Contacts of the helix formed by residues 293 - 304 (chain H) in PDB entry 6CAJ
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 PRO 293 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202H GLU 4.4 0.5 - - - +
203H ASN 3.0 22.4 - - - +
204H GLY* 3.3 26.7 - - - +
278H PRO* 4.2 11.7 - - + +
281H ILE* 3.6 26.9 - - + +
282H THR 3.3 17.5 - - - +
284H LEU* 3.7 23.6 - - + -
291H LEU 4.3 0.2 - - - +
292H THR* 1.3 90.7 - - - +
294H SER* 1.3 58.9 + - - +
295H ALA 3.2 0.7 + - - -
296H VAL* 3.9 8.4 + - + +
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Residues in contact with SER 294 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D SER* 3.0 36.8 + - - -
337D TYR* 2.7 26.6 + - - -
510F SER* 3.3 28.8 + - - +
511F SER* 5.1 1.0 + - - -
514F VAL* 5.6 0.7 - - - +
203H ASN 4.5 3.1 - - - -
292H THR* 3.1 12.2 + - - +
293H PRO* 1.3 76.4 - - - +
295H ALA* 1.3 56.5 + - - +
296H VAL 3.5 0.7 - - - -
297H SER* 3.9 8.2 + - - +
298H ASP 3.7 8.5 + - - -
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Residues in contact with ALA 295 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D TYR* 3.6 26.9 - - + -
291H LEU* 3.8 32.3 - - + -
292H THR* 3.0 18.3 + - + +
294H SER* 1.3 78.7 + - - +
296H VAL* 1.3 60.4 + - - +
297H SER 3.3 0.9 - - - -
298H ASP* 3.2 2.8 + - - +
299H GLU* 2.9 33.4 + - + +
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Residues in contact with VAL 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H VAL* 3.9 2.9 - - + -
201H VAL 3.7 21.8 - - - +
202H GLU 3.7 6.5 - - - +
204H GLY* 4.8 2.5 - - - +
235H PHE* 3.6 38.4 - - + -
284H LEU* 3.7 30.3 - - + -
286H THR* 5.6 0.2 - - + -
291H LEU* 5.2 6.1 - - + -
292H THR 4.7 5.4 - - - +
293H PRO 4.2 9.6 - - - +
294H SER 3.5 0.6 - - - -
295H ALA* 1.3 76.4 - - - +
297H SER* 1.3 59.3 + - - +
299H GLU* 3.3 6.9 + - - +
300H LEU* 2.9 39.2 + - + +
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Residues in contact with SER 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508F PRO* 3.4 19.9 - - - +
511F SER* 2.4 30.9 + - - -
202H GLU* 3.1 36.2 + - - -
203H ASN* 4.7 0.9 - - - -
294H SER* 3.9 11.0 + - - -
295H ALA 3.3 0.2 - - - -
296H VAL* 1.3 77.5 - - - +
298H ASP* 1.3 56.5 + - - +
300H LEU* 3.7 0.7 - - - +
301H ILE* 2.9 33.6 + - - +
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Residues in contact with ASP 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337D TYR* 3.2 40.1 + - + +
338D ARG* 3.8 12.0 - - - +
511F SER* 4.9 0.4 + - - -
514F VAL* 3.3 17.5 - - + +
517F ARG* 2.6 35.0 + - - -
294H SER 3.7 1.6 + - - -
295H ALA 3.2 10.0 + - - +
297H SER* 1.3 78.6 - - - +
299H GLU* 1.3 57.0 + - + +
301H ILE* 3.3 1.2 + - - +
302H LYS* 2.9 42.6 + - - +
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Residues in contact with GLU 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235H PHE* 4.6 15.5 - - + -
288H LEU* 3.4 33.8 - - + +
291H LEU* 4.7 13.1 - - + +
295H ALA* 2.9 22.2 + - + +
296H VAL* 3.3 7.2 + - - +
298H ASP* 1.3 76.6 - - + +
300H LEU* 1.3 60.0 + - - +
302H LYS* 3.4 29.3 + - - +
303H LEU* 2.9 31.3 + - + +
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Residues in contact with LEU 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H LEU* 5.4 0.9 - - + -
201H VAL 4.9 0.2 - - - -
202H GLU* 3.8 30.3 - - + +
235H PHE* 3.8 33.2 - - + +
236H VAL 3.9 9.9 - - - +
237H ARG* 3.4 47.9 + - + -
296H VAL* 2.9 30.1 + - + +
297H SER 4.0 2.9 - - - +
299H GLU* 1.3 75.3 - - - +
301H ILE* 1.3 62.0 + - - +
303H LEU* 3.7 21.3 - - + -
304H TYR* 2.9 20.6 + - - -
305H LEU* 3.6 4.5 + - - +
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Residues in contact with ILE 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504F LEU* 5.2 6.5 - - + -
507F ILE* 3.7 26.5 - - + -
511F SER* 3.8 16.2 - - - -
514F VAL* 3.8 28.7 - - + -
515F VAL* 4.1 10.8 - - + -
518F VAL* 4.3 25.8 - - + -
202H GLU* 4.0 11.2 - - - +
237H ARG* 5.3 2.7 - - - +
297H SER* 2.9 22.4 + - - +
298H ASP 3.3 3.1 + - - +
300H LEU* 1.3 75.7 - - - +
302H LYS* 1.3 63.2 + - - +
304H TYR* 3.2 35.2 - - + +
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Residues in contact with LYS 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D ARG* 3.3 31.1 - - - +
517F ARG* 4.4 6.7 - - - +
518F VAL* 4.9 11.0 - - + -
298H ASP* 2.9 42.5 + - - +
299H GLU* 3.4 31.8 + - - +
301H ILE* 1.3 76.4 - - + +
303H LEU* 1.3 60.0 + - - +
304H TYR* 3.8 12.7 - - - -
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Residues in contact with LEU 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H LEU* 3.7 29.8 - - + -
74H ARG* 2.8 44.9 + - - +
235H PHE* 6.0 3.6 - - + -
299H GLU 2.9 18.6 + - - +
300H LEU* 4.2 17.7 - - + +
302H LYS* 1.3 79.8 - - - +
304H TYR* 1.3 56.4 + - - +
305H LEU 4.1 10.1 - - - +
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Residues in contact with TYR 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504F LEU* 4.4 30.2 - - + +
518F VAL* 4.0 27.8 + - + +
519F LYS* 6.0 0.9 - - - +
74H ARG* 3.1 30.7 + - - +
237H ARG* 4.0 3.1 - - - +
300H LEU 2.9 12.6 + - - -
301H ILE* 3.2 28.0 - - + -
302H LYS* 3.8 14.6 - - - -
303H LEU* 1.3 76.6 - - - +
305H LEU* 1.3 65.7 + - - +
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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