Contacts of the strand formed by residues 441 - 450 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391B ASP 3.9 6.7 - - - -
393B GLN* 3.9 21.1 - - + -
395B ILE* 3.5 30.5 - - + -
399B GLY 3.8 21.8 - - - -
401B VAL* 3.7 21.3 - - + -
411B GLY 3.7 4.9 - - - -
412B ILE 3.4 25.1 - - - -
413B ARG* 3.4 53.4 - - + -
414B VAL* 4.3 4.0 - - - -
437B ILE* 3.3 6.5 - - - +
438B ARG* 2.9 29.4 + - - +
439B GLY 3.2 0.4 - - - -
440B ASP* 1.3 86.5 - - + +
442B TRP* 1.3 62.3 + - - +
443B LEU* 3.8 1.3 + - + -
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Residues in contact with TRP 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B GLN* 3.2 21.4 + - - -
365B GLU* 3.9 15.0 - - + -
366B THR* 3.6 21.0 - - + +
411B GLY* 3.0 22.0 - - - -
412B ILE* 2.8 18.6 + - + +
414B VAL* 3.9 25.8 - - + +
422B ILE* 5.1 7.9 - - + -
423B PHE* 3.5 36.6 - + - -
426B TYR* 3.9 7.2 - + - -
433B THR* 3.4 30.1 - - + -
436B ASN* 3.4 37.0 - - + -
437B ILE* 4.0 15.9 - - + -
441B PHE* 1.3 70.4 - - - +
443B LEU* 1.3 70.5 + - - +
444B LEU* 3.6 5.1 + - + +
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B ILE* 3.3 39.9 - - + -
409B ASP* 4.2 15.9 - - + -
410B ILE 3.7 7.6 - - - +
411B GLY* 4.5 2.0 - - - -
435B ALA 5.8 1.3 - - - +
436B ASN* 2.8 36.5 + - - +
438B ARG* 3.2 50.9 - - + +
441B PHE* 4.6 0.7 - - + -
442B TRP* 1.3 89.6 + - - +
444B LEU* 1.3 61.6 + - - +
445B GLY* 3.5 7.7 + - - +
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B TYR* 3.0 44.6 - - + +
362B GLY 4.7 0.2 - - - -
363B GLN* 2.7 48.3 + - + +
366B THR* 3.9 20.4 - - + +
369B THR* 4.0 7.4 - - + +
410B ILE* 3.0 23.0 + - + +
411B GLY* 3.9 14.1 - - - -
412B ILE* 3.9 21.8 - - + -
436B ASN* 5.8 0.7 + - - -
442B TRP* 3.9 9.0 - - + +
443B LEU* 1.3 72.6 - - - +
445B GLY* 1.3 57.9 + - - +
446B ASP* 3.4 2.9 - - - +
461B ARG* 3.1 11.8 + - - -
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Residues in contact with GLY 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409B ASP* 6.1 2.0 - - - +
410B ILE 4.3 1.2 + - - -
443B LEU* 3.2 9.4 - - - +
444B LEU* 1.3 79.0 - - - +
446B ASP* 1.3 59.2 + - - +
461B ARG* 3.3 25.7 + - - -
462B ALA* 2.9 32.3 + - - +
463B ASP* 4.3 2.5 + - - -
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Residues in contact with ASP 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B TYR* 2.5 33.0 + - - +
409B ASP* 3.6 5.2 - - - +
410B ILE* 2.9 35.0 + - + -
444B LEU* 3.4 5.5 - - - +
445B GLY* 1.3 79.4 - - - +
447B ARG* 1.3 62.8 + - - +
458B PHE* 3.6 16.8 - - + -
460B GLY 3.8 3.1 - - - -
461B ARG* 3.0 19.7 + - - -
462B ALA* 5.0 0.2 - - - -
1570B AMP 2.5 46.7 + - - -
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Residues in contact with ARG 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B GLU* 2.9 45.1 + - - +
408B GLY* 3.3 20.2 + - - +
409B ASP* 2.7 42.4 + - - -
410B ILE* 3.6 9.7 - - - +
446B ASP* 1.3 75.0 - - - +
448B GLY* 1.3 59.6 + - - +
458B PHE* 3.8 3.1 - - - -
459B MET* 3.0 29.6 + - + +
460B GLY 2.8 22.1 + - - +
461B ARG 4.6 0.7 - - - +
462B ALA* 4.3 19.7 - - - +
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Residues in contact with GLY 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B ILE* 3.4 22.4 - - - +
407B GLU* 3.2 4.2 - - - +
408B GLY 2.9 32.6 + - - +
410B ILE* 3.9 7.4 - - - +
447B ARG* 1.3 76.4 - - - +
449B ILE* 1.3 62.0 + - - -
457B GLN 3.3 11.4 - - - -
459B MET* 3.9 5.1 - - - +
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Residues in contact with ILE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B TYR* 4.8 2.4 - - + +
394B ILE* 4.2 4.3 - - - -
405B GLY* 3.5 37.5 - - - +
406B THR 3.9 4.0 - - - +
407B GLU* 3.8 21.5 - - + +
448B GLY* 1.3 78.3 - - - +
450B LYS* 1.3 66.8 + - - +
451B ASP* 5.5 0.9 - - - -
455B TYR 3.9 0.2 - - - +
456B PHE* 3.5 2.1 - - - +
457B GLN* 2.7 55.2 + - - +
459B MET* 3.9 30.1 - - + -
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Residues in contact with LYS 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B TYR* 5.4 0.2 - - - -
392B VAL 4.8 0.9 - - - +
393B GLN* 3.1 32.1 + - - +
394B ILE* 3.8 18.1 - - + +
401B VAL* 5.5 0.4 - - - +
402B LEU 4.9 10.1 + - - -
403B PRO 5.3 1.7 + - - +
404B PRO* 3.0 20.9 - - + +
405B GLY 2.9 25.9 + - - +
406B THR 4.8 1.0 + - - -
449B ILE* 1.3 77.2 - - - +
451B ASP* 1.3 68.1 + - - +
454B GLY* 3.7 28.5 - - - +
455B TYR 3.4 6.7 - - - +
456B PHE* 3.8 27.6 - - + +
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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