* 3.6 26.7 - - + -
441A PHE* 3.3 3.8 - - - -
442A TRP* 2.8 32.9 + - + +
444A LEU* 3.9 6.7 - - + -
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Residues in contact with ARG 413 (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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391A ASP* 3.0 49.5 + - + +
393A GLN* 5.2 0.6 - - - +
401A VAL* 3.9 15.2 - - - +
412A ILE* 1.3 75.7 - - - +
414A VAL* 1.3 57.7 + - - +
415A LYS 3.5 20.4 + - - +
416A PRO* 5.5 2.7 - - - -
417A ILE 4.0 3.4 - - - +
419A PRO* 3.4 19.4 - - - +
440A ASP* 3.6 25.9 + - - +
441A PHE* 3.4 38.7 - - + -
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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