Contacts of the strand formed by residues 354 - 359 (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 354 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288C ALA* 4.2 1.6 - - - -
352C GLY 4.3 0.2 - - - +
353C SER* 1.3 77.3 - - - +
355C LEU* 1.3 75.2 + - - +
371C ILE* 3.5 2.6 - - - +
372C GLY* 3.2 26.2 + - - -
416C GLY 2.6 25.7 + - - -
417C SER* 3.4 22.8 - - - -
419C LEU* 3.2 23.1 - - - +
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Residues in contact with LEU 355 (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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288C ALA* 4.0 11.0 - - + +
289C VAL* 3.8 13.9 - - - +
290C ALA* 3.7 28.4 - - + +
303C LEU* 3.5 37.7 - - + +
304C VAL 4.1 0.4 - - - -
305C GLY 3.9 11.9 - - - +
324C VAL* 3.9 22.2 - - + -
352C GLY 4.5 3.6 - - - +
354C SER* 1.3 83.5 - - - +
356C THR* 1.3 63.6 + - - +
357C PRO* 4.6 1.4 - - - +
369C VAL* 6.0 1.1 - - + -
370C ALA 3.4 4.5 - - - +
371C ILE* 3.7 25.1 - - + -
419C LEU* 4.6 7.0 - - - +
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Residues in contact with THR 356 (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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290C ALA* 5.2 1.6 - - - -
355C LEU* 1.3 75.6 - - - +
357C PRO* 1.3 83.0 + - - +
358C LEU* 4.8 0.9 - - + -
369C VAL* 3.9 5.5 - - - +
370C ALA* 3.0 52.0 + - + +
419C LEU* 3.5 33.9 - - + -
420C ARG* 3.8 4.9 + - - -
421C GLY* 3.0 17.3 + - - +
433C LEU* 4.1 13.5 - - + -
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Residues in contact with PRO 357 (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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290C ALA* 4.6 11.4 - - + -
291C ALA 3.5 23.8 - - - +
292C THR* 3.7 27.6 - - + +
355C LEU 4.6 0.9 - - - +
356C THR* 1.3 96.3 + - - +
358C LEU* 1.3 60.3 + - - +
359C GLY 3.4 3.3 + - - +
368C ASP 4.3 4.3 - - - +
369C VAL* 4.6 0.7 - - + -
420C ARG* 5.4 7.6 - - - +
421C GLY 3.0 18.2 - - - +
422C GLY* 3.8 1.6 - - - -
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Residues in contact with LEU 358 (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* 4.9 4.5 - - + -
356C THR* 3.3 1.0 + - + -
357C PRO* 1.3 73.3 - - - +
359C GLY* 1.3 60.4 + - - +
361C LEU* 4.8 14.9 - - + +
368C ASP* 3.0 22.6 + - + +
369C VAL 3.5 25.1 - - - +
370C ALA* 3.5 17.7 - - + +
386C VAL* 3.5 30.1 - - + -
421C GLY* 4.6 1.8 - - - -
422C GLY* 3.0 19.3 + - - +
431C PRO* 3.3 15.1 - - - +
432C ASP 4.4 5.0 - - - +
433C LEU* 3.8 42.6 - - + -
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Residues in contact with GLY 359 (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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292C THR* 5.8 0.4 + - - -
357C PRO* 3.4 5.9 + - - +
358C LEU* 1.3 79.3 - - - +
360C ASP* 1.3 57.2 + - - -
361C LEU 3.4 3.7 + - - -
367C ASN* 3.1 16.3 + - - -
368C ASP* 2.8 31.1 + - - +
422C GLY* 3.7 10.9 - - - -
431C PRO* 4.1 4.7 - - - -
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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