Contacts of the helix formed by residues 321 - 331 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227D SER* 4.9 9.0 - - - -
259D ASP 3.1 30.3 - - - -
260D ALA* 3.4 10.3 - - + +
261D GLY* 3.4 28.9 - - - -
317D VAL* 4.1 5.2 - - + -
318D THR* 2.9 11.9 + - - +
320D GLU* 1.3 105.4 - - + +
322D GLN* 1.3 64.1 + - - +
323D PRO* 3.4 2.2 - - - -
324D VAL* 3.4 24.0 + - + -
325D TYR* 3.1 39.5 + - + +
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Residues in contact with GLN 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D VAL* 3.4 22.3 + - - +
318D THR 3.5 4.9 + - - +
319D GLU* 3.1 28.7 + - - +
321D PHE* 1.3 77.0 - - - +
323D PRO* 1.4 63.9 - - + +
326D LYS* 2.8 71.9 + - - +
337D VAL* 3.8 11.1 - - - +
338D GLY* 3.3 26.9 + - - -
339D THR* 3.3 29.6 + - + +
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Residues in contact with PRO 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C LEU* 3.7 26.2 - - + +
319D GLU* 4.1 3.6 - - - +
320D GLU 3.8 11.9 - - - +
321D PHE 3.6 2.7 - - - -
322D GLN* 1.4 94.2 - - + +
324D VAL* 1.3 64.7 + - + +
326D LYS* 3.8 6.8 - - + +
327D GLU* 3.4 22.0 + - - +
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Residues in contact with VAL 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C LEU* 4.3 25.4 - - + +
258C THR* 3.7 22.2 - - - +
281C MET* 3.6 11.5 - - + +
261D GLY* 5.4 3.8 - - - -
262D PHE* 3.8 24.9 - - + -
320D GLU 5.6 0.7 - - - +
321D PHE* 3.4 31.1 + - + +
322D GLN 3.2 0.4 - - - -
323D PRO* 1.3 77.7 - - + +
325D TYR* 1.3 62.9 + - + +
327D GLU* 3.0 8.8 + - - +
328D LEU* 3.0 21.7 + - - +
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Residues in contact with TYR 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256D PHE* 3.8 20.4 - + - -
258D THR* 3.6 14.7 - - + +
260D ALA 2.9 30.0 + - - -
261D GLY* 3.9 6.6 - - - -
262D PHE* 3.6 22.8 - + - +
315D PHE* 3.9 18.2 - + + -
317D VAL* 3.7 33.0 - - + -
321D PHE* 3.1 37.8 + - + +
322D GLN 4.4 0.2 - - - +
324D VAL* 1.3 76.1 - - + +
326D LYS* 1.3 64.6 + - - +
328D LEU* 3.7 31.8 - - + +
329D LYS* 3.0 23.7 + - - +
337D VAL* 4.2 13.5 - - + +
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Residues in contact with LYS 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322D GLN* 2.8 65.4 + - - +
323D PRO* 3.8 7.6 - - + +
325D TYR* 1.3 71.4 - - - +
327D GLU* 1.3 64.9 + - + +
329D LYS* 3.2 17.7 - - - +
330D ASN* 3.2 17.5 + - - +
337D VAL* 4.2 19.8 - - + +
339D THR* 6.1 0.6 - - - +
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Residues in contact with GLU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C LEU* 5.6 3.6 - - + -
259C TYR* 3.2 31.2 + - + +
281C MET* 3.5 21.5 - - + +
323D PRO 3.4 10.7 + - - +
324D VAL 3.0 9.4 + - - +
326D LYS* 1.3 80.9 - - + +
328D LEU* 1.3 64.1 + - - +
330D ASN* 3.1 35.8 + - - +
331D LEU* 3.4 18.0 + - - +
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Residues in contact with LEU 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C MET* 3.6 11.3 - - - -
232D PHE* 4.0 17.0 - - + -
262D PHE* 3.8 13.9 - - + -
299D ILE* 3.7 34.5 - - + -
315D PHE* 3.7 22.4 - - + -
324D VAL 3.0 11.9 + - - +
325D TYR* 3.7 33.7 - - + +
326D LYS 3.4 0.2 - - - -
327D GLU* 1.3 75.6 - - - +
329D LYS* 1.3 62.4 + - - +
331D LEU* 3.0 15.8 + - - +
332D ILE* 3.2 37.6 + - + +
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Residues in contact with LYS 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D PHE* 4.3 7.1 - - + -
325D TYR 3.0 14.8 + - - +
326D LYS 3.2 11.7 - - - +
328D LEU* 1.3 76.5 - - - +
330D ASN* 1.3 74.5 + - - +
331D LEU 3.0 1.3 + - - -
332D ILE 3.2 20.2 + - - +
333D PRO 5.7 2.2 - - - -
335D SER* 3.2 39.0 + - - +
336D ALA* 4.0 8.5 - - - +
337D VAL* 3.8 24.5 - - + -
361D GLU* 5.7 2.6 + - - -
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Residues in contact with ASN 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326D LYS* 3.2 13.7 + - - +
327D GLU* 3.1 41.5 + - - +
329D LYS* 1.3 89.1 + - - +
331D LEU* 1.3 64.1 + - + +
332D ILE 3.5 1.2 - - - -
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Residues in contact with LEU 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C GLN* 4.5 17.0 - - + +
281C MET* 3.7 37.9 - - + +
310C MET* 4.1 25.4 - - + +
299D ILE* 3.7 26.9 - - + -
303D VAL* 3.3 19.2 - - - +
327D GLU* 3.6 14.6 - - - +
328D LEU 3.0 8.8 + - - +
330D ASN* 1.3 86.7 - - + +
332D ILE* 1.3 59.4 + - - +
333D PRO* 3.7 4.5 - - - +
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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