Contacts of the helix formed by residues 303 - 318 (chain B) in PDB entry 6VW1
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 303 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B ALA 4.9 3.6 - - - +
302B TRP* 1.3 75.4 - - - +
304B ALA* 1.3 61.0 + - - +
305B GLN* 3.6 14.7 - - - +
306B ARG* 3.0 26.4 + - - +
307B ILE* 2.9 33.4 + - - +
364B VAL* 4.6 7.4 - - + -
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Residues in contact with ALA 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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303B ASP* 1.3 72.1 - - - +
305B GLN* 1.3 66.9 + - - +
307B ILE* 4.2 12.0 - - - +
308B PHE* 3.0 31.5 + - + +
333B LEU* 3.4 33.0 - - + +
334B THR* 3.7 19.2 - - + +
362B THR* 3.7 17.2 - - + +
364B VAL* 5.4 1.6 - - - +
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Residues in contact with GLN 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 ASP* 3.6 15.1 + - - +
304B ALA* 1.3 78.9 - - - +
306B ARG* 1.3 57.1 + - - +
308B PHE* 3.5 2.2 + - - +
309B LYS* 2.9 57.1 + - - +
328B TRP* 4.1 28.0 + - - -
333B LEU* 4.9 7.3 - - - +
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Residues in contact with ARG 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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300B GLN* 4.7 6.3 + - - -
302B TRP* 3.4 56.6 - - + +
303B ASP* 3.0 27.6 + - - +
305B GLN* 1.3 75.0 - - - +
307B ILE* 1.3 62.9 + - - +
309B LYS* 3.8 7.0 - - - +
310B GLU* 2.9 44.8 + - - +
421B ILE 4.8 7.3 + - - -
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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
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297B MET* 3.7 30.1 - - + -
302B TRP* 4.1 16.8 - - + -
303B ASP 2.9 22.6 + - - +
304B ALA* 3.2 6.5 + - - +
306B ARG* 1.3 77.9 - - - +
308B PHE* 1.3 62.8 + - + +
310B GLU* 3.2 3.1 + - - +
311B ALA* 3.0 24.9 + - - +
362B THR* 3.8 23.8 - - + -
363B LYS 3.9 9.0 - - - +
364B VAL* 4.6 4.7 - - + -
368B ASP 4.3 1.3 - - - +
369B PHE* 3.9 23.3 - - + +
372B ALA* 3.6 26.7 - - + -
373B HIS* 4.8 2.4 - - - -
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Residues in contact with PHE 308 (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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304B ALA 3.0 27.5 + - - +
307B ILE* 1.3 75.6 - - + +
309B LYS* 1.3 60.8 + - - +
311B ALA* 3.3 5.3 + - + +
312B GLU* 2.9 29.1 + - - +
327B PHE* 4.4 2.0 - + - -
328B TRP* 3.7 22.2 - - + -
333B LEU* 3.9 29.8 - - + -
358B ILE* 3.8 29.6 - - + -
360B MET* 3.6 25.6 - - + -
362B THR* 3.3 25.6 - - + -
372B ALA* 3.7 26.9 - - + -
375B GLU* 5.3 0.2 - - + -
376B MET* 3.7 22.0 - - + +
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Residues in contact with LYS 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 GLN* 2.9 38.1 + - - +
306B ARG* 3.8 8.5 - - - +
308B PHE* 1.3 78.5 - - - +
310B GLU* 1.3 55.7 + - - +
312B GLU* 3.3 23.0 + - - +
313B LYS* 2.9 31.8 + - - +
328B TRP* 3.5 37.3 - - + +
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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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302B TRP* 4.2 6.5 - - + -
306B ARG* 2.9 44.8 + - - +
307B ILE 3.6 4.5 - - - +
309B LYS* 1.3 74.7 - - - +
311B ALA* 1.3 60.7 + - - +
313B LYS* 3.3 33.7 + - - +
314B PHE* 2.9 27.7 + - - +
369B PHE* 4.6 11.9 - - + -
373B HIS* 4.4 2.4 + - + -
417B HIS* 5.9 1.0 - - + -
421B ILE* 3.4 51.6 - - + +
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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
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307B ILE 3.0 14.2 + - - +
308B PHE* 3.3 10.7 + - - +
310B GLU* 1.3 76.2 - - - +
312B GLU* 1.3 62.4 + - - +
314B PHE* 3.1 4.2 + - - +
315B PHE* 3.0 28.7 + - + -
372B ALA* 4.5 3.1 - - + +
373B HIS* 3.6 45.2 - - + +
376B MET* 3.8 14.8 - - + -
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Residues in contact with GLU 312 (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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308B PHE 2.9 18.2 + - - +
309B LYS* 3.3 29.6 + - - +
310B GLU 3.3 0.2 - - - -
311B ALA* 1.3 75.7 - - - +
313B LYS* 1.3 58.2 + - - +
315B PHE* 3.2 5.3 + - + +
316B VAL* 2.9 32.9 + - - +
321B PRO 5.2 0.7 - - - +
322B ASN* 3.3 27.9 - - - +
323B MET* 2.7 37.3 + - + +
328B TRP* 3.1 23.1 + - + -
376B MET* 3.5 13.8 - - - -
380B GLN* 6.1 0.4 - - - +
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Residues in contact with LYS 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 LYS* 2.9 18.3 + - - +
310B GLU* 3.3 33.5 + - - +
312B GLU* 1.3 77.0 + - - +
314B PHE* 1.3 62.3 + - - +
316B VAL* 3.3 8.1 + - + +
317B SER* 2.9 23.8 + - - -
421B ILE* 5.4 4.5 - - + -
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Residues in contact with PHE 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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310B GLU 2.9 13.3 + - - +
311B ALA 3.1 7.8 + - - +
313B LYS* 1.3 76.4 - - - +
315B PHE* 1.3 82.3 + + - +
317B SER* 2.7 25.2 + - - -
318B VAL* 3.7 10.1 + - + +
373B HIS* 4.0 23.3 - + - +
408B MET* 4.0 32.5 - - + -
411B SER* 4.1 25.6 - - - -
412B ALA 5.2 0.9 - - - -
417B HIS* 3.8 18.6 - + - +
543B ASP* 4.2 0.9 - - - -
544B ILE* 4.2 15.7 - - + -
545B SER* 3.2 35.2 - - - -
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Residues in contact with PHE 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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311B ALA* 3.0 30.3 + - + -
312B GLU* 3.2 5.8 + - - +
314B PHE* 1.3 90.0 - + - +
316B VAL* 1.3 61.7 - - - +
318B VAL* 3.2 21.7 - - + +
320B LEU* 3.3 25.5 + - + +
321B PRO 4.8 0.2 - - - +
373B HIS* 3.5 14.4 - - - -
376B MET* 3.4 37.5 - - + -
377B GLY* 3.3 24.5 - - - -
380B GLN* 3.6 32.3 - - + +
408B MET* 3.5 40.4 - - + -
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Residues in contact with VAL 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 GLU 2.9 21.0 + - - +
313B LYS* 3.8 8.1 - - + +
314B PHE 3.2 0.2 - - - -
315B PHE* 1.3 76.4 - - - +
317B SER* 1.3 62.1 + - - +
318B VAL 3.1 1.4 + - - -
319B GLY* 3.2 12.1 + - - -
320B LEU 3.4 18.6 - - - +
321B PRO 4.0 1.6 - - - +
322B ASN* 3.2 40.4 - - - +
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Residues in contact with SER 317 (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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313B LYS* 2.9 14.5 + - - -
314B PHE* 2.7 22.2 + - - -
316B VAL* 1.3 78.1 - - - +
318B VAL* 1.3 58.5 + - - +
319B GLY 3.5 0.4 + - - -
545B SER* 3.9 8.2 - - - -
546B ASN* 3.2 51.6 + - - +
548B THR* 4.4 5.9 - - - +
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Residues in contact with VAL 318 (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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314B PHE* 4.0 10.5 - - + +
315B PHE* 3.2 22.2 - - + +
316B VAL 3.1 0.2 - - - -
317B SER* 1.3 89.6 - - - +
319B GLY* 1.3 57.6 + - - +
320B LEU* 4.2 18.2 - - + -
408B MET* 6.6 0.2 - - + -
544B ILE* 3.4 40.2 - - + +
545B SER* 4.1 2.9 - - - -
546B ASN 4.0 1.3 - - - +
547B SER 3.7 13.0 - - - +
548B THR* 3.4 14.5 - - - +
551B GLY* 3.2 31.1 - - - +
552B GLN 4.4 0.2 + - - -
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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