Contacts of the helix formed by residues 168 - 180 (chain G) in PDB entry 40ER
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 THR 168 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A GLU* 5.6 0.4 - - - +
70G ARG* 5.5 5.4 - - - +
145G LEU* 5.1 1.3 - - - -
151G HIS* 3.9 12.6 - - + +
152G ARG* 4.8 16.1 - - - +
165G TYR* 4.8 2.3 + - - -
166G ILE* 3.5 9.9 + - - +
167G LEU* 1.3 80.6 + - - +
169G HIS* 1.3 70.2 + - + +
170G LYS* 3.1 28.7 - - + +
171G ARG* 3.1 23.7 + - - +
172G ILE* 3.2 19.5 + - - +
298G HIS* 5.6 2.7 - - + +
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Residues in contact with HIS 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145G LEU* 4.0 25.1 - - + +
146G ILE* 5.7 4.3 - - + -
150G ILE 3.6 18.0 + - - -
151G HIS* 3.8 27.7 + + + -
168G THR* 1.3 75.8 - - + +
170G LYS* 1.3 61.8 + - - +
172G ILE* 3.4 4.3 + - - +
173G LEU* 3.2 24.3 + - - +
298G HIS* 3.7 21.8 - + + -
315G LEU* 3.5 20.8 - - + +
316G SER* 3.7 32.0 + - - -
319G LEU* 3.4 30.0 - - + +
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Residues in contact with LYS 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A HIS* 4.5 10.8 - - - -
363A PRO* 4.5 1.6 - - - +
364A GLU* 3.3 30.0 + - - +
226B ASP* 5.6 2.7 - - - -
70G ARG* 4.6 1.8 - - - +
168G THR* 3.1 18.1 - - + -
169G HIS* 1.3 77.8 - - - +
171G ARG* 1.3 62.9 + - - +
172G ILE 3.3 0.2 + - - -
173G LEU* 3.4 3.8 + - - +
174G LYS* 3.1 26.1 + - - +
293G VAL* 5.6 0.5 - - - +
296G GLU* 2.5 35.1 + - - +
297G VAL* 3.9 6.1 - - - +
298G HIS* 4.4 6.1 - - - +
315G LEU* 3.6 20.2 - - + -
402G AMP 2.9 26.9 + - - +
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Residues in contact with ARG 171 (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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342A PHE* 2.9 76.5 + - - -
343A TYR* 4.3 4.8 - - - +
226B ASP* 5.6 6.7 + - - +
229B LEU* 4.7 5.5 - - - +
41G LEU* 3.0 36.2 + - + +
42G ILE 4.3 0.2 - - - -
43G PRO* 3.4 28.2 - - - +
165G TYR* 3.2 32.8 + - + +
167G LEU* 4.7 3.8 - - + -
168G THR* 3.1 22.6 + - - +
170G LYS* 1.3 78.5 - - - +
172G ILE* 1.3 61.5 + - - +
175G PHE* 3.1 24.4 + - - +
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Residues in contact with ILE 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G MET* 5.6 0.4 - - - -
41G LEU* 4.0 6.1 - - + -
138G LEU* 3.8 31.9 - - + -
141G ALA* 5.1 1.8 - - + -
142G VAL* 4.0 25.1 - - + +
145G LEU* 3.6 30.3 - - + -
167G LEU* 3.5 25.8 - - + -
168G THR 3.2 14.3 + - - +
169G HIS 3.9 4.7 - - - +
170G LYS 3.2 0.2 - - - -
171G ARG* 1.3 75.4 - - - +
173G LEU* 1.3 55.0 + - - +
175G PHE* 3.3 2.6 + - - +
176G LEU* 2.7 40.8 + - + +
319G LEU* 4.0 12.8 - - + -
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Residues in contact with LEU 173 (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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169G HIS 3.2 14.4 + - - +
170G LYS* 4.0 3.6 - - - +
172G ILE* 1.3 78.8 - - - +
174G LYS* 1.3 64.1 + - - +
176G LEU* 3.0 18.1 + - + +
177G LYS* 3.1 15.4 + - + +
289G ILE* 3.8 27.4 - - + -
292G LEU* 4.5 12.1 - - + -
293G VAL* 3.6 25.1 - - + +
315G LEU* 3.6 28.9 - - + -
318G ILE* 4.6 15.9 - - + -
319G LEU* 4.4 15.7 - - + +
322G LEU* 6.1 2.7 - - + -
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Residues in contact with LYS 174 (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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339A ALA* 5.8 5.6 - - - -
342A PHE* 3.5 44.0 - - + +
170G LYS 3.1 17.5 + - - +
173G LEU* 1.3 76.3 - - - +
175G PHE* 1.3 63.2 + - - +
177G LYS* 3.5 1.1 + - - +
178G LEU* 3.0 37.3 + - + +
293G VAL* 4.0 32.9 + - + +
294G GLU* 5.7 1.4 - - - +
296G GLU* 3.9 27.9 + - + +
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Residues in contact with PHE 175 (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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332A ASN* 5.7 0.9 - - - -
342A PHE* 4.0 13.2 - + + -
343A TYR* 3.6 19.3 - - - -
32G PHE* 4.0 20.4 - + - -
36G HIS* 4.9 14.4 - + + -
40G ASP* 3.8 29.6 - - + -
41G LEU* 3.5 33.7 - - + -
138G LEU* 4.2 15.3 - - + -
171G ARG 3.1 18.1 + - - +
172G ILE 3.5 2.0 - - - +
174G LYS* 1.3 79.8 - - - +
176G LEU* 1.3 65.8 + - - +
179G PHE* 3.1 62.5 + + + +
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Residues in contact with LEU 176 (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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29G TYR* 3.6 37.5 - - + +
32G PHE* 3.7 32.1 - - + -
33G MET* 4.2 13.7 - - + -
138G LEU* 3.9 20.2 - - + -
172G ILE* 2.7 26.5 + - + +
173G LEU* 3.0 18.6 + - + +
175G PHE* 1.3 73.5 - - - +
177G LYS* 1.3 58.9 + - - +
180G ILE* 2.9 35.9 + - + +
322G LEU* 5.3 10.8 - - + -
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Residues in contact with LYS 177 (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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29G TYR* 3.2 26.1 + - - -
173G LEU* 3.1 11.3 + - + +
174G LYS 4.4 1.6 - - - +
176G LEU* 1.3 79.0 - - - +
178G LEU* 1.3 64.0 + - - +
180G ILE* 3.6 20.4 + - + +
185G LYS* 3.9 21.7 - - + +
189G MET* 5.4 3.1 - - - +
286G GLU* 3.6 17.5 + - - -
289G ILE* 4.0 22.2 - - + -
290G ASN* 3.7 27.1 - - - +
293G VAL* 5.0 12.6 - - + -
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Residues in contact with LEU 178 (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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335A ILE* 3.6 27.0 - - + +
336A MET* 6.3 0.2 - - - -
338A GLU* 4.5 15.3 - - + +
339A ALA* 4.6 20.2 - - + +
342A PHE* 4.4 20.9 - - + -
343A TYR* 5.8 0.2 - - + -
174G LYS* 3.0 28.0 + - + +
177G LYS* 1.3 81.2 - - - +
179G PHE* 1.3 84.0 + - + +
180G ILE 4.5 1.9 - - - +
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Residues in contact with PHE 179 (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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332A ASN* 3.2 40.2 - - - -
335A ILE* 4.4 17.7 - - + -
336A MET* 3.9 10.3 - - + -
342A PHE* 4.5 1.6 - + - -
343A TYR* 3.5 35.0 - + - -
32G PHE* 4.2 19.2 - - + -
175G PHE* 3.1 58.5 + + + +
178G LEU* 1.3 99.1 - - + +
180G ILE* 1.3 62.4 + - - +
181G THR* 3.6 1.9 + - - +
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Residues in contact with ILE 180 (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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28G VAL 5.2 2.2 - - - +
29G TYR* 4.1 24.5 - - + +
32G PHE* 3.7 39.5 - - + -
176G LEU* 2.9 26.2 + - + +
177G LYS* 3.6 37.1 - - + +
178G LEU 4.5 2.1 - - - +
179G PHE* 1.3 78.8 - - - +
181G THR* 1.3 78.9 + - + +
182G GLU* 5.3 2.4 - - - +
184G PRO* 3.9 19.5 - - + -
185G LYS* 5.3 2.5 - - + +
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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