Contacts of the helix formed by residues 296 - 308 (chain K) in PDB entry 6XAV
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 GLY 296 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105E LYS* 6.5 0.7 - - - -
106E GLU 5.4 6.5 - - - -
269K CYS* 4.2 2.0 - - - +
294K ASN 3.8 2.4 + - - -
295K LEU* 1.3 75.7 - - - +
297K LYS* 1.3 61.9 + - - -
298K LYS 3.4 2.5 - - - -
299K SER* 3.9 12.2 - - - -
300K LEU* 3.0 28.2 + - - +
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Residues in contact with LYS 297 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E GLU 5.6 2.0 + - - -
96G GLN* 3.4 35.0 + - + +
296K GLY* 1.3 70.5 - - - -
298K LYS* 1.3 64.9 + - - +
300K LEU* 3.5 4.8 + - - +
301K THR* 3.1 24.6 + - - -
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Residues in contact with LYS 298 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96G GLN* 4.2 15.3 - - + +
98G GLU* 5.0 1.8 - - - +
265K ARG* 5.6 11.0 - - + -
266K SER* 4.8 2.9 - - - +
296K GLY* 3.4 0.6 - - - -
297K LYS* 1.3 78.6 - - - +
299K SER* 1.3 57.8 + - - +
301K THR* 3.4 4.5 + - - -
302K GLU* 3.0 29.3 + - - +
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Residues in contact with SER 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265K ARG 4.5 2.0 - - - -
266K SER* 3.9 27.6 - - - +
269K CYS* 3.7 30.1 - - - -
295K LEU* 4.9 3.8 - - - -
296K GLY* 3.6 13.2 + - - -
297K LYS 3.3 0.4 - - - -
298K LYS* 1.3 79.9 - - - +
300K LEU* 1.3 55.6 + - - +
302K GLU* 3.4 2.1 + - - +
303K ILE* 2.9 29.6 + - - +
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Residues in contact with LEU 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G ALA* 6.6 0.2 - - + -
290K LEU* 6.4 2.0 - - + -
295K LEU* 5.5 6.2 - - + +
296K GLY 3.0 19.0 + - - +
297K LYS* 3.9 5.6 - - - +
299K SER* 1.3 76.9 - - - +
301K THR* 1.3 58.8 + - - +
303K ILE* 3.4 7.0 + - - +
304K LYS* 3.0 28.6 + - - +
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Residues in contact with THR 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G TRP* 5.0 5.7 - - - -
95G ASP* 3.7 25.4 - - - -
96G GLN* 4.4 4.7 - - - -
98G GLU* 3.3 25.9 - - - +
297K LYS 3.1 17.7 + - - -
298K LYS* 3.8 3.4 - - - -
299K SER 3.3 0.2 - - - -
300K LEU* 1.3 78.7 - - - +
302K GLU* 1.3 56.1 + - - +
304K LYS* 3.3 6.7 + - - +
305K ASP* 3.0 28.1 + - - +
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Residues in contact with GLU 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G GLU* 4.7 1.9 + - - +
266K SER* 4.2 19.1 - - - -
298K LYS 3.0 18.5 + - - +
299K SER 3.8 3.4 - - - +
301K THR* 1.3 73.4 - - - +
303K ILE* 1.3 64.8 + - - +
305K ASP* 3.4 6.9 + - - +
306K VAL* 3.1 23.7 + - - +
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Residues in contact with ILE 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299K SER 2.9 18.1 + - - +
300K LEU* 3.8 7.4 - - - +
302K GLU* 1.3 76.3 - - - +
304K LYS* 1.3 58.9 + - - +
306K VAL* 3.4 6.0 + - - +
307K LEU* 2.9 29.9 + - - +
313K SER* 4.7 10.2 - - - -
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Residues in contact with LYS 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62G TRP* 3.7 36.1 + - + +
75G ILE* 6.3 4.0 - - + -
95G ASP* 5.6 0.9 - - - +
300K LEU 3.0 18.3 + - - +
301K THR* 3.7 6.1 - - - +
303K ILE* 1.3 78.1 - - - +
305K ASP* 1.3 56.1 + - - +
307K LEU* 3.3 7.2 + - - +
308K ALA* 3.0 27.9 + - - +
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Residues in contact with ASP 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G GLU* 4.5 16.7 - - - +
62G TRP* 4.7 6.9 - - + -
301K THR 3.0 16.8 + - - +
302K GLU* 3.8 7.4 - - - +
303K ILE 3.3 0.2 - - - -
304K LYS* 1.3 77.2 - - - +
306K VAL* 1.3 60.9 + - - +
308K ALA* 3.4 18.1 + - - +
309K SER* 4.1 5.2 + - - -
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Residues in contact with VAL 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302K GLU 3.1 17.2 + - - +
303K ILE* 3.9 6.1 - - - +
304K LYS 3.3 0.2 - - - -
305K ASP* 1.3 77.2 - - - +
307K LEU* 1.3 60.1 + - - +
308K ALA 3.5 0.3 + - - -
309K SER* 3.6 16.1 + - - -
311K GLY* 4.1 9.7 + - - -
312K LEU* 4.2 14.2 + - + -
313K SER* 6.4 0.2 - - - -
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Residues in contact with LEU 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71G PRO* 5.0 6.9 - - - +
303K ILE 2.9 18.4 + - - +
304K LYS* 3.8 7.6 - - - +
305K ASP 3.3 0.2 - - - -
306K VAL* 1.3 76.0 - - - +
308K ALA* 1.3 62.3 + - - +
309K SER 3.2 1.3 - - - -
310K ARG* 3.2 14.4 + - - +
312K LEU 3.3 21.5 - - - +
313K SER* 3.8 18.4 - - - +
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Residues in contact with ALA 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G GLN* 4.1 24.9 - - + +
42G GLU* 4.6 12.6 - - + +
60G ARG* 5.2 0.9 - - - +
62G TRP* 5.7 2.7 - - + +
71G PRO 4.8 9.9 - - - +
72G THR* 4.0 30.4 - - - +
304K LYS 3.0 15.3 + - - +
305K ASP* 3.7 11.0 - - - +
306K VAL 3.3 1.0 - - - -
307K LEU* 1.3 77.9 - - - +
309K SER* 1.3 57.4 + - - +
310K ARG* 3.2 3.5 + - - +
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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