Contacts of the helix formed by residues 320 - 331 (chain B) in PDB entry 3V4K
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 ARG 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289B PHE* 3.1 53.2 - - + -
293B GLN* 5.2 1.6 + - - -
317B ASP* 3.4 5.4 + - - +
319B GLY* 1.3 75.9 - - - +
321B CYS* 1.3 65.9 + - - +
322B GLN 3.3 2.9 - - - -
323B GLU* 2.9 48.4 + - - +
324B GLY 3.0 18.2 + - - -
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Residues in contact with CYS 321 (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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287B PRO 4.6 4.8 - - - +
288B CYS* 4.4 10.8 - - - -
289B PHE* 4.4 9.4 - - - +
315B TYR* 3.4 52.5 - - - +
316B ASP* 3.9 5.4 - - - +
317B ASP* 3.2 41.2 + - - +
319B GLY 3.5 0.8 - - - -
320B ARG* 1.3 77.6 - - - +
322B GLN* 1.3 63.2 + - - +
324B GLY* 3.2 2.8 + - - -
325B LEU* 3.1 27.0 + - + +
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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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316B ASP* 3.0 33.5 + - - +
319B GLY 4.9 4.1 + - - +
320B ARG 3.3 0.6 - - - -
321B CYS* 1.3 73.3 - - - +
323B GLU* 1.3 66.6 + - - +
325B LEU* 3.2 5.6 + - - +
326B ARG* 2.9 58.1 + - - +
374B ARG* 5.8 2.2 - - - +
377B ALA 5.2 0.3 - - - +
378B ILE* 3.7 35.6 - - + +
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Residues in contact with GLU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 3.6 13.4 - - + -
319B GLY 5.4 0.6 + - - -
320B ARG* 2.9 56.2 + - - +
322B GLN* 1.3 76.9 - - - +
324B GLY* 1.3 58.3 + - - +
326B ARG* 3.3 18.6 + - - +
327B THR* 2.8 42.3 + - - +
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Residues in contact with GLY 324 (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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289B PHE* 3.7 21.7 - - - -
292B ALA* 3.4 21.8 - - - +
293B GLN 5.3 0.2 - - - -
320B ARG 3.0 10.9 + - - -
321B CYS 3.2 4.0 + - - -
322B GLN 3.2 0.2 - - - -
323B GLU* 1.3 77.6 - - - +
325B LEU* 1.3 56.5 + - - +
327B THR* 3.3 5.1 + - - -
328B LEU* 2.9 30.3 + - - +
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Residues in contact with LEU 325 (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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286B SER* 4.3 18.6 - - - +
287B PRO* 4.0 36.6 - - + +
292B ALA* 5.2 0.4 - - + -
314B ILE* 4.5 7.4 - - + -
315B TYR 5.3 2.5 - - - +
321B CYS* 3.1 16.0 + - + +
322B GLN* 3.2 7.4 + - - +
324B GLY* 1.3 76.4 - - - +
326B ARG* 1.3 57.6 + - - +
328B LEU* 3.3 4.3 + - + -
329B ALA* 2.9 30.3 + - - +
335B ILE* 3.6 22.1 - - + +
375B LEU* 4.3 13.9 - - + -
378B ILE* 4.2 33.0 - - + -
379B LEU* 3.9 7.2 - - + -
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Residues in contact with ARG 326 (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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322B GLN* 2.9 54.4 + - - +
323B GLU* 3.7 17.8 - - - +
325B LEU* 1.3 75.5 - - - +
327B THR* 1.3 58.5 + - - +
329B ALA* 3.4 2.0 + - - +
330B GLU* 2.9 30.4 + - - +
377B ALA 5.1 0.6 + - - -
378B ILE* 2.9 41.4 + - - +
379B LEU* 4.1 16.2 - - + +
380B GLN 4.5 10.1 - - - -
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Residues in contact with THR 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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289B PHE* 5.5 3.7 - - + -
293B GLN* 5.1 12.8 - - + -
296B ALA* 4.1 17.3 - - + -
323B GLU* 2.8 28.9 + - - +
324B GLY* 3.6 7.2 - - - +
326B ARG* 1.3 76.6 - - - +
328B LEU* 1.3 63.0 + - - +
330B GLU* 3.4 16.6 + - - +
331B ALA* 3.0 22.7 + - + +
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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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287B PRO* 4.2 17.9 - - + -
292B ALA* 3.9 14.1 + - + +
295B MET* 3.7 14.8 - - + -
296B ALA* 3.7 32.5 - - - +
299B ILE* 4.1 4.9 - - + -
307B LEU* 4.5 2.9 - - + -
309B ILE* 3.5 26.7 - - + -
324B GLY 2.9 15.8 + - - +
325B LEU* 3.6 7.4 - - + +
327B THR* 1.3 77.7 - - - +
329B ALA* 1.3 61.8 + - - +
331B ALA* 3.3 10.6 + - - +
332B GLY 3.4 0.7 + - - -
333B ALA* 3.1 38.1 + - + +
335B ILE* 4.2 9.4 - - + -
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Residues in contact with ALA 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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325B LEU 2.9 16.3 + - - +
326B ARG* 3.8 4.0 - - - +
328B LEU* 1.3 74.9 - - - +
330B GLU* 1.3 60.0 + - - +
332B GLY* 2.9 20.6 + - - -
333B ALA 3.6 18.1 + - - +
335B ILE* 4.1 7.3 - - + +
379B LEU* 4.0 22.4 - - + -
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Residues in contact with GLU 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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326B ARG 2.9 17.7 + - - +
327B THR* 3.6 17.3 + - - +
329B ALA* 1.3 76.4 - - - +
331B ALA* 1.3 61.7 + - - +
332B GLY* 3.3 1.6 + - - -
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Residues in contact with ALA 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ALA* 3.9 20.0 - - + +
299B ILE* 3.7 17.2 - - + +
300B SER* 3.9 22.4 + - - +
303B LYS* 4.9 10.2 + - - -
327B THR 3.0 16.2 + - - +
328B LEU 3.6 6.1 - - - +
329B ALA 3.2 0.6 - - - -
330B GLU* 1.3 74.8 - - - +
332B GLY* 1.3 57.3 + - - +
333B ALA 3.7 0.9 - - - -
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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