Contacts of the helix formed by residues 300 - 310 (chain G) in PDB entry 3A5Z
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 300 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G THR 4.1 5.8 - - - -
114G MET* 4.7 0.2 - - - -
245G LEU* 2.8 15.1 + - - +
299G LEU* 1.3 74.8 - - - +
301G VAL* 1.3 54.0 + - - -
302G ASP* 3.2 3.1 - - - -
303G ARG* 2.7 31.1 + - - +
304G LEU* 2.9 10.4 + - - +
993G KAA 3.3 30.6 + - - -
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Residues in contact with VAL 301 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ARG* 4.6 7.0 - - - +
23G MET* 3.8 26.9 - - - -
26G ILE* 4.3 11.7 - - + -
95G LEU* 3.8 15.3 - - + -
113G THR* 3.5 15.9 + - + +
114G MET 4.1 3.4 - - - -
115G LEU* 3.6 35.7 - - + +
299G LEU* 3.3 10.4 + - + +
300G GLY* 1.3 70.7 - - - +
302G ASP* 1.3 57.7 + - - +
304G LEU* 4.0 3.1 - - + -
305G VAL* 2.8 42.4 + - + +
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Residues in contact with ASP 302 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ARG* 2.8 41.9 + - - +
112G PHE* 3.2 13.2 - - + +
113G THR* 2.6 33.7 + - - +
300G GLY 3.2 1.2 - - - -
301G VAL* 1.3 76.9 - - - +
303G ARG* 1.3 58.1 + - + +
305G VAL* 3.6 0.4 + - - -
306G MET* 2.9 28.2 + - - +
314G LEU* 3.6 23.7 - - + +
317G VAL* 3.5 7.4 - - + +
318G ILE* 3.6 20.7 - - + +
993G KAA 5.6 2.0 - - + +
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Residues in contact with ARG 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G TYR* 2.8 36.6 + - + +
108G HIS* 3.0 36.6 + - - -
243G ILE* 3.5 14.4 - - + -
244G GLU* 3.1 52.2 + - - +
245G LEU* 3.8 14.4 - - + -
300G GLY* 2.7 10.1 + - - +
302G ASP* 1.3 74.5 - - - +
304G LEU* 1.3 67.1 + - - +
306G MET* 3.3 12.3 + - + +
307G LEU* 3.1 27.5 + - - +
314G LEU* 3.9 14.4 - - + -
993G KAA 3.5 30.6 + - - +
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Residues in contact with LEU 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G ILE* 4.9 2.7 - - + -
26G ILE* 4.3 20.9 - - + -
134G LEU* 4.9 7.2 - - + -
135G LEU* 3.8 28.3 - - + -
138G VAL* 3.9 28.7 - - + -
139G LEU* 3.8 24.3 - - + +
245G LEU* 4.3 10.9 - - + +
299G LEU* 4.1 24.0 - - + -
300G GLY 2.9 11.0 + - - +
301G VAL* 3.4 9.9 - - + +
303G ARG* 1.3 76.9 - - - +
305G VAL* 1.3 63.4 + - - +
307G LEU* 3.2 8.2 + - - +
308G ALA* 3.0 21.0 + - - +
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Residues in contact with VAL 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ARG* 4.0 32.1 - - + +
22G ILE* 3.9 32.5 - - + -
23G MET* 5.6 0.2 - - - -
301G VAL* 2.8 36.8 + - + +
302G ASP 3.9 3.4 - - - +
304G LEU* 1.3 69.5 - - + +
306G MET* 1.3 66.2 + - - +
308G ALA* 4.3 0.2 - - - -
309G LEU* 3.1 47.7 + - + +
317G VAL* 3.7 16.4 - - + -
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Residues in contact with MET 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G TYR* 3.3 35.2 - - + -
243G ILE* 4.0 23.8 - - + -
302G ASP 2.9 19.1 + - - +
303G ARG* 3.4 14.1 - - + +
305G VAL* 1.3 76.9 - - - +
307G LEU* 1.3 64.5 + - + +
310G GLY 3.1 2.6 + - - -
311G ALA* 2.8 44.1 + - + +
312G GLU 4.4 0.7 - - - +
313G THR* 3.2 44.0 - - - +
314G LEU* 3.6 9.4 - - - -
317G VAL* 3.6 13.4 - - + +
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Residues in contact with LEU 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G LEU* 3.8 14.4 - - + -
240G TYR* 3.6 29.6 - - + +
241G LYS* 3.6 37.9 + - + +
243G ILE* 3.5 31.9 - - + -
245G LEU* 3.8 33.7 - - + -
303G ARG 3.1 14.1 + - - +
304G LEU* 3.5 6.3 - - - +
306G MET* 1.3 79.2 - - + +
308G ALA* 1.3 65.5 + - - +
310G GLY* 3.1 14.4 + - - -
311G ALA 5.6 0.2 - - - -
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Residues in contact with ALA 308 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G ILE* 3.8 24.2 - - + -
138G VAL* 4.3 12.1 - - + +
139G LEU* 3.4 18.5 - - + +
304G LEU 3.0 15.3 + - - +
305G VAL 3.3 4.5 + - - +
307G LEU* 1.3 76.1 - - - +
309G LEU* 1.3 64.1 + - + +
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Residues in contact with LEU 309 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ASN* 4.1 44.7 + - + +
18G LYS* 3.8 33.0 - - + -
19G ARG 4.6 1.6 - - - +
22G ILE* 4.5 11.0 - - + -
305G VAL* 3.1 39.1 + - + +
308G ALA* 1.3 83.9 - - + +
310G GLY* 1.3 62.2 + - - +
311G ALA 3.5 3.8 + - - +
317G VAL* 4.2 7.4 - - + -
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Residues in contact with GLY 310 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241G LYS* 5.5 4.5 - - - -
306G MET 3.1 2.0 + - - -
307G LEU* 3.1 13.7 + - - -
308G ALA 3.5 0.4 - - - -
309G LEU* 1.3 79.5 - - - +
311G ALA* 1.3 68.1 + - - +
312G GLU* 3.6 9.2 + - - +
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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