Contacts of the strand formed by residues 432 - 437 (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 ASP 432 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 4.8 2.7 - - - -
25C PHE* 3.8 7.4 - - + -
358C LEU* 4.4 4.6 - - - +
361C LEU* 5.4 0.4 - - - -
421C GLY* 3.5 20.4 - - - -
422C GLY 3.6 5.0 + - - -
423C ARG 3.1 12.7 + - - +
424C ASP* 3.5 4.3 - - - +
425C LEU* 3.5 24.5 + - + -
426C ASP* 3.6 4.1 - - - +
430C TYR 2.6 9.7 - - - +
431C PRO* 1.3 74.6 - - - +
433C LEU* 1.3 63.3 + - - +
445C VAL* 5.4 0.9 - - + -
446C TYR 3.4 9.4 - - - +
447C ARG* 3.0 18.2 - - + +
448C GLY 2.7 24.3 + - - +
2004C CA 2.3 28.3 - - - -
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Residues in contact with LEU 433 (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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3C LEU* 4.1 30.1 - - + -
25C PHE* 4.3 1.4 - - - -
356C THR* 4.1 12.8 - - + -
358C LEU* 3.8 25.1 - - + -
370C ALA* 4.6 2.5 - - + -
384C VAL* 4.9 7.2 - - + -
386C VAL* 5.2 0.7 - - + -
402C LEU* 4.3 11.9 - - + -
419C LEU* 4.3 4.3 - - + -
420C ARG 3.7 16.6 - - - +
432C ASP* 1.3 80.0 - - - +
434C ILE* 1.3 75.8 - - - +
435C VAL* 3.8 22.7 - - + -
444C VAL 3.7 1.0 - - - +
445C VAL* 3.3 5.2 - - - +
446C TYR* 2.8 43.6 + - + +
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Residues in contact with ILE 434 (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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23C VAL* 3.7 28.3 - - + +
24C GLU 3.8 28.5 - - - +
25C PHE* 3.6 38.8 - - + -
35C VAL* 4.2 24.0 - - + -
419C LEU* 3.5 4.5 - - - -
420C ARG* 2.8 40.5 + - + +
433C LEU* 1.3 78.2 - - - +
435C VAL* 1.3 67.3 + - - +
443C ALA* 4.7 4.5 - - + -
444C VAL 3.4 8.3 - - - +
445C VAL* 4.4 14.6 - - + +
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Residues in contact with VAL 435 (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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23C VAL* 4.8 0.2 - - - -
384C VAL* 3.9 9.0 - - + -
402C LEU* 5.7 0.2 - - + -
415C PHE* 3.9 22.2 - - + -
416C GLY* 3.6 28.0 - - - +
418C ALA 3.4 3.4 - - - +
419C LEU* 3.6 15.5 - - + -
433C LEU* 3.8 17.0 - - + -
434C ILE* 1.3 79.7 - - - +
436C GLY* 1.3 66.5 + - - +
443C ALA* 3.3 5.1 - - - +
444C VAL* 2.8 39.2 + - + +
446C TYR* 3.7 25.6 - - + -
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Residues in contact with GLY 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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20C GLY 3.5 19.7 - - - -
23C VAL* 4.5 5.7 - - - +
414C PHE 3.4 2.3 - - - +
415C PHE* 3.4 0.3 - - - -
416C GLY* 2.7 32.9 + - - -
418C ALA* 2.7 24.8 + - - -
435C VAL* 1.3 75.6 - - - +
437C SER* 1.3 59.3 + - - -
438C PHE 3.9 0.9 - - - -
442C LYS 4.2 2.7 - - - -
443C ALA* 4.5 2.0 - - - -
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Residues in contact with SER 437 (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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20C GLY 3.9 0.2 + - - -
406C TRP* 3.5 24.8 - - - -
413C ASP* 3.5 12.5 - - - +
414C PHE 3.7 8.7 - - - -
415C PHE* 3.9 12.1 + - - -
435C VAL 5.4 0.2 - - - -
436C GLY* 1.3 75.4 - - - -
438C PHE* 1.3 66.8 + - - +
439C GLY 2.9 4.4 + - - -
440C VAL* 3.1 27.4 + - - +
442C LYS 3.0 28.0 + - - -
443C ALA* 5.5 0.2 - - - -
444C VAL* 5.8 0.9 - - - -
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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