Contacts of the helix formed by residues 175 - 186 (chain A) in PDB entry 5M4G
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 ILE 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A LEU* 4.0 12.1 - - + -
37A ASN* 4.0 15.1 + - - +
39A ALA* 3.8 39.3 - - + +
40A VAL* 3.8 24.7 - - + -
41A GLN 5.7 0.2 - - - +
143A VAL* 6.4 0.2 - - + -
145A LEU* 4.3 15.9 - - + -
172A ASN* 2.9 34.6 + - - +
174A THR* 1.3 80.4 - - - +
176A LEU* 1.3 66.3 + - - +
178A PRO* 3.4 11.9 - - - +
179A GLU* 3.5 12.0 - - - +
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Residues in contact with LEU 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.1 33.0 - - + -
34A LEU* 4.3 14.6 - - + -
46A VAL* 3.9 17.9 - - + -
48A LEU* 4.1 13.5 - - + -
145A LEU* 3.8 21.2 - - + +
146A THR 3.5 34.8 + - - +
147A LEU* 3.9 10.1 - - + +
172A ASN* 4.7 0.6 + - - -
174A THR 3.4 0.8 - - - -
175A ILE* 1.3 81.5 - - - +
177A HIS* 1.3 68.0 + - - +
179A GLU* 2.9 15.4 + - - +
180A ILE* 2.9 23.2 + - + -
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Residues in contact with HIS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 4.2 3.6 - + - -
146A THR 4.9 1.6 + - - -
147A LEU* 4.0 15.4 - - + +
148A ARG 3.3 21.3 - - - +
149A GLY* 3.7 20.9 - - - -
150A VAL 3.9 18.8 + - - -
151A ASN* 5.0 1.6 + - - -
158A CYS* 3.5 33.2 - - - -
173A ASN 5.6 0.2 + - - -
174A THR 4.2 1.4 + - - +
176A LEU* 1.3 76.8 - - - +
178A PRO* 1.3 75.5 - - + +
180A ILE* 3.5 6.9 - - - +
181A VAL* 3.0 52.8 + - + +
379A VAL* 6.0 0.6 - - - +
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Residues in contact with PRO 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A THR 3.4 17.7 - - - +
175A ILE* 3.4 12.1 - - - +
177A HIS* 1.3 102.4 - - + +
179A GLU* 1.3 60.4 + - + +
181A VAL* 3.8 6.8 - - + +
182A GLU* 3.1 27.9 + - - +
383A PRO* 6.5 1.1 - - + -
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 4.2 5.8 - - + -
33A ARG* 3.0 47.5 + - + +
34A LEU* 3.9 22.9 - - + -
37A ASN* 2.8 35.9 + - - +
175A ILE 3.5 16.4 - - - +
176A LEU 2.9 7.4 + - - +
178A PRO* 1.3 81.1 - - + +
180A ILE* 1.3 64.4 + - - +
182A GLU* 3.3 1.4 + - - +
183A CYS* 3.1 27.4 + - - -
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Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU* 3.8 26.6 - - + +
48A LEU* 4.4 19.3 - - + -
70A PHE* 3.7 39.0 - - + +
73A TRP* 3.7 35.4 - - + -
74A ALA* 5.1 0.2 - - + -
147A LEU* 3.7 16.2 - - + -
176A LEU* 2.9 25.5 + - + +
177A HIS 3.5 5.2 - - - +
179A GLU* 1.3 73.9 - - - +
181A VAL* 1.3 68.8 + - - +
183A CYS* 3.3 4.0 + - - +
184A ARG* 3.1 22.1 + - + +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 3.8 19.7 - - + -
177A HIS* 3.0 49.7 + - + +
178A PRO* 3.8 7.0 - - + +
180A ILE* 1.3 78.0 - - - +
182A GLU* 1.3 66.8 + - - +
184A ARG* 3.0 13.2 + - - +
185A VAL* 3.1 12.6 + - - +
379A VAL* 4.1 14.0 - - + +
380A GLY* 3.3 37.7 - - - +
383A PRO* 6.1 2.9 - - + -
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ARG* 3.6 34.6 + - - +
178A PRO 3.1 19.4 + - - +
179A GLU* 3.3 5.6 + - - +
180A ILE 3.3 0.4 - - - -
181A VAL* 1.3 79.0 - - - +
183A CYS* 1.3 62.3 + - - +
185A VAL* 3.3 11.5 + - - +
186A PHE* 3.3 34.3 - - + -
380A GLY* 4.9 0.3 - - - +
383A PRO* 4.7 9.1 - - - +
401A ARG* 2.7 45.3 + - - -
404A GLN* 5.3 0.2 + - - -
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Residues in contact with CYS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ARG* 2.9 45.2 + - - +
30A LEU* 3.8 30.3 - - - -
33A ARG* 4.0 17.7 - - - +
73A TRP* 3.4 25.8 - - + -
179A GLU 3.1 18.9 + - - -
180A ILE 3.6 4.7 - - - +
182A GLU* 1.3 78.0 - - - +
184A ARG* 1.3 62.5 + - - +
186A PHE* 3.0 9.6 + - - +
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Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A SER* 3.9 14.8 - - - -
70A PHE* 3.4 56.6 - - - +
73A TRP* 3.5 40.6 - - + +
180A ILE* 3.1 10.5 + - - +
181A VAL 3.0 10.6 + - - +
183A CYS* 1.3 77.9 - - - +
185A VAL* 1.3 53.8 + - - +
186A PHE 3.3 1.1 + - - -
187A LYS* 2.8 35.6 + - - +
191A GLU* 5.5 1.8 - - - +
374A ILE* 3.9 14.9 - - - +
375A ASP* 2.9 28.1 + - - +
378A ASP* 2.8 30.1 + - - +
379A VAL* 3.6 20.6 - - + +
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Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A VAL 3.1 13.6 + - - +
182A GLU* 3.5 12.3 - - - +
183A CYS 3.2 0.8 - - - -
184A ARG* 1.3 77.9 - - - +
186A PHE* 1.3 76.0 + - + +
187A LYS* 3.7 12.9 + - - +
371A PHE* 4.1 15.9 - - + -
379A VAL 3.5 22.0 - - - +
380A GLY* 3.8 14.4 - - - +
401A ARG* 3.9 14.1 - - - +
407A MET* 3.7 43.2 - - + +
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Residues in contact with PHE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ARG* 3.0 32.2 + - - +
33A ARG* 5.2 7.6 - - - -
182A GLU* 3.3 39.9 - - + -
183A CYS* 3.0 5.8 + - - +
184A ARG 3.2 0.9 - - - +
185A VAL* 1.3 85.0 - - + +
187A LYS* 1.3 63.4 + - - +
188A THR 3.8 0.3 + - - -
191A GLU* 3.9 1.4 - - - +
404A GLN* 3.7 51.4 - - + -
405A PRO 3.5 19.5 - - - +
406A GLY* 3.8 3.4 - - - -
407A MET* 4.1 16.8 - - + -
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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