Contacts of the helix formed by residues 298 - 309 (chain B) in PDB entry 3VI4
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 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A ALA 5.7 0.4 - - - -
308A LEU* 3.8 28.3 - - - -
320A GLU* 2.6 29.2 + - - -
350A ARG* 4.9 2.5 + - - +
232B PHE* 5.0 0.9 - - - -
264B PHE* 4.7 2.2 - - - -
265B ALA* 3.6 13.4 - - - +
297B PRO* 1.3 76.3 - - - +
299B ILE* 1.3 68.1 + - - +
300B ALA* 3.9 3.5 + - - -
301B HIS* 2.8 29.1 + - - +
302B LEU* 3.2 9.5 + - - +
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Residues in contact with ILE 299 (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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281A MET* 3.8 22.7 - - + +
282A ALA* 3.5 35.1 + - + +
310A MET* 4.2 15.0 - - + -
232B PHE* 3.9 20.3 - - + -
262B PHE* 4.5 2.7 - - + -
264B PHE* 4.9 2.8 - - + +
297B PRO 3.9 0.8 + - - -
298B SER* 1.3 69.8 - - - +
300B ALA* 1.3 52.6 + - - +
302B LEU* 3.0 8.5 + - + +
303B VAL* 2.8 47.1 + - + +
328B LEU* 3.5 31.4 - - + -
331B LEU* 4.2 15.7 - - + +
332B ILE* 4.8 2.9 - - + -
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Residues in contact with ALA 300 (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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308A LEU 4.7 2.9 + - - +
310A MET* 3.7 35.3 - - + +
319A GLN* 5.5 0.7 - - - -
320A GLU* 3.5 39.7 - - + +
348A PHE* 4.9 2.9 - - + -
298B SER* 3.1 2.6 - - - +
299B ILE* 1.3 78.4 - - - +
301B HIS* 1.3 57.1 + - - +
303B VAL* 3.3 5.0 + - - +
304B GLN* 3.0 25.8 + - - +
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Residues in contact with HIS 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A PHE* 3.4 35.9 - + + -
236B MET* 2.8 33.1 - - + +
277B ASN* 3.8 18.3 + - + -
278B ASP 4.8 2.9 - - - -
279B GLY* 3.7 24.6 + - - -
297B PRO* 3.9 9.2 - - + -
298B SER* 2.8 30.9 + - - +
300B ALA* 1.3 71.2 - - - +
302B LEU* 1.3 61.3 + - - +
304B GLN* 3.1 17.2 + - - +
305B LYS* 3.0 31.0 + - + +
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PHE* 3.5 48.5 - - + +
235B ILE* 3.8 35.9 - - + -
236B MET* 3.6 36.8 - - + +
239B ALA* 6.4 0.2 - - + -
297B PRO* 4.1 3.8 - - + -
298B SER 3.2 9.4 + - - +
299B ILE* 3.0 8.6 + - - +
301B HIS* 1.3 73.8 - - - +
303B VAL* 1.3 67.7 + - + +
305B LYS* 4.4 1.6 - - + +
306B LEU* 2.8 42.9 + - + +
332B ILE* 5.6 9.6 - - + -
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Residues in contact with VAL 303 (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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310A MET* 4.2 6.7 - - - -
318A PRO* 4.0 32.3 - - + -
299B ILE* 2.8 28.5 + - + +
300B ALA* 3.3 11.4 - - - +
302B LEU* 1.3 78.4 - - - +
304B GLN* 1.3 64.5 + - - +
306B LEU* 4.9 2.5 - - - -
307B SER* 3.1 29.6 + - - -
331B LEU 3.2 26.9 - - - +
332B ILE* 4.4 10.1 - - + -
333B PRO* 4.1 19.5 - - + +
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Residues in contact with GLN 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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317A ARG* 5.4 6.9 + - - +
347A GLU* 4.1 10.5 - - - +
348A PHE* 4.0 30.2 - - + -
300B ALA 3.0 13.2 + - - +
301B HIS* 3.1 13.6 + - - +
303B VAL* 1.3 78.0 - - - +
305B LYS* 1.3 89.7 + - - +
307B SER* 3.6 3.4 - - - -
308B GLU* 2.9 43.5 + - + +
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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
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236B MET* 3.7 31.4 - - + -
239B ALA* 4.2 6.0 - - + +
240B VAL* 4.1 15.0 - - + -
278B ASP 5.3 0.9 - - - -
279B GLY* 3.7 26.2 - - - -
280B GLN* 6.1 0.8 - - - +
301B HIS* 3.0 22.7 + - - +
302B LEU* 4.2 2.2 - - + +
304B GLN* 1.3 99.1 - - - +
306B LEU* 1.3 65.2 + - + +
308B GLU* 3.5 24.5 + - - +
309B ASN* 2.7 34.8 + - - +
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Residues in contact with LEU 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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235B ILE* 3.9 29.4 - - + -
239B ALA* 4.0 10.5 - - + -
254B LEU* 4.7 2.5 - - + -
302B LEU* 2.8 30.6 + - + +
303B VAL* 4.3 2.0 - - - +
305B LYS* 1.3 70.3 - - - +
307B SER* 1.3 58.5 + - - +
309B ASN 3.0 2.4 + - - -
310B ASN 2.9 26.2 + - - -
311B ILE* 3.0 48.3 + - + +
313B THR* 3.3 26.0 - - + +
332B ILE* 3.7 29.2 - - + -
333B PRO 6.1 0.2 - - - +
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Residues in contact with SER 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B VAL* 3.1 23.7 + - - -
304B GLN* 3.8 3.1 - - - -
306B LEU* 1.3 78.1 - - - +
308B GLU* 1.3 57.7 + - - +
310B ASN* 4.1 5.7 + - - +
311B ILE 5.6 0.4 - - - -
333B PRO* 5.8 10.0 - - - +
365B GLU* 3.1 22.0 + - - +
426B ARG* 3.0 23.7 + - - -
428B LEU* 3.6 17.0 - - - +
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Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B GLN* 2.9 28.5 + - + +
305B LYS* 3.5 36.5 + - - +
306B LEU 3.1 0.6 - - - -
307B SER* 1.3 78.0 - - - +
309B ASN* 1.3 66.1 + - - +
310B ASN* 3.5 6.5 + - - +
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Residues in contact with ASN 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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239B ALA 3.0 31.3 + - - +
240B VAL* 4.4 8.0 - - - +
252B ARG* 2.8 31.7 + - - +
305B LYS* 2.7 38.5 + - - +
308B GLU* 1.3 85.4 - - - +
310B ASN* 1.3 68.5 + - - +
311B ILE* 3.2 17.2 + - + +
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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