Contacts of the strand formed by residues 470 - 474 (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 ALA 470 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468C ALA* 3.2 6.9 - - - +
469C ALA* 1.3 81.4 - - - +
471C ILE* 1.3 64.8 + - - +
472C ILE* 4.8 0.7 - - + -
491C ALA* 3.7 5.8 - - - -
492C ALA* 3.2 14.6 - - + +
494C ILE* 3.8 17.0 - - + -
545C PHE* 5.6 0.4 - - + -
546C LEU* 3.4 24.0 - - + -
552C VAL* 3.2 14.7 - - + +
553C ILE 3.0 23.0 + - - -
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Residues in contact with ILE 471 (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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459C ALA* 4.4 2.7 - - + +
460C VAL* 4.4 5.8 - - + -
463C ALA* 4.1 23.8 - - + -
470C ALA* 1.3 75.8 - - - +
472C ILE* 1.3 57.9 + - - +
473C VAL* 3.9 1.0 + - - +
484C LEU* 3.6 40.8 - - + -
489C PRO* 3.7 37.0 - - + -
491C ALA* 4.3 3.8 - - + +
492C ALA 2.7 9.3 + - - +
493C VAL* 3.2 10.5 - - + -
494C ILE 2.8 30.0 + - - -
553C ILE* 3.1 18.4 - - + +
555C VAL* 4.0 15.0 - - + -
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Residues in contact with ILE 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C ALA* 4.8 0.2 - - + -
471C ILE* 1.3 73.7 - - - +
473C VAL* 1.3 57.3 + - - +
474C LEU* 4.8 2.2 - - + -
494C ILE* 3.3 27.8 - - + +
496C VAL* 4.5 16.2 - - + -
533C VAL* 4.3 18.2 - - + +
536C GLY* 4.2 3.1 - - - -
537C ILE* 3.7 40.6 - - + +
546C LEU* 4.8 2.9 - - + -
552C VAL* 4.2 26.7 - - + -
553C ILE 2.7 11.0 + - - +
554C VAL* 3.3 14.1 - - + +
555C VAL* 2.8 32.1 + - - +
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Residues in contact with VAL 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471C ILE 4.3 1.3 - - - +
472C ILE* 1.3 75.3 - - - +
474C LEU* 1.3 74.7 + - - +
475C THR* 3.7 1.0 + - + +
480C SER* 4.2 17.3 - - - +
481C ALA* 4.2 11.9 - - + +
484C LEU* 3.4 28.7 - - + -
493C VAL* 3.7 20.2 - - + -
494C ILE 2.9 9.2 + - - +
495C ALA* 3.4 3.8 - - - -
496C VAL 2.9 24.7 + - - -
555C VAL* 3.5 31.9 - - + -
565C THR* 5.3 0.2 - - + -
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Residues in contact with LEU 474 (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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472C ILE* 4.8 3.4 - - + -
473C VAL* 1.3 84.3 - - - +
475C THR* 1.3 61.7 + - - +
480C SER* 3.9 2.6 + - - -
496C VAL* 3.6 15.3 - - + +
529C VAL* 3.8 44.0 - - + +
532C ARG* 4.2 34.1 - - + +
533C VAL* 3.8 25.8 - - + +
555C VAL 3.3 9.4 + - - +
556C THR* 3.9 11.8 - - + -
565C THR* 4.4 2.6 + - - -
580C FBP 3.5 35.1 + - - +
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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