Contacts of the helix formed by residues 303 - 317 (chain B) in PDB entry 3VRY
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 SER 303 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B GLY 5.1 1.6 - - - -
301B SER 2.6 13.0 + - - -
302B MET* 1.3 72.0 - - - +
304B VAL* 1.3 61.4 + - - +
305B GLU* 3.7 17.7 + - - +
306B ALA* 3.5 21.0 + - - +
307B PHE* 2.8 30.5 + - - +
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Residues in contact with VAL 304 (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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302B MET 3.5 2.3 + - - +
303B SER* 1.3 73.7 + - - +
305B GLU* 1.3 63.0 + - + +
307B PHE* 3.7 4.4 - - - +
308B LEU* 2.8 50.4 + - + +
330B THR* 4.0 12.8 - - - +
332B GLU* 3.9 28.5 - - + +
334B ILE* 4.0 22.9 - - + -
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Residues in contact with GLU 305 (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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303B SER* 3.7 10.9 + - - +
304B VAL* 1.3 83.0 - - + +
306B ALA* 1.3 63.3 + - + +
308B LEU* 3.9 7.5 - - - +
309B ALA* 3.3 21.0 + - - +
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Residues in contact with ALA 306 (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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303B SER* 3.2 27.5 + - - +
304B VAL 3.1 0.2 - - - -
305B GLU* 1.3 80.5 - - + +
307B PHE* 1.3 66.0 + - - +
309B ALA* 3.1 6.8 + - - +
310B GLU* 3.1 21.1 + - - +
410B VAL* 4.5 12.0 - - + +
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Residues in contact with PHE 307 (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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297B MET* 5.5 3.6 - - + -
302B MET* 5.1 9.0 - - + +
303B SER 2.8 20.7 + - - +
304B VAL* 3.8 4.0 - - - +
306B ALA* 1.3 73.3 - - - +
308B LEU* 1.3 60.4 + - + +
310B GLU* 3.2 9.9 + - + +
311B ALA* 2.7 45.6 + - + +
314B MET* 4.9 9.2 - - - -
328B VAL* 3.8 15.0 - - + -
334B ILE* 3.3 35.9 - - + -
336B ILE* 3.5 39.5 - - + -
407B LEU* 4.3 12.1 - - + -
410B VAL* 4.1 27.5 - - + +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B TRP* 5.2 1.6 - - - +
261B GLU* 3.9 13.0 - - + +
304B VAL* 2.8 34.3 + - + +
305B GLU* 4.2 6.1 - - - +
306B ALA 3.1 0.2 - - - -
307B PHE* 1.3 87.0 - - + +
309B ALA* 1.3 59.7 + - - +
311B ALA* 3.5 4.8 + - + +
312B ASN* 2.6 46.9 + - - +
328B VAL* 4.8 12.3 - - + -
330B THR* 3.4 46.2 - - + +
334B ILE* 4.9 2.0 - - + -
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Residues in contact with ALA 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 GLU 3.3 15.6 + - - +
306B ALA* 3.1 6.7 + - - +
308B LEU* 1.3 74.0 - - - +
310B GLU* 1.3 65.9 + - - +
312B ASN* 3.1 17.3 + - - +
313B VAL* 3.3 15.1 + - - +
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Residues in contact with GLU 310 (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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306B ALA 3.1 12.1 + - - +
307B PHE* 3.3 9.4 - - - +
309B ALA* 1.3 76.9 - - - +
311B ALA* 1.3 57.0 + - - +
313B VAL* 2.9 30.4 + - - +
314B MET* 2.9 39.1 + - + +
382B TYR* 3.3 15.4 + - - -
406B GLY 4.0 0.7 - - - +
409B ARG* 2.6 40.1 + - - +
410B VAL* 3.9 22.2 - - + +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B TRP* 3.9 19.3 - - + +
307B PHE* 2.7 38.4 + - + +
308B LEU* 3.5 13.7 - - + +
309B ALA 3.2 0.2 - - - -
310B GLU* 1.3 72.7 - - - +
312B ASN* 1.3 58.4 + - - +
314B MET* 3.1 16.4 + - - +
315B LYS* 3.0 30.7 + - - +
325B LEU* 5.2 2.7 - - + -
328B VAL* 5.0 5.2 - - + -
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Residues in contact with ASN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B TRP* 3.9 26.1 + - - +
308B LEU* 2.6 34.7 + - - +
309B ALA* 3.1 11.5 + - - +
310B GLU 3.1 0.6 - - - -
311B ALA* 1.3 81.1 - - - +
313B VAL* 1.3 62.3 + - + +
315B LYS* 3.8 9.2 + - - +
316B THR* 3.1 20.8 - - - +
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Residues in contact with VAL 313 (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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309B ALA 3.3 11.2 + - - +
310B GLU* 2.9 20.4 + - - +
312B ASN* 1.3 77.4 - - + +
314B MET* 1.3 63.9 + - - +
316B THR* 2.5 31.8 + - - +
317B LEU* 3.5 8.8 + - + +
382B TYR* 3.9 30.1 - - + -
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Residues in contact with MET 314 (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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307B PHE* 4.9 11.7 - - + -
310B GLU* 2.9 29.4 + - + +
311B ALA* 3.1 19.7 + - - +
313B VAL* 1.3 76.8 - - - +
315B LYS* 1.3 56.1 + - - +
317B LEU* 2.9 37.4 + - - +
325B LEU* 3.8 19.9 - - + +
336B ILE* 6.0 0.4 - - - -
382B TYR* 4.0 11.4 - - - +
405B PHE* 3.5 29.6 - - + +
406B GLY 3.4 28.3 - - - +
407B LEU* 3.9 15.5 - - + +
410B VAL* 4.9 1.3 - - + -
602B B43 4.2 15.5 - - + -
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Residues in contact with LYS 315 (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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118B GLU* 5.8 1.6 + - - -
255B TRP* 5.5 5.7 - - - +
260B TRP* 3.5 43.7 - - + -
311B ALA 3.0 14.8 + - - +
312B ASN* 3.9 7.9 - - - +
313B VAL 3.3 0.2 - - - -
314B MET* 1.3 75.3 - - - +
316B THR* 1.3 58.4 + - + +
317B LEU 3.3 0.2 - - - -
318B GLN* 3.3 38.7 + - - +
324B LYS* 3.4 18.6 - - - +
325B LEU* 3.2 30.2 + - - +
326B HIS* 4.2 8.3 + - - +
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Residues in contact with THR 316 (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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312B ASN 3.1 20.4 - - - +
313B VAL* 2.5 22.5 + - - +
315B LYS* 1.3 77.6 - - + +
317B LEU* 1.3 61.6 + - - +
318B GLN* 2.9 15.6 + - - +
380B ARG* 3.2 22.5 + - - -
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B VAL* 3.8 10.8 - - + +
314B MET* 2.9 27.8 + - - +
316B THR* 1.3 78.6 - - - +
318B GLN* 1.3 60.2 + - - +
319B HIS 3.8 0.7 + - - -
322B LEU* 3.7 25.6 - - + +
323B VAL 5.0 1.6 - - - +
376B PHE* 3.8 16.2 - - + -
377B ILE* 5.3 3.4 - - + -
380B ARG* 3.8 38.6 - - + +
382B TYR* 3.5 50.9 - - + -
405B PHE* 4.0 11.9 - - + -
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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