Contacts of the helix formed by residues 299 - 313 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B SER 4.9 0.2 - - - +
298B GLY* 1.3 70.9 - - - -
300B PRO* 1.3 70.2 - - - +
301B VAL* 3.2 19.4 + - - +
302B GLU* 3.0 36.2 + - + +
303B TYR* 3.0 23.3 + - - +
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Residues in contact with PRO 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLN* 3.7 34.3 - - - +
298B GLY 3.3 7.2 - - - +
299B ASP* 1.3 88.7 - - - +
301B VAL* 1.3 52.5 + - - +
303B TYR* 3.4 3.1 + - + +
304B THR* 2.7 38.8 + - - -
326B TYR* 4.0 6.8 - - + -
328B ASP* 6.0 3.8 - - + +
338B TYR* 3.6 50.0 - - + +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ASP* 3.2 12.0 + - - +
300B PRO* 1.3 76.9 - - - +
302B GLU* 1.3 63.6 + - + +
304B THR* 3.3 8.0 + - - -
305B LYS* 3.2 44.3 + - - +
337B THR* 5.2 6.1 - - + -
338B TYR* 4.3 20.6 - - + -
341B ALA* 4.2 24.2 - - + -
345B ASN* 5.1 0.8 + - - +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ASP* 3.0 35.4 + - + +
300B PRO 3.4 0.2 - - - -
301B VAL* 1.3 78.6 - - + +
303B TYR* 1.3 62.9 + - - +
305B LYS* 3.2 15.2 + - + +
306B LYS* 3.0 23.1 + - - +
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Residues in contact with TYR 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B THR* 2.9 33.5 + - - +
271B ASP* 5.8 0.4 - - + -
275B THR* 3.5 15.7 - - + -
293B VAL* 3.4 27.5 - - + +
294B ARG 3.8 5.5 + - - -
295B GLN* 3.3 39.7 - - + +
297B SER 5.1 2.9 - - - +
299B ASP 3.0 18.6 + - - +
300B PRO* 3.5 8.1 - - + +
302B GLU* 1.3 77.5 - - - +
304B THR* 1.3 61.6 + - - +
306B LYS* 3.2 9.7 + - + +
307B ILE* 2.9 50.1 + - + +
324B ILE* 4.2 8.1 - - + -
393B ASP* 3.9 14.6 - - - -
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Residues in contact with THR 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B PRO 2.7 22.6 + - - -
301B VAL* 3.5 8.5 - - - -
302B GLU 3.3 0.2 - - - -
303B TYR* 1.3 74.3 - - - +
305B LYS* 1.3 58.0 + - - +
307B ILE* 4.1 0.3 - - - +
308B SER* 2.9 33.1 + - - -
324B ILE* 3.9 19.0 - - + +
326B TYR* 2.7 34.4 + - - +
341B ALA* 3.7 15.1 - - - +
342B ALA* 3.9 5.8 - - - -
345B ASN* 3.7 26.5 - - + +
347B MSE 4.3 1.6 - - + -
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B VAL* 3.2 34.9 + - - +
302B GLU* 3.2 14.8 + - + +
304B THR* 1.3 76.4 - - - +
306B LYS* 1.3 57.1 + - - +
308B SER* 3.7 1.4 - - - -
309B HIS* 2.9 30.5 + - - +
345B ASN* 3.9 27.1 - - - +
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Residues in contact with LYS 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B THR* 4.3 21.5 - - + -
276B ASP* 2.5 38.9 + - - +
279B LEU* 4.2 12.9 - - + +
302B GLU 3.0 12.4 + - - +
303B TYR* 3.5 14.1 - - + +
305B LYS* 1.3 78.6 - - - +
307B ILE* 1.3 57.5 + - + +
309B HIS* 3.5 7.7 + - - +
310B HIS* 3.1 26.0 + - - +
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Residues in contact with ILE 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B THR* 4.6 1.1 - - + -
275B THR* 4.3 9.4 - - + -
279B LEU* 4.0 26.7 - - + -
282B PHE* 5.7 1.1 - - + -
293B VAL* 3.9 22.9 - - + -
303B TYR* 2.9 54.4 + - + +
304B THR 4.1 2.0 - - - +
306B LYS* 1.3 74.6 - - + +
308B SER* 1.3 60.4 + - - +
310B HIS* 3.2 4.6 + - + +
311B TYR* 2.9 55.0 + - + -
324B ILE* 4.1 14.1 - - + -
347B MSE 4.1 1.1 - - + -
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B THR 2.9 21.0 + - - -
305B LYS* 3.7 4.3 - - - -
307B ILE* 1.3 78.2 - - - +
309B HIS* 1.3 56.6 + - - +
312B HIS* 2.9 50.1 + - - +
319B LYS* 5.3 0.5 - - - -
345B ASN* 2.5 41.5 + - - +
347B MSE 4.1 11.2 - - - -
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Residues in contact with HIS 309 (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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305B LYS 2.9 14.9 + - - +
306B LYS* 3.5 12.1 - - + +
308B SER* 1.3 74.7 - - - +
310B HIS* 1.3 61.5 + - + +
313B ASP* 2.8 72.7 + - + +
314B VAL* 3.2 20.8 + - + +
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Residues in contact with HIS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 3.7 50.2 - - + +
282B PHE* 2.7 38.2 + + - +
283B ARG* 5.1 2.9 - - + -
306B LYS 3.1 11.8 + - - +
307B ILE* 3.2 12.1 + - + +
309B HIS* 1.3 79.3 - - + +
311B TYR* 1.3 62.7 + + - +
314B VAL* 3.2 34.3 + - + +
315B LEU* 2.8 53.2 + - + +
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Residues in contact with TYR 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B PHE* 3.4 35.8 - + - -
287B SER 4.4 3.4 - - - -
290B TYR 4.9 0.5 + - - -
292B GLY* 3.5 24.8 + - - -
293B VAL* 3.7 5.2 - - + +
307B ILE* 2.9 45.0 + - + +
308B SER 4.0 1.1 - - - +
310B HIS* 1.3 81.0 - + + +
312B HIS* 1.3 73.5 + - + +
315B LEU* 3.4 16.8 - - + +
316B LYS 3.2 8.1 + - - -
317B LEU* 2.9 47.6 + - + +
322B LYS* 3.6 34.2 - - + +
347B MSE 3.6 15.9 - - + -
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Residues in contact with HIS 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B SER* 2.9 38.1 + - - +
311B TYR* 1.3 87.1 - - + +
313B ASP* 1.3 67.1 + - - +
316B LYS* 3.3 22.8 - - - +
317B LEU* 3.4 22.9 - - + +
318B PRO 3.6 17.8 + - - -
319B LYS* 3.5 28.8 - - + -
320B PHE 4.4 0.2 + - - -
321B SER* 4.9 2.6 + - - -
322B LYS* 5.7 1.4 + - - +
345B ASN 3.4 5.4 - - - -
346B GLY 3.3 27.0 + - - -
347B MSE 3.7 16.8 - - - -
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B HIS* 2.8 53.9 + - + +
312B HIS* 1.3 84.1 - - - +
314B VAL* 1.3 60.8 + - - +
316B LYS* 2.8 32.6 + - - +
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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