Contacts of the helix formed by residues 508 - 522 (chain C) in PDB entry 3VI7
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 LYS 508 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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506C GLU* 3.0 44.2 + - - +
507C LYS* 1.3 74.8 - - + +
509C GLN* 1.3 58.3 + - - +
510C ASP* 3.5 2.9 - - + +
511C VAL* 3.6 26.8 + - + +
512C LYS* 3.1 20.0 + - - +
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Residues in contact with GLN 509 (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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506C GLU 4.4 1.2 - - - +
507C LYS* 2.7 32.5 + - - +
508C LYS* 1.3 70.1 - - - +
510C ASP* 1.3 58.7 + - - +
512C LYS* 3.6 24.3 - - + +
513C GLU* 2.8 38.0 + - + +
761D LEU 5.3 4.9 + - - +
762D VAL* 6.1 2.5 - - - +
765D PRO* 4.0 28.7 - - - +
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Residues in contact with ASP 510 (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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508C LYS* 3.5 1.8 - - + -
509C GLN* 1.3 74.3 - - - +
511C VAL* 1.3 69.6 + - + +
513C GLU* 5.4 0.7 - - - -
514C GLN* 3.2 28.4 + - - +
796D GLN* 5.5 5.2 + - - -
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Residues in contact with VAL 511 (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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506C GLU* 3.9 18.8 - - + +
508C LYS* 3.6 28.1 + - + +
510C ASP* 1.3 77.9 - - + +
512C LYS* 1.3 60.6 + - - +
514C GLN* 3.7 6.5 + - - +
515C MET* 3.2 46.8 + - + +
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Residues in contact with LYS 512 (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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503C PRO* 3.4 30.5 - - + +
504C TRP* 3.5 17.9 + - - +
506C GLU* 3.7 17.7 + - - +
508C LYS 3.1 18.7 + - - +
509C GLN* 3.6 24.0 - - - +
510C ASP 3.2 0.2 - - - -
511C VAL* 1.3 73.5 - - - +
513C GLU* 1.3 61.1 + - + +
514C GLN 3.2 1.8 - - - -
515C MET* 3.2 2.9 + - - +
516C PHE* 2.8 63.7 + - + -
598C LYS* 5.1 10.7 - - - +
599C LEU* 6.2 2.0 - - - +
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Residues in contact with GLU 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C GLN* 2.8 21.4 + - + +
510C ASP* 4.9 0.7 - - - +
512C LYS* 1.3 77.8 - - + +
514C GLN* 1.3 57.7 + - - +
516C PHE* 4.2 10.8 - - - +
517C ASN* 2.6 37.5 + - - +
778D ARG* 4.3 8.7 + - - -
779D LYS* 3.4 30.0 + - - -
782D GLN* 4.0 14.5 + - - +
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Residues in contact with GLN 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C ASP 3.2 18.4 + - - +
511C VAL* 3.7 9.3 + - - +
512C LYS 3.2 0.6 - - - -
513C GLU* 1.3 75.6 - - - +
515C MET* 1.3 84.7 + - - +
517C ASN* 3.1 7.8 + - + +
518C GLU* 2.9 55.9 + - + +
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Residues in contact with MET 515 (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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501C CYS 3.9 11.7 - - - +
503C PRO* 3.7 35.9 - - + -
506C GLU* 6.3 0.4 - - - -
511C VAL* 3.2 39.6 + - + +
512C LYS 3.2 3.6 + - - +
514C GLN* 1.3 91.6 - - - +
516C PHE* 1.4 62.7 + - - +
518C GLU* 3.2 8.6 + - + +
519C LEU* 3.0 33.3 + - + +
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Residues in contact with PHE 516 (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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502C PHE* 3.8 27.8 - + - -
503C PRO* 3.9 28.0 - - + -
504C TRP* 3.7 36.3 - + - -
512C LYS* 2.8 56.6 + - + +
513C GLU* 4.2 15.5 - - - +
515C MET* 1.4 71.0 - - - +
517C ASN* 1.3 59.8 + - - +
519C LEU* 3.4 1.7 + - - +
520C LEU* 3.1 46.7 + - + +
563C PHE* 4.2 30.7 - + - -
779D LYS* 5.9 2.2 - - - +
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Residues in contact with ASN 517 (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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513C GLU* 2.6 38.2 + - - +
514C GLN* 3.1 10.8 + - + +
516C PHE* 1.3 77.3 - - - +
518C GLU* 1.3 64.2 + - - +
520C LEU* 4.5 5.9 - - - +
521C THR* 2.9 36.1 + - - +
522C TYR* 5.8 0.2 - - - -
779D LYS* 4.4 6.3 + - - +
782D GLN* 5.0 11.6 + - - +
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Residues in contact with GLU 518 (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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514C GLN* 2.9 47.2 + - + +
515C MET* 3.2 9.8 + - + +
517C ASN* 1.3 70.9 - - - +
519C LEU* 1.3 58.1 + - + +
522C TYR* 2.6 66.7 + - + +
523C ASN* 3.8 4.3 - - - +
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Residues in contact with LEU 519 (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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498C PHE* 4.5 9.0 - - + -
501C CYS* 3.7 41.3 - - + +
502C PHE* 3.7 43.7 - - + -
503C PRO* 4.4 2.9 - - + -
515C MET* 3.0 23.5 + - + +
516C PHE 3.8 0.2 - - - +
517C ASN 3.3 0.2 - - - -
518C GLU* 1.3 80.5 - - + +
520C LEU* 1.3 53.9 + - - +
523C ASN* 2.9 28.9 + - + +
524C ALA* 2.7 34.2 + - - -
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Residues in contact with LEU 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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502C PHE* 3.8 28.5 - - + -
516C PHE* 3.1 32.6 + - + +
517C ASN* 4.1 7.0 - - - +
519C LEU* 1.3 77.7 - - - +
521C THR* 1.3 60.7 + - - +
524C ALA* 3.5 8.7 - - + +
525C PRO* 3.2 18.4 - - - +
560C LEU* 4.2 17.7 - - + +
563C PHE* 4.0 26.7 - - + +
564C LYS* 3.3 46.0 - - + -
567C LEU* 5.5 0.2 - - + -
779D LYS* 6.0 3.1 - - + +
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Residues in contact with THR 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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517C ASN* 2.9 26.2 + - - +
518C GLU 4.1 0.7 - - - -
520C LEU* 1.3 76.0 - - - +
522C TYR* 1.3 96.9 + - + +
525C PRO* 3.4 15.9 - - - +
564C LYS* 5.3 3.8 - - - +
792D LYS* 6.4 0.2 - - - +
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Residues in contact with TYR 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 GLU* 2.6 53.7 + - + +
521C THR* 1.3 101.8 - - + +
523C ASN* 1.3 68.2 + - - +
525C PRO* 3.7 4.6 - - - +
526C HIS* 3.2 24.9 + - - -
792D LYS* 4.5 13.9 + - - -
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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