Contacts of the helix formed by residues 321 - 332 (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 PHE 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B SER* 4.9 9.0 - - - -
259B ASP 3.2 30.7 - - - -
260B ALA* 3.6 8.3 - - + +
261B GLY* 3.5 28.9 - - - -
317B VAL* 4.1 5.4 - - + -
318B THR* 3.1 13.7 + - - +
320B GLU* 1.3 109.8 - - + +
322B GLN* 1.3 64.1 + - - +
323B PRO* 3.4 3.8 - - - -
324B VAL* 3.5 23.3 + - + +
325B TYR* 3.1 38.1 + + + +
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Residues in contact with GLN 322 (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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317B VAL* 3.2 37.4 + - - +
318B THR 3.5 2.4 + - - +
319B GLU* 3.4 25.3 + - - +
321B PHE* 1.3 75.1 - - - +
323B PRO* 1.4 72.7 - - + +
325B TYR 3.2 1.0 + - - -
326B LYS* 2.9 60.6 + - - +
337B VAL* 3.5 17.1 - - - +
338B GLY* 3.2 17.4 + - - -
339B THR* 3.4 25.2 - - - +
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Residues in contact with PRO 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.8 27.5 - - + +
319B GLU 4.3 3.1 - - - +
320B GLU 4.1 11.2 - - - +
321B PHE* 3.5 4.3 - - - -
322B GLN* 1.4 96.8 - - + +
324B VAL* 1.3 62.2 + - + +
326B LYS* 4.0 13.0 - - + +
327B GLU* 3.4 22.0 + - - +
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 4.1 29.2 - - + +
258A THR* 4.7 12.8 - - + +
281A MET* 3.7 18.9 - - + +
261B GLY* 5.6 3.4 - - - -
262B PHE* 3.8 26.5 - - + -
320B GLU 5.8 0.2 - - - +
321B PHE* 3.5 29.1 + - + +
322B GLN 3.2 0.4 - - - -
323B PRO* 1.3 78.3 - - + +
325B TYR* 1.3 63.4 + - + +
327B GLU* 3.3 5.0 + - - +
328B LEU* 2.9 25.0 + - - +
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Residues in contact with TYR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B PHE* 3.9 19.3 - + - -
258B THR* 3.5 13.6 - - + +
260B ALA 2.8 29.0 + - - -
261B GLY* 3.8 6.2 + - - -
262B PHE* 3.6 30.7 - + - +
315B PHE* 4.0 16.2 - + + -
317B VAL* 3.6 36.8 - - + -
321B PHE* 3.1 35.0 + + + +
322B GLN 3.2 2.6 + - - +
324B VAL* 1.3 78.8 - - + +
326B LYS* 1.3 65.5 + - - +
328B LEU* 3.6 22.1 - - + +
329B LYS* 2.8 23.9 + - - +
337B VAL* 4.2 13.4 - - + +
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Residues in contact with LYS 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B GLU* 5.8 0.6 + - - -
322B GLN* 2.9 58.0 + - - +
323B PRO* 4.0 11.4 - - + +
325B TYR* 1.3 74.1 - - - +
327B GLU* 1.3 64.7 + - - +
329B LYS* 2.9 21.3 + - - +
330B ASN* 3.0 22.2 + - - +
337B VAL* 4.2 15.0 - - + +
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Residues in contact with GLU 327 (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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259A TYR* 3.0 37.3 + - + +
281A MET* 3.4 22.4 + - + +
323B PRO 3.4 11.2 + - - +
324B VAL 3.3 3.3 + - - +
325B TYR 3.2 0.2 - - - -
326B LYS* 1.3 80.5 - - - +
328B LEU* 1.3 61.1 + - - +
330B ASN* 3.2 35.8 + - - +
331B LEU* 3.5 21.5 + - - +
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Residues in contact with LEU 328 (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 9.6 - - - -
232B PHE* 3.7 18.4 - - + -
262B PHE* 3.7 22.9 - - + -
299B ILE* 3.5 36.3 - - + -
315B PHE* 3.8 21.8 - - + -
324B VAL 2.9 14.4 + - - +
325B TYR* 3.6 23.1 - - + +
326B LYS 3.2 0.2 - - - -
327B GLU* 1.3 74.5 - - - +
329B LYS* 1.3 55.0 + - - +
331B LEU* 2.8 24.2 + - - -
332B ILE* 3.1 32.0 + - + +
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Residues in contact with LYS 329 (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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315B PHE* 4.5 8.0 - - + -
325B TYR 2.8 13.9 + - - +
326B LYS 3.0 13.7 - - - +
328B LEU* 1.3 76.0 - - - +
330B ASN* 1.3 70.3 + - - +
331B LEU 3.1 1.2 + - - -
332B ILE 3.2 21.0 - - - +
335B SER* 3.1 44.9 + - - +
336B ALA* 4.2 6.3 - - - +
337B VAL* 3.8 24.7 - - + -
361B GLU* 5.7 3.0 + - - -
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Residues in contact with ASN 330 (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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312A ARG* 5.7 2.6 + - - -
326B LYS* 3.0 27.8 + - - +
327B GLU* 3.2 33.0 + - - +
328B LEU 3.2 0.6 - - - -
329B LYS* 1.3 88.5 + - - +
331B LEU* 1.3 60.6 + - + +
332B ILE 5.1 0.4 - - - -
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Residues in contact with LEU 331 (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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280A GLN* 4.1 18.4 - - + +
281A MET* 3.7 39.0 - - + +
310A MET* 3.6 29.9 - - + +
299B ILE* 4.2 15.9 - - + -
303B VAL* 3.2 20.1 - - - +
327B GLU* 3.6 22.4 - - - +
328B LEU 2.8 7.3 + - - +
330B ASN* 1.3 81.4 - - + +
332B ILE* 1.3 61.8 + - - +
333B PRO* 3.5 7.2 - - - +
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Residues in contact with ILE 332 (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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232B PHE* 5.7 0.2 - - + -
235B ILE* 6.4 0.4 - - + -
299B ILE* 4.8 3.4 - - + +
302B LEU* 5.6 9.9 - - + -
303B VAL* 4.4 13.7 - - + +
306B LEU* 3.7 32.3 - - + -
311B ILE 5.9 0.7 - - - +
313B THR* 4.4 2.5 - - - +
315B PHE* 3.4 32.1 - - + -
328B LEU* 3.1 32.4 + - + +
329B LYS* 3.2 6.2 + - - +
330B ASN 5.1 0.9 - - - -
331B LEU* 1.3 81.4 - - - +
333B PRO* 1.4 74.8 - - + +
334B LYS 3.4 1.0 + - - +
335B SER* 2.7 39.2 + - - +
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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