Contacts of the helix formed by residues 299 - 313 (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 ASP 299 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298C GLY* 1.3 69.5 - - - -
300C PRO* 1.3 72.6 - - - +
301C VAL* 2.9 25.1 + - - +
302C GLU* 3.1 32.7 + - + +
303C TYR* 3.0 22.2 + - - +
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Residues in contact with PRO 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C GLN* 3.8 33.7 - - + +
298C GLY 3.4 5.2 - - - +
299C ASP* 1.3 85.6 - - - +
301C VAL* 1.3 54.2 + - + +
303C TYR* 3.6 2.9 - - + +
304C THR* 2.7 37.7 + - - -
326C TYR* 4.0 10.6 - - + -
328C ASP* 6.5 0.4 - - + -
338C TYR* 3.4 47.8 - - + +
341C ALA* 6.0 0.2 - - - -
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Residues in contact with VAL 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ASP* 2.9 15.4 + - - +
300C PRO* 1.3 70.5 - - + +
302C GLU* 1.3 69.2 + - + +
304C THR* 3.2 8.1 + - - -
305C LYS* 3.1 50.4 + - + +
337C THR* 6.3 2.7 - - + -
338C TYR* 5.1 12.3 - - + -
341C ALA* 4.1 25.6 - - + -
345C ASN* 5.1 2.0 + - - +
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Residues in contact with GLU 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ASP* 3.1 33.2 + - + +
301C VAL* 1.3 81.0 - - + +
303C TYR* 1.3 63.3 + - - +
305C LYS* 3.2 13.7 + - + +
306C LYS* 3.0 23.8 + - - +
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Residues in contact with TYR 303 (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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270C THR* 2.8 30.8 + - - +
271C ASP* 5.7 2.0 - - + -
275C THR* 3.5 13.9 - - + -
293C VAL* 3.3 31.2 - - + +
294C ARG 3.7 6.5 + - - -
295C GLN* 3.4 41.7 - - + +
296C ASP 5.9 0.4 - - - -
297C SER 5.1 4.3 - - - +
299C ASP 3.0 17.4 + - - +
300C PRO 3.6 5.6 - - - +
302C GLU* 1.3 77.2 - - - +
304C THR* 1.3 63.8 + - - +
306C LYS* 3.2 9.2 + - + +
307C ILE* 2.9 51.5 + - + +
324C ILE* 4.2 10.8 - - + -
393C ASP* 3.9 14.1 - - - -
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Residues in contact with THR 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C PRO 2.7 22.5 + - - -
301C VAL* 3.4 9.0 - - - -
303C TYR* 1.3 77.1 - - - +
305C LYS* 1.3 56.8 + - - +
307C ILE* 3.5 0.9 + - - +
308C SER* 2.9 32.6 + - - -
324C ILE* 3.8 17.4 - - + +
326C TYR* 2.6 32.2 + - - +
341C ALA* 3.7 26.2 - - - +
342C ALA* 4.0 6.5 - - - -
345C ASN* 3.8 13.7 - - + +
347C MSE 4.4 2.7 - - + -
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Residues in contact with LYS 305 (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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301C VAL* 3.1 36.5 + - - +
302C GLU* 3.2 15.1 + - + +
304C THR* 1.3 76.3 - - - +
306C LYS* 1.3 58.1 + - - +
308C SER* 2.9 20.1 + - - -
309C HIS* 3.0 18.5 + - - +
345C ASN* 3.6 26.9 - - - +
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Residues in contact with LYS 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C THR* 4.2 20.0 - - + -
276C ASP* 2.8 35.4 + - - -
279C LEU* 4.3 17.7 - - + +
302C GLU 3.0 13.2 + - - +
303C TYR* 3.5 13.0 - - + +
305C LYS* 1.3 77.4 - - - +
307C ILE* 1.3 57.4 + - + +
309C HIS* 3.5 8.5 + - - +
310C HIS* 3.1 26.5 + - - +
502C EDO 4.2 6.3 + - - -
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Residues in contact with ILE 307 (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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270C THR* 4.7 1.3 - - + -
275C THR* 4.2 16.2 - - + -
279C LEU* 4.3 18.8 - - + -
282C PHE* 6.3 0.2 - - + -
293C VAL* 3.9 19.3 - - + -
303C TYR* 2.9 59.1 + - + +
304C THR 4.0 2.7 - - - +
306C LYS* 1.3 74.0 - - + +
308C SER* 1.3 67.7 + - - +
310C HIS* 3.2 6.1 + - + +
311C TYR* 3.0 49.7 + - + -
324C ILE* 4.1 4.7 - - + -
347C MSE 4.0 9.6 - - + -
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Residues in contact with SER 308 (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 2.9 16.4 + - - -
305C LYS* 2.9 22.9 + - - -
307C ILE* 1.3 78.6 - - - +
309C HIS* 1.3 54.8 + - - +
311C TYR* 3.3 0.7 + - - +
312C HIS* 2.8 38.2 + - - +
345C ASN* 3.1 34.4 + - - +
346C GLY 5.4 0.2 - - - -
347C MSE 3.8 18.8 - - - -
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Residues in contact with HIS 309 (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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305C LYS 3.0 17.6 + - - +
306C LYS* 3.5 8.6 + - - +
308C SER* 1.3 77.3 + - - +
310C HIS* 1.3 60.0 + - - +
313C ASP* 2.9 71.8 + - + +
314C VAL* 3.2 23.1 + - + +
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Residues in contact with HIS 310 (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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279C LEU* 3.7 53.9 - - + +
282C PHE* 2.9 36.6 + + - -
283C ARG* 5.2 2.9 - - + -
306C LYS 3.1 13.8 + - - +
307C ILE* 3.2 10.1 + - + +
309C HIS* 1.3 80.2 + - - +
311C TYR* 1.3 61.3 + + - +
314C VAL* 3.2 33.9 - - + +
315C LEU* 2.9 44.6 + - + +
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Residues in contact with TYR 311 (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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282C PHE* 3.4 38.4 - + - -
287C SER 4.2 10.5 - - - -
290C TYR 4.9 1.0 + - - -
292C GLY* 3.4 24.3 + - - -
293C VAL* 3.6 7.1 - - + +
307C ILE* 3.0 42.8 + - + +
308C SER* 4.0 3.6 - - - +
310C HIS* 1.3 80.5 - + + +
312C HIS* 1.3 58.9 + - + +
315C LEU* 3.4 16.4 - - + +
316C LYS 3.2 8.3 + - - -
317C LEU* 2.9 46.0 + - + +
322C LYS* 3.6 33.1 - - + +
347C MSE 3.8 19.1 - - + -
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Residues in contact with HIS 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C SER* 2.8 20.1 + - - +
311C TYR* 1.3 75.3 - - + +
313C ASP* 1.3 82.1 + - - +
316C LYS* 3.2 26.2 + - - +
317C LEU 2.7 26.0 + - - +
318C PRO* 4.5 3.4 - - + -
319C LYS* 3.7 49.3 + - + -
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Residues in contact with ASP 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C SER 4.8 0.2 - - - +
309C HIS* 2.9 50.5 + - + +
312C HIS* 1.3 96.6 - - - +
314C VAL* 1.3 58.8 + - - +
316C LYS* 2.7 31.1 + - - +
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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