Contacts of the helix formed by residues 298 - 309 (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 SER 298 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308C LEU* 4.0 19.1 - - - -
320C GLU* 2.7 28.1 + - - -
350C ARG* 4.3 2.5 + - - +
232D PHE* 4.8 1.6 - - - -
264D PHE* 4.9 2.2 - - - -
265D ALA* 3.5 22.4 - - - +
297D PRO* 1.3 76.7 - - - +
299D ILE* 1.3 66.6 + - - +
300D ALA* 3.7 4.2 + - - -
301D HIS* 2.9 28.0 + - - +
302D LEU* 3.2 9.5 + - - +
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Residues in contact with ILE 299 (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* 3.8 8.7 - - + +
282C ALA* 3.3 35.4 + - + +
310C MET* 4.0 20.4 - - + -
232D PHE* 3.9 19.8 - - + -
262D PHE* 4.4 2.7 - - + -
264D PHE* 5.2 1.9 - - + +
297D PRO 4.0 0.6 + - - -
298D SER* 1.3 70.3 - - - +
300D ALA* 1.3 65.3 + - - +
302D LEU* 3.0 8.1 + - - +
303D VAL* 2.9 31.2 + - + +
328D LEU* 3.7 32.3 - - + -
331D LEU* 3.7 25.4 - - + -
332D ILE* 4.6 3.6 - - + -
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Residues in contact with ALA 300 (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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308C LEU 4.7 3.6 + - - +
310C MET* 3.4 38.5 - - + +
319C GLN* 5.5 0.9 - - - -
320C GLU* 3.5 34.5 - - + +
348C PHE* 4.8 3.7 - - + -
298D SER* 3.1 3.5 + - - +
299D ILE* 1.3 78.2 - - - +
301D HIS* 1.3 61.2 + - - +
303D VAL* 3.4 5.4 - - - +
304D GLN* 3.2 22.2 + - - +
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Residues in contact with HIS 301 (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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320C GLU* 4.8 0.2 - - - +
348C PHE* 3.9 31.7 - + + -
236D MET* 3.4 25.5 - - + +
277D ASN* 3.2 35.8 + - - +
278D ASP 4.1 3.3 + - - -
279D GLY* 3.8 18.2 - - - -
297D PRO* 4.1 3.5 - - + +
298D SER* 2.9 25.5 + - - +
300D ALA* 1.3 76.9 - - - +
302D LEU* 1.3 59.9 + - - +
304D GLN* 3.3 10.0 + - - +
305D LYS* 3.0 34.4 + - + +
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Residues in contact with LEU 302 (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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232D PHE* 3.5 44.6 - - + +
235D ILE* 3.8 35.7 - - + -
236D MET* 3.8 24.7 - - + +
239D ALA* 6.3 0.4 - - + -
297D PRO* 3.8 18.8 - - + -
298D SER 3.2 11.4 + - - +
299D ILE* 3.0 8.6 + - - +
301D HIS* 1.3 73.5 - - - +
303D VAL* 1.3 60.0 + - + +
305D LYS* 4.3 4.0 - - + +
306D LEU* 2.7 49.0 + - + +
332D ILE* 5.3 9.4 - - + -
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Residues in contact with VAL 303 (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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310C MET* 4.4 7.0 - - - -
318C PRO* 4.0 29.6 - - + -
299D ILE* 2.9 23.3 + - + +
300D ALA* 3.4 11.4 - - - +
301D HIS 3.3 0.2 - - - -
302D LEU* 1.3 74.6 - - - +
304D GLN* 1.3 63.0 + - - +
306D LEU* 4.1 6.9 - - - +
307D SER* 3.0 31.4 + - - +
331D LEU 3.3 24.2 - - - +
332D ILE* 4.0 15.5 - - + -
333D PRO* 4.0 19.0 - - + +
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Residues in contact with GLN 304 (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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317C ARG* 5.5 4.4 - - - +
347C GLU* 3.6 26.5 + - - -
348C PHE* 3.9 25.0 - - + -
300D ALA 3.2 9.7 + - - +
301D HIS* 3.6 11.5 - - - +
302D LEU 3.2 0.6 - - - -
303D VAL* 1.3 79.5 - - - +
305D LYS* 1.3 81.0 + - - +
307D SER* 3.1 4.3 + - - -
308D GLU* 2.8 50.0 + - + +
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Residues in contact with LYS 305 (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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236D MET* 3.6 35.0 - - + -
239D ALA* 4.7 5.6 - - + -
240D VAL* 4.0 13.2 - - + -
278D ASP 5.6 0.9 - - - -
279D GLY* 4.3 15.5 - - - -
280D GLN* 5.8 3.4 - - - +
301D HIS* 3.0 28.6 + - - +
302D LEU* 3.1 4.5 + - + +
304D GLN* 1.3 98.3 + - - +
306D LEU* 1.3 62.1 + - + +
308D GLU* 2.7 29.0 + - - +
309D ASN* 2.6 39.2 + - - +
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Residues in contact with LEU 306 (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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235D ILE* 4.0 25.1 - - + -
239D ALA* 4.6 7.2 - - + -
254D LEU* 4.6 1.6 - - + -
302D LEU* 2.7 41.0 + - + +
303D VAL* 4.1 3.4 - - - +
305D LYS* 1.3 72.6 - - + +
307D SER* 1.3 52.5 + - - +
309D ASN 2.5 20.7 - - - +
310D ASN* 3.8 0.7 - - - -
311D ILE* 3.0 53.6 + - + +
313D THR* 3.7 26.0 - - + +
332D ILE* 3.8 28.7 - - + -
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Residues in contact with SER 307 (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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303D VAL* 3.0 20.3 + - - +
304D GLN* 3.1 6.1 + - - -
305D LYS 3.1 0.8 - - - -
306D LEU* 1.3 75.2 - - - +
308D GLU* 1.3 58.5 + - - +
309D ASN 2.8 13.1 - - - +
310D ASN* 6.0 0.2 - - - -
333D PRO* 4.6 13.2 - - - +
365D GLU* 4.4 10.6 + - - -
426D ARG* 2.8 31.6 + - - +
428D LEU* 3.9 15.6 - - - +
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Residues in contact with GLU 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D GLN* 2.8 44.5 + - + +
305D LYS* 2.7 33.3 + - - +
307D SER* 1.3 70.7 - - - +
309D ASN* 1.3 67.4 + - - +
310D ASN* 5.2 0.7 - - - +
426D ARG* 5.6 1.4 - - - -
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Residues in contact with ASN 309 (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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239D ALA 2.9 33.4 + - - +
240D VAL* 3.9 14.2 - - - +
247D TRP* 6.3 0.7 - - + -
252D ARG* 4.2 10.1 + - - +
305D LYS* 2.6 31.8 + - - +
306D LEU 2.5 22.0 - - - +
307D SER 2.8 7.8 - - - +
308D GLU* 1.3 83.0 + - - +
310D ASN* 1.3 57.7 + - - +
311D ILE* 4.0 12.8 - - + -
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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