Contacts of the helix formed by residues 175 - 186 (chain B) in PDB entry 7CAL
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 LEU 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B VAL* 3.7 20.9 - - + +
74B ALA* 3.8 20.2 - - + -
172B LEU* 3.4 25.5 + - + +
173B TRP 3.1 2.0 - - - -
174B ARG* 1.3 75.5 - - + +
176B ARG* 1.3 62.5 + - - +
177B ARG 3.2 2.9 - - - -
178B VAL* 3.1 17.4 + - + +
179B SER* 3.2 13.4 + - - -
207B PHE* 4.1 30.3 - - + -
701B 3PE 4.2 35.9 - - + +
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Residues in contact with ARG 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B TYR* 4.6 7.9 + - - -
137B TRP* 3.8 58.8 + - + +
140B PHE* 4.3 15.5 - - + -
141B ASP* 4.1 14.8 - - - +
173B TRP 3.8 16.7 + - - +
174B ARG* 4.7 3.7 - - - +
175B LEU* 1.3 75.8 - - - +
177B ARG* 1.3 99.7 + - - +
178B VAL 3.2 0.2 - - - -
179B SER* 3.8 8.1 - - - +
180B SER* 2.9 36.4 + - - -
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Residues in contact with ARG 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLU* 5.6 8.3 + - - +
66B LEU* 4.4 20.4 - - - +
67B VAL* 4.2 14.4 - - + +
70B VAL* 4.2 11.0 - - + -
102B PHE* 3.8 34.3 + - - -
105B ASP* 3.5 32.9 + - - +
106B ILE* 6.0 2.4 - - - +
109B THR* 5.6 1.2 - - - +
133B TYR* 5.2 4.8 + - - -
141B ASP* 5.3 4.8 - - - +
174B ARG* 3.7 14.4 + - - +
175B LEU 3.2 0.6 - - - -
176B ARG* 1.3 119.0 - - - +
178B VAL* 1.3 60.4 + - - +
180B SER* 3.8 7.4 + - - -
181B LEU* 3.6 19.1 + - - +
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Residues in contact with VAL 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 4.0 27.8 - - + +
70B VAL* 3.7 26.7 - - + -
71B ILE* 4.5 10.8 - - + -
175B LEU* 3.1 12.7 + - + +
177B ARG* 1.3 79.0 - - - +
179B SER* 1.3 64.0 + - - +
180B SER 3.3 0.2 - - - -
181B LEU* 3.1 16.0 + - + +
182B PHE* 3.2 35.9 + - + -
701B 3PE 4.2 26.2 - - + -
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B LEU 3.2 15.6 + - - -
176B ARG* 3.6 7.4 + - - -
178B VAL* 1.3 77.1 - - - +
180B SER* 1.3 58.8 + - - +
181B LEU 3.2 1.2 + - - -
182B PHE* 3.7 4.6 + - - +
183B ALA* 3.5 18.9 + - - +
200B LYS* 5.6 0.7 - - - -
701B 3PE 3.1 41.7 + - - +
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ARG* 2.9 27.1 + - - -
177B ARG* 3.8 8.9 + - - -
179B SER* 1.3 75.0 - - - +
181B LEU* 1.3 58.6 + - - +
182B PHE 3.6 0.2 - - - -
183B ALA* 4.1 10.1 - - - +
184B ARG* 3.8 27.5 + - - +
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Residues in contact with LEU 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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63B GLU 5.4 1.3 - - - +
64B MET* 4.2 26.7 - - + -
67B VAL* 3.7 32.5 - - + -
177B ARG 3.6 14.0 + - - +
178B VAL* 3.1 9.7 + - + +
180B SER* 1.3 78.6 + - - +
182B PHE* 1.3 70.4 + - + +
183B ALA 3.2 1.3 - - - -
184B ARG* 3.7 21.8 - - - +
185B LEU* 3.0 53.4 + - + +
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Residues in contact with PHE 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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178B VAL* 3.2 41.5 + - + +
179B SER* 3.7 5.4 + - - +
181B LEU* 1.3 87.5 - - + +
183B ALA* 1.3 62.2 + - - +
185B LEU* 4.3 3.5 - - + +
186B GLU* 3.3 32.3 + - - +
196B ILE* 4.3 27.7 - - + +
199B THR* 4.1 38.4 - - + -
200B LYS* 4.0 39.7 - - + -
203B SER* 4.5 8.5 - - - -
701B 3PE 4.4 14.4 - - + -
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Residues in contact with ALA 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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179B SER 3.5 14.5 + - - +
180B SER* 4.5 8.3 - - - +
181B LEU 3.2 0.4 - - - -
182B PHE* 1.3 80.7 - - - +
184B ARG* 1.3 56.5 + - - +
186B GLU* 3.9 9.9 + - - +
187B LYS* 2.7 37.6 + - - +
200B LYS* 5.9 1.7 - - - +
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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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60B ARG* 5.6 6.9 - - - +
63B GLU* 3.7 32.8 + - - +
64B MET* 5.7 4.2 - - - +
180B SER* 3.8 24.9 + - - +
181B LEU* 3.3 24.9 + - - +
182B PHE 3.3 0.2 - - - -
183B ALA* 1.3 79.1 - - - +
185B LEU* 1.3 74.3 + - + +
186B GLU 3.2 1.4 + - - -
187B LYS* 3.4 12.4 + - - +
188B ASP* 3.4 21.4 + - - +
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Residues in contact with LEU 185 (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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64B MET* 6.1 4.5 - - + -
181B LEU* 3.0 43.2 + - + +
182B PHE* 4.5 5.6 - - + +
183B ALA 3.5 0.2 - - - -
184B ARG* 1.3 85.1 - - + +
186B GLU* 1.3 62.8 + - - +
187B LYS 3.3 0.4 + - - -
188B ASP* 3.6 23.6 + - - +
191B PHE* 3.7 46.3 - - + +
192B ASN 4.6 0.7 - - - +
196B ILE* 4.0 34.1 - - + +
310C ARG* 4.2 1.6 + - - -
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Residues in contact with GLU 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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182B PHE 3.3 20.9 + - - +
183B ALA* 4.1 9.8 - - - +
184B ARG 3.2 1.0 - - - -
185B LEU* 1.3 79.8 - - - +
187B LYS* 1.3 54.8 + - + +
192B ASN 5.6 0.2 - - - -
193B TYR* 3.9 25.8 + - + -
196B ILE* 3.8 18.5 - - + +
197B ARG* 2.8 39.8 + - - -
200B LYS* 4.0 11.4 + - - +
701B 3PE 5.4 4.3 - - - -
303C THR* 6.2 0.2 - - - +
306C THR* 4.3 17.3 + - + +
310C ARG* 2.4 36.2 + - - +
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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