Contacts of the strand formed by residues 455 - 460 (chain C) in PDB entry 3VI4
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 SER 455 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454C ALA* 1.3 77.0 - - - +
456C ALA* 1.3 60.0 + - - +
457C SER 4.0 0.8 + - - -
487C CYS 3.4 1.6 - - - +
488C LEU* 3.3 6.9 - - - -
489C ASN* 3.1 43.2 + - - +
541C GLU* 5.4 2.8 + - - -
569C PHE* 3.5 6.9 - - - -
591C LYS 5.4 2.2 - - - -
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Residues in contact with ALA 456 (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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455C SER* 1.3 72.8 - - - +
457C SER* 1.3 63.3 + - - +
487C CYS 3.4 5.4 - - - -
488C LEU* 3.5 15.7 - - + -
567C LEU* 4.2 18.8 - - + -
569C PHE* 3.4 24.4 - - + -
591C LYS 5.3 2.7 + - - +
592C SER 6.1 1.3 - - - -
593C ARG* 6.2 0.7 - - - -
594C ILE* 3.4 28.5 - - + +
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Residues in contact with SER 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C SER* 4.0 1.6 + - - -
456C ALA* 1.3 76.8 - - - +
458C LEU* 1.3 62.5 + - - +
459C THR* 5.4 3.0 + - - -
486C PHE* 3.4 11.0 - - - +
487C CYS* 2.9 54.5 + - - +
541C GLU* 4.2 10.6 + - - -
567C LEU* 4.5 0.5 - - - +
594C ILE* 4.6 2.5 - - - -
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Residues in contact with LEU 458 (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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456C ALA 4.0 0.4 + - - -
457C SER* 1.3 77.6 - - - +
459C THR* 1.3 77.3 + - - +
460C ILE* 5.2 2.7 - - + +
484C LEU* 3.7 24.2 - - + -
485C SER 3.3 20.4 - - - +
505C LEU* 5.3 1.1 - - + -
565C ILE* 5.1 9.0 - - + -
566C ALA 5.4 0.2 - - - -
567C LEU* 3.8 27.4 - - + +
594C ILE* 3.8 44.9 - - + +
596C ASP* 3.4 32.3 - - + +
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Residues in contact with THR 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457C SER* 5.4 2.5 + - - -
458C LEU* 1.3 84.8 + - - +
460C ILE* 1.3 65.6 + - - +
461C PHE* 3.9 0.9 + - - +
483C ASN 3.6 3.8 - - - +
484C LEU* 3.9 0.3 - - - -
485C SER* 3.2 48.3 + - - -
487C CYS* 6.2 0.2 - - - -
596C ASP* 4.6 1.3 - - - -
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Residues in contact with ILE 460 (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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458C LEU* 5.2 3.1 - - + -
459C THR* 1.3 74.9 - - - +
461C PHE* 1.3 65.1 + - - +
462C PRO 3.3 23.7 - - - +
463C ALA* 5.1 2.4 - - - -
465C PHE* 6.4 0.7 - - + -
482C ILE* 3.4 22.7 - - + -
483C ASN 3.4 4.5 - - - +
484C LEU* 5.0 12.8 - - + -
548C ILE* 5.3 5.8 - - + -
565C ILE* 4.6 22.9 - - + -
596C ASP* 3.6 37.1 + - + +
597C LYS* 4.9 2.7 - - - +
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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