Contacts of the strand formed by residues 441 - 450 (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 PHE 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A ASP* 4.2 2.0 - - - -
393A GLN* 3.9 22.4 - - + -
395A ILE* 3.7 25.1 - - + -
399A GLY 3.6 25.6 - - - -
401A VAL* 3.8 15.9 - - + -
411A GLY* 3.9 9.9 - - - -
412A ILE 3.3 19.3 - - - +
413A ARG* 3.4 55.4 - - + -
414A VAL* 4.2 4.0 - - - -
437A ILE* 3.4 5.4 - - - +
438A ARG* 3.0 34.5 + - - +
439A GLY 3.4 0.2 - - - -
440A ASP* 1.3 87.4 - - + +
442A TRP* 1.3 64.8 + - - +
443A LEU 3.8 0.3 + - - -
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Residues in contact with TRP 442 (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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363A GLN* 3.1 21.5 + - - -
365A GLU* 3.9 16.4 - - + -
366A THR* 3.6 25.2 - - + +
411A GLY* 3.1 7.2 - - - -
412A ILE* 2.8 32.0 + - + +
414A VAL* 3.9 25.9 - - + +
422A ILE* 5.2 7.2 - - + -
423A PHE* 3.6 32.1 - + - -
426A TYR* 3.9 8.7 - + - -
433A THR* 3.5 26.7 - - + -
436A ASN* 3.5 48.5 - - + -
437A ILE* 4.0 12.3 - - + -
441A PHE* 1.3 72.0 - - - +
443A LEU* 1.3 71.6 + - - +
444A LEU* 3.7 5.4 + - + +
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Residues in contact with LEU 443 (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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363A GLN* 4.4 0.3 - - - +
395A ILE* 3.6 31.0 - - + -
409A ASP* 4.1 15.5 - - + -
410A ILE 4.0 3.8 - - - +
435A ALA 4.9 4.3 - - - +
436A ASN* 2.9 42.1 + - + +
438A ARG* 3.6 48.0 - - + +
442A TRP* 1.3 90.3 + - - +
444A LEU* 1.3 61.6 + - - +
445A GLY* 3.5 8.0 + - - +
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Residues in contact with LEU 444 (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* 3.3 43.1 - - + +
362A GLY 4.8 0.2 - - - -
363A GLN* 2.8 45.8 + - + +
366A THR* 3.8 22.7 - - + +
369A THR* 3.9 10.1 - - + +
410A ILE* 3.2 27.4 + - + +
411A GLY* 3.9 4.3 - - - -
412A ILE* 3.9 27.6 - - + -
442A TRP* 3.9 10.5 - - + +
443A LEU* 1.3 72.6 - - - +
445A GLY* 1.3 57.2 + - - +
446A ASP* 3.3 1.9 + - - +
461A ARG* 2.8 14.4 + - - -
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Residues in contact with GLY 445 (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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409A ASP* 5.9 3.5 - - - +
410A ILE 4.5 1.2 + - - -
443A LEU* 3.2 10.7 + - - +
444A LEU* 1.3 78.6 - - - +
446A ASP* 1.3 57.7 + - - +
461A ARG* 3.4 23.8 + - - -
462A ALA* 2.9 32.3 + - - +
463A ASP* 4.3 3.6 + - - -
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Residues in contact with ASP 446 (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* 2.5 32.2 + - - +
409A ASP* 3.8 2.8 - - - -
410A ILE* 3.0 31.6 + - + +
444A LEU* 3.3 4.8 - - - +
445A GLY* 1.3 78.1 - - - +
447A ARG* 1.3 64.5 + - - +
458A PHE* 3.6 20.9 - - + -
460A GLY 3.8 3.1 - - - -
461A ARG* 3.0 17.0 - - - -
462A ALA* 4.7 1.3 - - - -
1570A AMP 2.6 45.3 + - - -
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Residues in contact with ARG 447 (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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407A GLU* 3.0 40.5 + - - +
408A GLY* 3.2 29.4 - - - -
409A ASP* 3.1 36.1 + - - -
410A ILE* 3.6 8.9 - - - +
445A GLY 4.2 0.4 + - - -
446A ASP* 1.3 76.2 - - - +
448A GLY* 1.3 58.0 + - - +
458A PHE* 4.0 3.6 - - - -
459A MET* 3.0 28.9 + - + +
460A GLY 2.8 21.2 + - - +
461A ARG 4.7 0.9 - - - +
462A ALA* 4.0 17.5 - - + -
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Residues in contact with GLY 448 (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* 3.4 11.1 - - - +
407A GLU* 3.4 4.0 - - - +
408A GLY 2.8 35.8 + - - +
410A ILE* 3.8 15.2 - - - +
447A ARG* 1.3 76.1 - - - +
449A ILE* 1.3 62.7 - - - -
457A GLN 3.2 12.3 - - - -
459A MET* 4.0 5.4 - - - +
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Residues in contact with ILE 449 (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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382A TYR* 5.8 2.7 - - + +
394A ILE* 4.0 4.5 - - - +
405A GLY* 3.5 39.7 - - - +
406A THR 4.0 4.0 - - - +
407A GLU* 3.8 21.1 - - + +
448A GLY* 1.3 78.9 - - - +
450A LYS* 1.3 66.6 + - - +
451A ASP* 5.5 0.7 - - + -
455A TYR 3.7 0.7 - - - +
456A PHE* 3.4 4.0 - - - +
457A GLN* 2.8 51.2 + - + +
459A MET* 3.9 32.3 - - + -
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Residues in contact with LYS 450 (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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382A TYR* 5.5 0.2 - - - -
392A VAL 4.8 1.1 - - - +
393A GLN* 3.0 32.3 + - - +
394A ILE* 3.8 20.6 - - + +
401A VAL* 5.4 0.8 - - - +
402A LEU 5.0 10.4 + - - -
403A PRO 5.6 1.1 + - - +
404A PRO* 3.2 18.9 - - + +
405A GLY 2.9 25.9 + - - +
406A THR 4.6 1.2 + - - -
449A ILE* 1.3 78.3 - - - +
451A ASP* 1.3 66.5 + - - +
454A GLY* 3.7 29.3 - - - +
455A TYR 3.3 3.6 - - - +
456A PHE* 4.0 24.9 - - + +
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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