Contacts of the strand formed by residues 348 - 353 (chain C) in PDB entry 1VLP
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 LEU 348 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C ARG* 6.1 2.5 - - - +
320C PHE* 3.5 44.6 - - + +
321C SER 4.5 7.9 - - - +
322C LYS 3.0 15.0 + - - +
323C ILE* 4.0 22.0 - - + -
324C ILE* 2.8 31.5 + - - +
347C MSE 1.3 77.8 - - - +
349C ALA* 1.3 57.4 + - - +
350C THR* 6.1 0.4 - - + -
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Residues in contact with ALA 349 (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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173C ARG* 4.3 12.0 + - - +
324C ILE 3.4 3.8 - - - -
326C TYR* 3.9 10.5 - - + -
339C SER* 4.6 9.0 - - - +
342C ALA* 3.7 22.7 - - + -
347C MSE 3.9 0.6 + - - -
348C LEU* 1.3 75.9 - - - +
350C THR* 1.3 70.9 + - - +
351C PHE* 3.9 22.1 - - + -
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Residues in contact with THR 350 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ARG* 3.3 23.8 - - + -
211C LEU* 3.9 25.9 - - + +
267C LEU* 4.9 1.9 - - - +
323C ILE* 3.7 26.3 - - + +
324C ILE 2.9 7.6 + - - +
325C CYS* 3.3 25.6 - - - +
326C TYR* 2.9 24.9 + - - -
348C LEU* 6.1 0.4 - - + -
349C ALA* 1.3 79.2 - - - +
351C PHE* 1.3 69.5 + - - +
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Residues in contact with PHE 351 (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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172C ILE* 3.5 31.4 - - + -
173C ARG 3.0 9.4 + - - +
174C PHE* 3.2 10.0 - - + +
175C SER* 2.8 28.1 + - - -
211C LEU* 5.1 0.9 - - - +
325C CYS* 4.3 4.5 - - - -
326C TYR* 3.3 34.3 - + + +
330C LEU* 3.7 21.3 - - + -
335C ALA* 3.3 35.4 - - + -
338C TYR* 3.8 8.5 - - + -
339C SER* 3.8 16.6 - - - -
349C ALA* 3.9 21.1 - - + -
350C THR* 1.3 78.8 - - - +
352C GLY* 1.3 59.3 + - - +
353C ILE* 4.0 13.0 - - + -
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Residues in contact with GLY 352 (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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175C SER* 3.7 12.8 - - - -
177C PHE* 4.2 15.7 - - - -
325C CYS* 4.1 6.3 - - - -
326C TYR 2.9 10.2 + - - -
327C SER* 3.7 23.3 - - - +
330C LEU* 3.7 14.6 + - - +
351C PHE* 1.3 72.0 - - - +
353C ILE* 1.3 61.0 + - - -
354C GLY 3.9 2.0 + - - -
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Residues in contact with ILE 353 (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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163C LYS* 6.4 0.2 - - + -
167C LEU* 3.6 36.8 - - + -
174C PHE* 4.1 12.6 - - + -
175C SER 3.0 10.9 + - - +
176C GLU* 3.6 0.9 - - - -
177C PHE* 3.0 18.9 + - - +
330C LEU* 3.8 30.7 - - + +
331C ASN* 4.7 8.5 - - - +
332C VAL* 5.2 1.6 - - + +
335C ALA* 4.9 5.6 - - + -
351C PHE* 4.3 11.7 - - + -
352C GLY* 1.3 74.7 - - - +
354C GLY* 1.3 61.2 + - - +
356C ASN* 4.2 15.3 - - + +
357C PHE* 3.5 37.6 - - + +
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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