Contacts of the strand formed by residues 422 - 427 (chain B) 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 422 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B SER* 3.9 6.3 + - - -
421B ASP* 1.3 68.9 - - - +
423B PHE* 1.3 59.9 + - - +
424B LYS* 4.0 17.2 + - - +
435B GLU* 3.8 21.3 + - - -
436B VAL 5.1 0.9 - - - -
437B ILE* 3.8 24.9 - - - +
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Residues in contact with PHE 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366B ASN* 4.4 5.4 - - + -
367B GLY* 4.2 10.8 - - - -
368B LYS 4.0 18.2 - - - +
369B LEU* 3.7 30.7 - - + -
375B ILE* 4.3 5.2 - - + -
410B ILE* 3.7 22.7 - - + -
421B ASP* 2.9 22.4 + - + +
422B SER* 1.3 74.4 - - - +
424B LYS* 1.3 72.2 + - - +
425B ILE* 3.6 26.9 - - + -
434B VAL 3.7 0.5 - - - +
435B GLU* 3.9 0.9 - - - -
436B VAL* 3.0 44.6 + - + -
438B LEU* 3.8 23.8 - - + -
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Residues in contact with LYS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B GLU 4.1 0.7 - - - +
366B ASN* 3.5 1.4 - - - -
367B GLY* 3.1 28.3 + - - +
422B SER* 4.0 15.2 + - - +
423B PHE* 1.3 82.6 - - - +
425B ILE* 1.3 62.7 + - - +
426B ARG* 4.3 2.7 - - + -
433B GLU* 3.2 52.5 - - + +
434B VAL 3.3 7.6 - - - +
435B GLU* 3.4 38.0 + - + +
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Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 5.6 0.2 - - - +
111B PHE* 4.8 2.0 - - + -
113B LEU* 4.9 4.5 - - + -
364B LEU* 4.3 18.6 - - + -
365B GLU 3.5 5.8 - - - +
366B ASN* 4.0 2.2 - - + -
375B ILE* 4.2 3.6 - - + -
377B TYR* 3.3 36.6 - - + +
408B ILE* 3.8 36.1 - - + -
410B ILE* 5.8 0.2 - - + -
423B PHE* 3.6 28.5 - - + -
424B LYS* 1.3 72.4 - - - +
426B ARG* 1.3 64.4 + - - +
427B PRO* 4.6 1.1 - - - +
432B GLU 4.4 0.5 - - - +
433B GLU 3.7 1.2 - - - -
434B VAL* 3.0 45.2 + - + +
436B VAL* 4.4 11.7 - - + -
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Residues in contact with ARG 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B SER 3.0 25.9 + - - -
310B ASN* 2.8 36.2 - - - +
364B LEU* 3.5 5.0 - - - -
365B GLU* 2.8 71.1 + - - +
424B LYS* 5.3 2.7 - - + -
425B ILE* 1.3 77.9 - - - +
427B PRO* 1.4 76.1 + - - +
428B LEU* 3.7 7.8 + - - +
429B GLY 3.9 6.5 - - - +
430B PHE 2.9 24.4 + - - +
431B THR* 4.4 4.5 - - - +
432B GLU 3.6 12.6 - - - +
433B GLU* 3.9 25.8 - - + -
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Residues in contact with PRO 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B ILE* 3.5 31.2 - - + -
115B PHE* 4.7 1.1 - - + -
362B VAL* 4.2 15.9 - - + -
363B ILE 3.3 7.2 - - - +
364B LEU* 3.9 11.9 - - + -
425B ILE 4.6 0.4 - - - +
426B ARG* 1.4 84.6 + - + +
428B LEU* 1.3 66.2 + - - +
429B GLY 3.3 0.3 + - - -
430B PHE* 3.1 56.3 + - + +
432B GLU 3.4 16.6 - - - +
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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