Contacts of the helix formed by residues 175 - 186 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 4.0 14.1 - - + -
37B ASN* 4.0 11.6 + - - +
39B ALA* 3.7 37.9 - - + +
40B VAL* 3.7 23.6 - - + -
145B LEU* 4.2 16.6 - - + -
172B ASN* 2.9 32.8 + - - +
174B THR* 1.3 79.2 - - - +
176B LEU* 1.3 65.8 + - - +
177B HIS 3.5 0.2 + - - -
178B PRO* 3.5 7.9 - - - +
179B GLU* 3.5 14.6 - - - +
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.1 34.8 - - + -
34B LEU* 4.3 7.4 - - + -
46B VAL* 3.9 25.1 - - + -
48B LEU* 4.1 15.3 - - + -
145B LEU* 3.9 20.6 - - + +
146B THR 3.5 33.3 + - - +
147B LEU* 4.0 8.7 - - + +
172B ASN* 4.7 0.6 + - - -
174B THR 3.5 0.6 - - - -
175B ILE* 1.3 82.5 - - - +
177B HIS* 1.3 68.2 + - - +
179B GLU* 3.0 6.6 + - - +
180B ILE* 2.9 31.2 + - + +
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Residues in contact with HIS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 4.2 4.2 - + - -
146B THR 4.9 1.2 + - - -
147B LEU* 4.0 16.1 - - + +
148B ARG 3.2 21.3 - - - +
149B GLY* 3.7 19.8 - - - -
150B VAL 3.9 18.1 + - - -
151B ASN* 5.6 0.8 - - - -
158B CYS* 3.6 33.1 - - - -
174B THR 4.1 2.3 + - - +
176B LEU* 1.3 77.9 - - - +
178B PRO* 1.3 75.0 - - + +
180B ILE* 3.5 6.5 + - - +
181B VAL* 3.0 51.8 + - + +
379B VAL* 6.1 0.8 - - - +
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Residues in contact with PRO 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B THR 3.4 17.3 - - - +
175B ILE* 3.5 10.1 - - - +
177B HIS* 1.3 102.1 - - + +
179B GLU* 1.3 60.2 + - + +
181B VAL* 3.6 6.6 + - + +
182B GLU* 3.0 29.8 + - - +
383B PRO* 6.5 0.7 - - + -
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Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.3 4.7 - - + -
33B ARG* 3.2 55.6 + - + +
34B LEU* 4.0 18.8 - - + -
37B ASN* 2.8 38.1 + - - +
175B ILE 3.5 16.4 - - - +
176B LEU 3.0 7.2 + - - +
178B PRO* 1.3 80.2 - - + +
180B ILE* 1.3 66.1 + - - +
182B GLU* 3.3 2.0 + - - +
183B CYS* 3.0 19.9 + - - -
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Residues in contact with ILE 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.9 26.4 - - + +
48B LEU* 4.5 20.2 - - + -
70B PHE* 3.8 33.0 - - + +
73B TRP* 3.8 34.1 - - + -
74B ALA* 5.1 0.2 - - + -
147B LEU* 3.7 23.1 - - + -
176B LEU* 2.9 25.8 + - + +
177B HIS 3.5 5.8 - - - +
179B GLU* 1.3 72.7 - - - +
181B VAL* 1.3 68.8 + - - +
183B CYS* 3.3 4.0 + - - +
184B ARG* 3.0 22.5 + - - +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PHE* 3.8 19.3 - - + -
177B HIS* 3.0 48.8 + - + +
178B PRO* 3.8 6.5 - - + +
180B ILE* 1.3 76.9 - - - +
182B GLU* 1.3 66.9 + - - +
184B ARG* 3.0 12.8 + - - +
185B VAL* 3.0 13.7 + - + +
379B VAL* 4.0 14.1 - - + +
380B GLY* 3.3 36.8 - - - +
383B PRO* 6.1 2.5 - - + -
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Residues in contact with GLU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG* 3.6 34.5 - - - +
178B PRO 3.0 18.8 + - - +
179B GLU* 3.3 5.6 + - - +
181B VAL* 1.3 78.7 - - - +
183B CYS* 1.3 61.7 + - - +
185B VAL* 3.2 7.7 + - - +
186B PHE* 3.2 39.1 - - + -
383B PRO* 4.8 8.7 - - - +
401B ARG* 2.7 45.1 + - - -
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Residues in contact with CYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 3.1 28.9 + - - +
30B LEU* 3.9 30.7 - - - -
33B ARG* 3.8 20.2 - - - +
73B TRP* 3.4 26.4 + - + -
179B GLU 3.0 18.8 + - - -
180B ILE 3.6 5.6 - - - +
181B VAL 3.2 0.2 - - - -
182B GLU* 1.3 77.2 - - - +
184B ARG* 1.3 57.9 + - - +
186B PHE* 3.0 26.2 + - - +
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Residues in contact with ARG 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B SER* 3.8 16.0 - - - -
70B PHE* 3.5 56.2 - - - +
73B TRP* 3.5 41.9 + - + +
180B ILE* 3.0 11.5 + - - +
181B VAL 3.0 9.8 + - - +
183B CYS* 1.3 75.9 - - - +
185B VAL* 1.3 58.4 + - - +
186B PHE 3.3 0.9 + - - -
187B LYS* 2.8 29.3 + - - +
191B GLU* 5.4 1.8 - - - +
374B ILE* 3.6 22.9 - - - +
375B ASP* 3.0 18.8 + - - -
378B ASP* 2.8 30.6 + - - +
379B VAL* 3.7 19.9 - - + +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B VAL 3.0 18.9 + - - +
182B GLU* 3.5 9.6 - - - +
183B CYS 3.2 0.4 - - - -
184B ARG* 1.3 78.4 - - - +
186B PHE* 1.3 75.2 + - + +
187B LYS* 3.7 12.0 + - - +
371B PHE* 4.1 14.3 - - + -
379B VAL 3.5 22.7 - - - +
380B GLY* 3.8 14.6 - - - +
401B ARG* 3.9 13.9 - - - +
406B GLY 3.7 0.9 - - - +
407B MET* 3.6 45.2 - - + -
408B VAL 4.5 0.3 + - - -
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Residues in contact with PHE 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 2.8 38.0 + - - +
33B ARG* 5.2 7.2 - - - -
182B GLU* 3.2 46.4 - - + -
183B CYS* 3.0 8.4 + - - +
185B VAL* 1.3 85.7 - - + +
187B LYS* 1.3 64.3 + - - +
191B GLU* 4.0 0.9 - - - +
404B GLN* 3.8 42.8 - - + -
405B PRO 3.3 28.0 - - - +
406B GLY* 3.8 2.7 - - - -
407B MET* 4.1 18.2 - - + -
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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