Contacts of the helix formed by residues 300 - 312 (chain D) in PDB entry 6Q0V
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 ASP 300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249D ARG* 5.5 0.2 - - - -
250D MET* 4.5 1.3 - - - -
275D ARG 4.5 1.7 + - - +
298D PHE* 3.3 15.3 - - - +
299D SER* 1.4 79.6 - - - +
301D SER* 1.4 64.6 + - - +
302D GLU* 3.2 29.5 + - - +
303D CYS* 3.6 29.6 + - + +
304D ALA* 3.3 15.4 + - - +
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Residues in contact with SER 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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249D ARG* 5.3 7.1 - - - +
250D MET* 3.4 34.3 - - - +
299D SER 4.5 0.4 + - - -
300D ASP* 1.4 71.8 + - - +
302D GLU* 1.4 61.7 + - - +
303D CYS 3.2 0.2 - - - -
304D ALA 3.2 2.3 + - - -
305D LYS* 3.0 45.7 + - - +
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Residues in contact with GLU 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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300D ASP* 3.2 11.1 + - - +
301D SER* 1.4 79.4 + - - +
303D CYS* 1.4 61.5 + - - +
305D LYS* 3.5 26.0 + - + +
306D LYS* 2.9 51.0 + - + +
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Residues in contact with CYS 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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273D PHE* 3.6 31.2 - - - +
274D GLY* 3.9 16.8 - - - -
275D ARG 5.2 0.9 - - - +
298D PHE* 4.1 6.9 - - + -
300D ASP* 3.6 31.8 + - + +
301D SER 3.2 0.4 - - - -
302D GLU* 1.4 76.1 - - - +
304D ALA* 1.4 61.2 + - - +
306D LYS* 3.6 6.8 + - - +
307D ALA* 3.3 21.1 + - - +
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Residues in contact with ALA 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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250D MET* 3.5 26.5 - - + +
252D LEU* 3.3 20.1 - - + +
298D PHE* 3.7 30.7 - - + -
300D ASP 3.3 11.4 + - - +
301D SER 3.2 10.0 + - - +
303D CYS* 1.4 75.7 - - - +
305D LYS* 1.4 62.2 + - - +
307D ALA 3.5 0.7 + - - -
308D LEU* 3.3 19.2 + - - +
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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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250D MET* 3.8 14.8 - - + -
301D SER* 3.0 35.9 + - - +
302D GLU* 3.6 31.3 - - + +
303D CYS 3.4 0.2 - - - -
304D ALA* 1.4 75.7 - - - +
306D LYS* 1.4 58.9 + - + +
308D LEU* 3.4 7.9 + - - +
309D GLU* 3.1 26.5 + - - +
325D HIS* 5.0 7.2 - - + +
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Residues in contact with LYS 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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543C THR* 5.1 13.2 - - + -
273D PHE* 3.7 14.3 - - + +
302D GLU* 2.9 52.7 + - + +
303D CYS* 4.0 8.3 - - - +
304D ALA 3.4 0.2 - - - -
305D LYS* 1.4 76.5 - - + +
307D ALA* 1.4 59.3 + - - +
309D GLU* 3.5 19.8 + - - +
310D GLN* 3.1 38.5 + - + +
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Residues in contact with ALA 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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252D LEU* 4.5 1.1 - - + -
270D PHE* 4.1 10.9 - - + -
273D PHE* 3.7 23.3 - - + -
298D PHE* 3.7 33.0 - - + -
303D CYS 3.3 7.2 + - - +
304D ALA 3.6 9.4 - - - +
305D LYS 3.3 0.2 - - - -
306D LYS* 1.4 78.4 - - - +
308D LEU* 1.3 55.7 + - - +
310D GLN 3.7 0.3 + - - -
311D LEU* 3.1 36.1 + - - +
323D VAL* 4.9 2.0 - - - -
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Residues in contact with LEU 308 (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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252D LEU* 3.7 19.3 - - + -
304D ALA 3.3 8.3 + - - +
305D LYS* 3.4 11.4 - - - +
307D ALA* 1.3 76.5 - - - +
309D GLU* 1.3 63.0 + - - +
312D ASN* 3.0 47.4 + - + +
323D VAL* 3.4 38.8 - - + +
324D GLY* 3.8 11.9 - - - -
325D HIS* 3.5 28.9 - - + +
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Residues in contact with GLU 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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305D LYS 3.1 13.7 + - - +
306D LYS* 3.7 19.3 - - - +
308D LEU* 1.3 82.6 - - - +
310D GLN* 1.3 76.4 + - + +
312D ASN* 4.8 1.4 + - - +
314D PHE* 4.1 12.1 - - - -
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Residues in contact with GLN 310 (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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541C GLY 5.5 1.2 + - - -
542C GLN* 4.5 11.9 - - - +
543C THR* 4.7 5.0 - - + +
546C SER* 2.9 31.2 + - - +
553C LYS* 4.6 2.8 + - - -
273D PHE* 3.7 25.6 - - + -
306D LYS* 3.1 22.6 + - + +
309D GLU* 1.3 94.6 + - - +
311D LEU* 1.3 64.0 + - - +
314D PHE* 3.5 17.2 - - - -
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Residues in contact with LEU 311 (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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549C SER* 3.4 21.8 - - - +
553C LYS* 3.7 28.0 - - + +
269D ILE* 3.8 6.7 - - + -
270D PHE* 3.5 35.0 - - + -
273D PHE* 3.7 20.2 - - + -
307D ALA 3.1 21.1 + - - +
310D GLN* 1.3 83.6 - - - +
312D ASN* 1.3 64.1 + - - +
313D GLY 3.3 0.7 + - - -
314D PHE* 3.3 25.7 + - - +
321D MET* 3.5 27.6 - - + +
323D VAL* 4.1 6.7 - - + -
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Residues in contact with ASN 312 (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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308D LEU* 3.0 28.2 + - + +
309D GLU 5.0 1.2 - - - +
311D LEU* 1.3 74.7 - - - +
313D GLY* 1.3 61.0 + - - +
314D PHE* 3.3 19.4 - - - -
321D MET 3.8 2.6 - - - +
322D LYS* 3.7 14.6 + - - +
323D VAL* 3.3 41.3 + - + +
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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