Contacts of the helix formed by residues 331 - 345 (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 ASN 331 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329C SER 3.9 1.2 + - - -
330C LEU* 1.3 76.5 - - - +
332C VAL* 1.3 65.4 + - - +
333C GLU* 3.1 13.3 + - - +
334C LYS* 2.7 54.2 + - - +
335C ALA* 2.9 22.8 + - - +
353C ILE* 4.7 8.0 - - - +
356C ASN* 3.8 27.4 - - - +
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Residues in contact with VAL 332 (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* 3.9 45.8 - - + +
166C THR* 3.7 29.6 - - + -
167C LEU* 4.0 25.8 - - + -
331C ASN* 1.3 75.7 - - - +
333C GLU* 1.3 63.6 + - - +
335C ALA* 3.2 2.8 + - - +
336C ILE* 3.0 34.4 + - + +
353C ILE* 5.2 2.2 - - + +
356C ASN* 4.7 1.7 + - - +
357C PHE* 6.1 0.2 - - + -
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Residues in contact with GLU 333 (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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331C ASN* 3.1 13.1 + - - +
332C VAL* 1.3 80.0 - - - +
334C LYS* 1.3 69.8 + - + +
336C ILE* 3.3 8.4 + - - +
337C THR* 3.2 28.9 + - - +
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Residues in contact with LYS 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328C ASP 4.3 4.1 + - - +
329C SER* 3.1 37.5 + - - +
330C LEU* 3.7 14.8 - - + -
331C ASN* 2.7 34.5 + - - +
333C GLU* 1.3 79.6 - - + +
335C ALA* 1.4 57.4 + - - +
337C THR* 3.3 3.9 + - - -
338C TYR* 2.8 66.6 + - + +
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Residues in contact with ALA 335 (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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167C LEU* 3.8 22.4 - - + -
172C ILE* 4.1 3.1 - - + -
330C LEU* 3.8 2.4 - - + +
331C ASN 2.9 14.0 + - - +
332C VAL 3.5 8.1 - - - +
334C LYS* 1.4 77.0 - - - +
336C ILE* 1.3 56.2 + - - +
339C SER* 2.9 32.2 + - - -
351C PHE* 3.3 40.8 - - + -
353C ILE* 4.9 2.7 - - + -
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Residues in contact with ILE 336 (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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166C THR* 4.3 5.6 - - + -
167C LEU* 5.2 0.4 - - + -
170C ASN* 3.9 32.5 - - + +
172C ILE* 4.0 21.1 - - + -
332C VAL* 3.0 38.0 + - + +
333C GLU* 3.8 7.4 - - - +
335C ALA* 1.3 76.4 - - - +
337C THR* 1.3 66.4 + - - +
339C SER* 3.4 4.3 - - - -
340C HIS* 3.3 19.4 + - - +
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Residues in contact with THR 337 (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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333C GLU* 3.2 19.8 + - - +
334C LYS* 4.0 3.8 - - - -
336C ILE* 1.3 81.4 - - - +
338C TYR* 1.3 68.7 + - + +
340C HIS* 3.2 20.5 + - + +
341C ALA* 3.3 11.1 + - - +
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Residues in contact with TYR 338 (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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295C GLN* 5.1 0.9 - - - -
300C PRO* 3.4 39.3 - - + +
301C VAL* 5.1 11.4 - - + -
326C TYR* 4.0 32.0 + + + -
328C ASP 5.4 1.9 + - - -
330C LEU* 4.0 24.0 - - + -
334C LYS* 2.8 61.1 + - + +
337C THR* 1.3 76.4 - - + +
339C SER* 1.3 59.4 + - - +
341C ALA* 3.2 8.9 + - + +
342C ALA* 3.0 28.6 + - - +
351C PHE* 3.8 12.8 - + + -
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Residues in contact with SER 339 (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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170C ASN 5.3 0.5 + - - -
172C ILE* 4.3 17.7 - - - +
335C ALA 2.9 20.6 + - - -
336C ILE* 3.4 8.7 - - - -
337C THR 3.3 0.2 - - - -
338C TYR* 1.3 75.0 - - - +
340C HIS* 1.3 61.6 + - - +
342C ALA* 3.3 6.3 + - - +
343C LYS* 3.0 48.4 + - - +
349C ALA* 4.6 5.3 - - - +
351C PHE* 3.8 12.4 - - - -
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Residues in contact with HIS 340 (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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336C ILE 3.3 7.4 + - - +
337C THR* 3.2 16.6 + - + +
339C SER* 1.3 77.8 - - - +
341C ALA* 1.3 61.3 + - - +
343C LYS* 3.3 11.6 + - + +
344C GLU* 2.9 64.7 + - + +
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Residues in contact with ALA 341 (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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300C PRO 6.0 0.2 - - - -
301C VAL* 4.1 32.8 - - + -
304C THR* 3.7 7.5 - - + +
326C TYR* 5.1 0.9 - - + +
337C THR 3.3 8.5 + - - +
338C TYR* 3.2 12.3 + - - +
340C HIS* 1.3 82.0 - - - +
342C ALA* 1.3 65.1 + - - +
344C GLU* 3.5 3.7 + - - -
345C ASN* 2.7 38.4 + - - +
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Residues in contact with ALA 342 (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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304C THR* 4.0 11.6 - - - +
326C TYR* 3.7 15.3 - - - +
338C TYR 3.0 8.0 + - - +
339C SER 3.6 7.6 - - - +
341C ALA* 1.3 75.6 - - - +
343C LYS* 1.3 64.8 + - + +
345C ASN* 3.0 9.4 + - - +
346C GLY 3.0 0.2 + - - -
347C MSE 3.0 43.3 + - + +
348C LEU 4.7 0.2 - - - +
349C ALA* 3.7 22.7 - - + +
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Residues in contact with LYS 343 (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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170C ASN 4.8 10.5 + - - -
320C PHE* 3.4 27.2 - - + -
339C SER* 3.0 40.0 + - - +
340C HIS* 3.6 10.5 - - + +
342C ALA* 1.3 77.8 - - + +
344C GLU* 1.3 66.3 + - + +
345C ASN 3.1 0.9 + - - -
346C GLY 3.3 8.3 + - - -
347C MSE 4.3 1.8 - - - +
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Residues in contact with GLU 344 (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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319C LYS* 6.0 0.5 + - - -
340C HIS* 2.9 51.9 + - + +
341C ALA* 3.8 7.4 - - - +
342C ALA 3.3 0.2 - - - -
343C LYS* 1.3 78.4 - - - +
345C ASN* 1.3 65.9 + - - +
346C GLY 3.5 0.6 + - - -
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Residues in contact with ASN 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C VAL* 5.1 1.6 + - - +
304C THR* 3.8 20.2 - - + +
305C LYS* 3.6 40.2 - - - +
308C SER* 3.1 30.8 + - - +
319C LYS* 5.2 5.4 - - - +
341C ALA* 2.7 29.1 + - - +
342C ALA 3.0 4.0 + - - +
344C GLU* 1.3 85.9 - - - +
346C GLY* 1.3 61.5 + - - +
347C MSE 3.4 0.8 + - - -
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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