Contacts of the helix formed by residues 519 - 535 (chain C) 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 ASP 519 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517C SER 3.8 1.0 + - - -
518C HIS* 1.3 71.2 - - - +
520C PRO* 1.3 77.8 - - - +
521C GLU* 3.0 25.7 + - - +
522C GLN* 3.1 23.5 + - + +
523C LEU* 3.0 20.1 + - - +
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Residues in contact with PRO 520 (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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511C LEU* 5.9 3.8 - - + -
518C HIS 3.3 9.8 - - - +
519C ASP* 1.3 89.1 - - - +
521C GLU* 1.3 58.2 + - - +
523C LEU* 4.3 5.8 - - + -
524C THR* 2.9 30.9 + - - -
546C PHE* 3.8 29.4 - - + -
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Residues in contact with GLU 521 (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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519C ASP* 3.0 19.7 + - - +
520C PRO* 1.3 78.6 - - - +
522C GLN* 1.3 74.7 + - - +
524C THR* 3.8 6.6 - - - -
525C LYS* 3.6 21.5 + - + +
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Residues in contact with GLN 522 (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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518C HIS* 6.5 0.9 - - + -
519C ASP* 3.1 24.8 + - + +
521C GLU* 1.3 94.6 + - - +
523C LEU* 1.3 57.9 + - - +
524C THR 3.3 0.4 - - - -
525C LYS* 3.2 17.3 + - - +
526C GLU* 3.0 27.0 + - - +
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Residues in contact with LEU 523 (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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487C ALA* 4.3 5.8 - - + -
511C LEU* 3.4 34.1 - - + -
515C PHE* 3.8 44.6 - - + +
518C HIS* 3.9 19.7 - - + +
519C ASP 3.0 15.5 + - - +
520C PRO* 4.0 7.2 - - + +
522C GLN* 1.3 72.7 - - - +
524C THR* 1.3 60.3 + - - +
526C GLU* 4.2 15.9 - - - -
527C LEU* 2.9 51.1 + - + +
546C PHE* 4.2 10.1 - - + -
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Residues in contact with THR 524 (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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520C PRO 2.9 17.8 + - - -
521C GLU* 3.8 7.6 - - - +
523C LEU* 1.3 76.3 - - - +
525C LYS* 1.3 58.3 + - + +
527C LEU* 3.2 2.5 + - - +
528C GLN* 2.9 52.8 + - - +
544C ILE* 3.9 31.3 + - + +
546C PHE* 3.7 17.3 - - - -
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Residues in contact with LYS 525 (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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521C GLU* 3.6 15.0 + - + +
522C GLN* 3.2 21.7 + - - +
524C THR* 1.3 79.0 - - + +
526C GLU* 1.3 57.1 + - - +
528C GLN* 3.7 14.6 - - - +
529C GLN* 2.9 31.2 + - - +
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Residues in contact with GLU 526 (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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485C HIS* 3.0 32.5 + - + +
515C PHE* 4.2 7.8 - - - -
518C HIS* 4.4 12.3 + - - -
522C GLN 3.0 14.5 + - - +
523C LEU* 3.7 20.4 - - + +
524C THR 3.3 0.4 - - - -
525C LYS* 1.3 78.1 - - - +
527C LEU* 1.3 56.0 + - - +
529C GLN* 4.1 4.4 - - - +
530C HIS* 3.0 26.5 + - - +
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Residues in contact with LEU 527 (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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482C LEU* 4.3 10.5 - - + -
485C HIS* 3.6 42.4 - - + +
487C ALA* 4.3 3.1 - - + -
488C VAL* 3.9 24.2 - - + -
509C VAL* 4.7 7.9 - - + -
511C LEU* 4.8 2.9 - - + -
523C LEU* 2.9 32.6 + - + +
524C THR 3.9 2.9 - - - +
526C GLU* 1.3 74.4 - - - +
528C GLN* 1.3 60.7 + - - +
530C HIS* 3.5 4.9 - - + +
531C VAL* 3.0 32.7 + - - +
544C ILE* 4.0 15.5 - - + -
546C PHE* 4.0 28.3 - - + -
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Residues in contact with GLN 528 (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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524C THR* 2.9 36.5 + - - +
525C LYS* 3.7 16.9 - - - +
527C LEU* 1.3 74.7 - - - +
529C GLN* 1.3 64.9 - - - +
531C VAL* 3.2 7.0 + - - +
532C LYS* 3.1 30.4 + - - +
540C TYR* 3.7 21.2 - - + +
541C PRO* 3.1 32.4 + - + +
542C ARG* 3.4 21.4 + - - +
543C LYS* 4.9 0.8 - - - +
544C ILE* 4.1 6.7 - - + +
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Residues in contact with GLN 529 (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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525C LYS 2.9 17.8 + - - +
526C GLU* 4.1 5.2 - - - +
528C GLN* 1.3 71.8 - - - +
530C HIS* 1.3 67.9 + - - +
532C LYS* 3.0 31.8 + - - +
533C SER* 2.9 31.9 + - - +
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Residues in contact with HIS 530 (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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481C ALA 2.7 29.0 + - - -
482C LEU* 4.5 3.8 - - + -
484C GLU* 3.9 13.5 - - + -
485C HIS* 3.5 50.5 + + + +
526C GLU 3.0 20.4 + - - +
527C LEU* 3.5 8.5 - - - +
529C GLN* 1.3 75.2 - - - +
531C VAL* 1.3 70.6 + - + +
533C SER* 2.8 24.0 + - - -
534C VAL* 3.2 31.0 - - + +
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Residues in contact with VAL 531 (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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478C VAL* 4.8 4.5 - - + +
481C ALA* 4.3 4.9 - - + -
482C LEU* 3.4 45.5 - - + +
527C LEU 3.0 11.6 + - - +
528C GLN 3.2 7.1 + - - +
530C HIS* 1.3 79.4 - - + +
532C LYS* 1.3 61.0 + - - +
534C VAL* 3.2 7.3 + - - +
535C THR* 3.2 41.6 + - + +
536C ALA 5.6 0.4 - - - +
537C PRO* 6.1 0.2 - - + -
539C LYS 4.3 2.9 - - - +
540C TYR* 3.7 27.1 - - + +
541C PRO* 3.8 12.1 - - + -
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Residues in contact with LYS 532 (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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141C LYS* 3.7 13.7 + - - -
528C GLN* 3.1 17.8 + - - +
529C GLN* 3.0 32.6 + - - +
531C VAL* 1.3 75.9 - - - +
533C SER* 1.3 59.3 + - - +
535C THR 3.1 16.9 - - - +
537C PRO* 3.9 30.0 - - + +
540C TYR* 3.6 51.8 + - + -
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Residues in contact with SER 533 (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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141C LYS* 3.3 25.8 + - - +
166C GLU* 4.7 4.7 - - - +
529C GLN* 2.9 22.5 + - - +
530C HIS* 2.8 25.8 + - - -
532C LYS* 1.3 77.5 - - - +
534C VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 534 (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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141C LYS* 3.2 16.6 - - - +
143C THR* 3.9 17.1 + - - +
144C ASP* 4.0 4.3 - - - +
481C ALA* 3.8 24.7 - - + +
484C GLU* 3.5 25.2 - - + +
530C HIS* 3.2 40.2 - - + +
531C VAL* 3.6 7.2 - - - +
533C SER* 1.3 84.0 - - - +
535C THR* 1.3 63.4 + - - +
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Residues in contact with THR 535 (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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141C LYS* 3.5 8.2 - - - +
144C ASP* 2.5 28.0 + - - -
477C GLU* 5.0 4.0 + - - +
481C ALA* 4.2 16.2 - - + -
531C VAL* 3.2 25.2 + - + +
532C LYS 3.1 18.4 - - - +
534C VAL* 1.3 77.1 - - - +
536C ALA* 1.3 71.3 + - - +
537C PRO* 3.3 0.3 - - - +
539C LYS* 3.1 41.8 + - + +
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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