Contacts of the helix formed by residues 299 - 313 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298D GLY* 1.3 70.3 - - - -
300D PRO* 1.4 71.0 - - - +
301D VAL* 3.1 14.2 + - - +
302D GLU* 2.8 39.2 + - + +
303D TYR* 3.0 23.5 + - - +
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Residues in contact with PRO 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D GLN* 3.7 34.1 - - - +
298D GLY 3.4 6.9 - - - +
299D ASP* 1.4 87.2 - - - +
301D VAL* 1.3 58.6 + - + +
303D TYR* 3.5 3.1 + - + +
304D THR* 2.7 32.8 + - - -
326D TYR* 4.0 9.6 - - + -
328D ASP* 6.0 2.2 - - + +
338D TYR* 3.4 46.0 - - + +
341D ALA* 6.0 0.2 - - - -
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Residues in contact with VAL 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D ASP* 3.1 9.8 + - - +
300D PRO* 1.3 75.7 - - + +
302D GLU* 1.3 65.7 + - - +
304D THR* 3.2 7.6 + - - -
305D LYS* 3.0 52.2 + - + +
337D THR* 5.7 5.2 - - + -
338D TYR* 4.9 14.1 - - + -
341D ALA* 4.1 25.8 - - + -
345D ASN* 5.1 0.2 - - - +
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Residues in contact with GLU 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299D ASP* 2.8 28.8 + - + +
301D VAL* 1.3 73.5 - - - +
303D TYR* 1.3 62.9 + - - +
305D LYS* 3.2 12.9 + - - +
306D LYS* 3.0 22.7 + - - +
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Residues in contact with TYR 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D THR* 2.8 41.4 + - - +
271D ASP* 5.6 1.3 - - + -
275D THR* 3.5 15.0 - - + -
293D VAL* 3.5 18.8 - - + +
294D ARG 3.5 8.0 + - - -
295D GLN* 3.3 43.1 - - + +
296D ASP 5.9 0.2 - - - -
297D SER 5.0 4.0 - - - +
299D ASP 3.0 18.2 + - - +
300D PRO 3.6 5.2 - - - +
301D VAL 3.2 0.2 - - - -
302D GLU* 1.3 73.1 - - - +
304D THR* 1.3 68.2 + - - +
306D LYS* 3.2 9.7 + - + +
307D ILE* 2.9 45.5 + - + +
324D ILE* 4.0 9.0 - - + -
393D ASP* 3.8 15.9 - - - -
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Residues in contact with THR 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D PRO 2.7 19.8 + - - -
301D VAL* 3.2 12.6 + - - -
303D TYR* 1.3 77.1 - - - +
305D LYS* 1.3 57.4 + - - +
307D ILE* 3.9 1.2 - - - +
308D SER* 2.9 29.1 + - - -
324D ILE* 3.8 18.0 - - + +
326D TYR* 2.7 32.3 + - - +
341D ALA* 4.0 6.8 - - - +
342D ALA* 4.0 14.1 - - - -
345D ASN* 3.9 23.1 - - + +
347D MSE 4.3 3.6 - - + -
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Residues in contact with LYS 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D VAL* 3.0 37.9 + - + +
302D GLU* 3.5 13.0 - - - +
303D TYR 3.2 0.2 - - - -
304D THR* 1.3 76.3 - - - +
306D LYS* 1.3 61.4 + - - +
308D SER* 3.9 3.1 - - - -
309D HIS* 3.0 24.8 + - - +
345D ASN* 3.4 34.2 - - - +
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Residues in contact with LYS 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D THR* 4.2 22.4 - - + -
276D ASP* 4.0 20.6 - - - +
279D LEU* 4.2 13.4 - - + +
302D GLU 3.0 16.4 + - - +
303D TYR* 3.7 9.4 - - + +
305D LYS* 1.3 75.1 - - - +
307D ILE* 1.3 57.5 + - + +
309D HIS* 3.5 8.1 + - - +
310D HIS* 3.1 26.3 + - - +
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Residues in contact with ILE 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270D THR* 4.8 0.9 - - + -
275D THR* 4.3 9.0 - - + -
279D LEU* 4.1 26.2 - - + -
282D PHE* 6.1 0.4 - - + -
293D VAL* 4.0 17.0 - - + -
303D TYR* 2.9 57.2 + - + +
304D THR 4.0 2.9 - - - +
306D LYS* 1.3 72.8 - - + +
308D SER* 1.3 63.0 + - - +
310D HIS* 3.2 5.9 + - + +
311D TYR* 2.9 54.4 + - + +
324D ILE* 4.2 5.6 - - + -
347D MSE 3.9 13.2 - - + -
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Residues in contact with SER 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D THR 2.9 19.6 + - - -
305D LYS* 3.9 3.1 - - - -
307D ILE* 1.3 76.7 - - - +
309D HIS* 1.3 57.9 + - - +
311D TYR* 4.5 0.7 - - - +
312D HIS* 2.9 37.6 + - - +
319D LYS* 5.7 3.3 - - - +
345D ASN* 2.6 33.6 + - - +
346D GLY* 4.7 2.1 + - - -
347D MSE 3.9 19.2 - - - +
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Residues in contact with HIS 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D LYS 3.0 18.0 + - - +
306D LYS* 3.6 8.1 - - - +
307D ILE 3.2 0.2 - - - -
308D SER* 1.3 74.7 - - - +
310D HIS* 1.3 61.1 + - - +
313D ASP* 2.7 67.8 + - + +
314D VAL* 3.2 21.7 + - + +
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Residues in contact with HIS 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D LEU* 3.5 57.4 - - + +
282D PHE* 2.8 34.2 + + - +
283D ARG* 5.1 2.9 - - + -
306D LYS 3.1 11.4 + - - +
307D ILE* 3.2 9.6 + - + +
309D HIS* 1.3 81.2 - - + +
311D TYR* 1.3 61.7 + + - +
314D VAL* 3.2 33.7 - - + +
315D LEU* 2.8 46.7 + - + +
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Residues in contact with TYR 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D PHE* 3.3 37.9 - + - -
287D SER 4.2 10.5 - - - -
290D TYR 4.9 1.0 + - - -
292D GLY* 3.5 22.7 + - - -
293D VAL* 3.6 6.6 - - + +
307D ILE* 2.9 42.3 + - + +
308D SER* 4.1 3.6 - - - +
310D HIS* 1.3 78.9 - + + +
312D HIS* 1.3 59.2 + - + +
315D LEU* 3.4 16.8 - - + +
316D LYS 3.2 7.6 + - - -
317D LEU* 2.9 48.2 + - + +
318D PRO 6.1 0.2 - - - +
321D SER* 5.8 0.9 - - - +
322D LYS* 3.5 34.4 - - + +
323D ILE 4.9 0.2 - - - -
347D MSE 3.7 19.3 - - + -
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Residues in contact with HIS 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308D SER* 2.9 22.6 + - - +
311D TYR* 1.3 79.5 - - + +
313D ASP* 1.3 79.2 + - - +
316D LYS* 3.2 25.9 - - - +
317D LEU 2.8 25.6 + - - +
318D PRO* 4.8 3.6 - - + -
319D LYS* 3.7 48.4 - - + +
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Residues in contact with ASP 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D HIS* 2.7 56.1 + - + +
312D HIS* 1.3 90.8 - - - +
314D VAL* 1.3 62.8 + - + +
316D LYS* 2.5 34.2 + - - +
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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