Contacts of the helix formed by residues 433 - 445 (chain C) in PDB entry 2VGB
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 TYR 433 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C ALA 4.3 3.1 - - - -
64C ALA* 4.3 9.4 - - - +
66C ALA 2.7 30.0 + - - -
67C ASP 3.3 19.1 + - - -
68C THR* 3.6 6.1 - - - -
69C PHE* 3.8 39.0 - + + -
72C HIS* 3.6 39.9 - + + +
431C ALA 3.3 3.0 + - - -
432C VAL* 1.3 71.8 - - - +
434C HIS* 1.3 64.9 + - - +
435C ARG* 3.2 27.4 - - + -
436C GLN* 3.1 39.6 + - + +
437C LEU* 3.0 17.7 + - - +
443D ARG* 4.5 0.7 + - - -
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Residues in contact with HIS 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA* 5.6 5.4 - - + +
429C GLU 4.0 6.0 + - - -
432C VAL* 3.0 39.7 + - + +
433C TYR* 1.3 70.5 - - - +
435C ARG* 1.3 60.3 + - - +
437C LEU* 2.8 12.2 + - + +
438C PHE* 2.5 36.0 + - + +
464C PHE* 3.9 27.3 - + + -
488C ARG* 4.0 14.9 + - + +
489C PRO 4.5 4.7 - - - -
490C ARG* 3.0 65.0 + - + -
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Residues in contact with ARG 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ALA 4.4 11.6 + - - +
65C MET* 4.1 18.5 + - - +
66C ALA 3.6 13.4 + - - -
67C ASP* 3.2 19.4 + - - +
433C TYR* 3.1 33.7 + - + +
434C HIS* 1.3 80.4 - - - +
436C GLN* 1.3 62.8 + - - +
438C PHE* 4.1 3.2 - - - +
439C GLU* 3.1 37.7 + - + +
443D ARG* 2.8 69.6 + - + +
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Residues in contact with GLN 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE* 3.2 37.6 - - - +
436A GLN* 2.9 30.9 + - - +
440A GLU* 5.1 0.5 - - - +
69C PHE* 4.1 13.9 + - - +
433C TYR* 3.1 30.6 + - + +
435C ARG* 1.3 77.4 - - - +
437C LEU* 1.3 67.6 + - - +
439C GLU* 3.1 6.7 + - - +
440C GLU* 2.8 47.4 + - + +
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Residues in contact with LEU 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 5.3 9.9 - - + -
361C ASN* 4.9 12.3 - - - +
398C GLY* 6.4 1.8 - - - -
432C VAL* 3.7 25.1 - - + -
433C TYR 3.0 13.2 + - - +
434C HIS* 2.8 12.4 + - - +
436C GLN* 1.3 79.1 - - - +
438C PHE* 1.3 63.3 + - - +
440C GLU* 3.2 7.8 + - + +
441C LEU* 3.0 49.6 + - + +
488C ARG* 3.8 29.6 - - + -
510C ARG* 5.4 3.8 - - - +
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Residues in contact with PHE 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C HIS* 2.5 21.4 + - - +
435C ARG* 4.1 2.7 - - - +
437C LEU* 1.3 69.4 - - - +
439C GLU* 1.3 66.8 + - + +
441C LEU* 3.1 7.5 + - + -
442C ARG* 3.0 57.0 + - + +
457C ILE* 4.3 11.9 - - + -
460C VAL* 3.8 19.1 - - + -
461C GLU* 3.9 29.6 - - + -
464C PHE* 3.6 38.4 - + + -
487C TYR* 4.0 32.1 - + + +
488C ARG 5.7 0.4 - - - +
442D ARG* 4.7 10.5 - - - -
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Residues in contact with GLU 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435C ARG* 3.1 28.6 + - + +
436C GLN* 3.1 7.9 + - + +
438C PHE* 1.3 77.2 - - + +
440C GLU* 1.3 59.8 + - + +
442C ARG* 3.5 11.9 + - - +
443C ARG* 2.9 40.6 + - - +
439D GLU* 3.1 36.0 - - - +
442D ARG* 4.1 18.4 + - - +
443D ARG* 3.1 33.2 + - - +
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Residues in contact with GLU 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR* 3.1 23.8 - - + +
69A PHE* 2.9 24.8 + - - +
70A LEU* 2.8 40.7 + - + +
436A GLN* 5.1 0.2 - - - +
436C GLN* 2.8 45.2 + - + +
437C LEU* 3.7 7.2 - - + +
439C GLU* 1.3 77.6 - - + +
441C LEU* 1.3 52.6 + - - +
443C ARG* 3.3 8.9 + - - +
444C ALA* 2.8 39.0 + - - +
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Residues in contact with LEU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A LEU* 3.9 20.4 - - + -
361C ASN* 3.9 32.1 - - + +
362C LEU* 4.7 1.6 - - + -
437C LEU* 3.0 45.0 + - + +
438C PHE* 3.8 4.3 - - - +
440C GLU* 1.3 72.5 - - - +
442C ARG* 1.3 68.9 + - - +
444C ALA* 3.0 4.1 + - - +
445C ALA* 2.7 28.8 + - - +
486C ARG* 4.0 25.7 + - - +
487C TYR* 4.3 23.1 - - + +
488C ARG* 4.1 13.5 - - + -
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Residues in contact with ARG 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C PHE* 3.0 50.8 + - + +
439C GLU* 3.7 9.7 - - - +
441C LEU* 1.3 76.0 - - - +
443C ARG* 1.3 65.2 + - - +
444C ALA 3.0 0.5 + - - -
445C ALA* 3.1 18.3 - - - +
457C ILE* 4.2 9.4 - - + -
487C TYR* 4.6 9.5 - - - -
438D PHE* 4.7 11.3 - - - -
439D GLU* 3.9 22.4 + - - +
442D ARG* 2.7 40.6 - - - +
461D GLU* 3.6 31.8 + - - -
464D PHE* 6.2 1.4 - - - +
465D LYS* 5.0 2.9 + - - +
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Residues in contact with ARG 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 4.6 21.5 - - + +
439C GLU* 2.9 25.1 + - - +
440C GLU* 3.4 8.3 - - - +
442C ARG* 1.3 80.1 - - - +
444C ALA* 1.3 61.3 + - - +
445C ALA 4.3 1.9 - - - +
67D ASP* 3.4 29.7 + - - +
433D TYR* 4.7 0.6 + - - -
435D ARG* 2.9 60.2 + - + +
439D GLU* 3.3 28.7 + - - +
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Residues in contact with ALA 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 6.2 0.4 - - - +
70A LEU* 4.6 3.6 - - + -
362C LEU* 3.9 31.3 - - + +
440C GLU 2.8 21.8 + - - +
441C LEU* 3.8 2.2 - - + +
443C ARG* 1.3 76.9 - - - +
445C ALA* 1.3 64.9 - - - +
446C PRO* 3.4 6.2 - - - +
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Residues in contact with ALA 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C LEU* 5.7 2.0 - - - +
441C LEU 2.7 21.7 + - - +
442C ARG 3.1 13.0 - - - +
443C ARG 4.3 1.7 - - - +
444C ALA* 1.3 72.6 - - - +
446C PRO* 1.4 73.9 - - + +
447C LEU* 5.8 0.3 - - - +
486C ARG* 3.9 25.5 - - - +
487C TYR* 4.1 9.2 - - + +
465D LYS* 3.4 20.1 + - - +
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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