Contacts of the helix formed by residues 175 - 186 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C VAL* 3.7 20.4 - - + -
74C ALA* 3.8 19.5 - - + -
171C ARG 5.8 0.4 - - - +
172C LEU* 3.4 24.0 - - + +
173C TRP 3.1 1.6 - - - -
174C ARG* 1.3 74.9 - - + +
176C ARG* 1.3 62.1 - - - +
177C ARG 3.2 2.7 - - - -
178C VAL* 3.1 17.9 + - + +
179C SER* 3.2 12.9 + - - -
207C PHE* 4.1 30.5 - - + -
701C 3PE 4.0 37.5 - - + +
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Residues in contact with ARG 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C TYR* 4.6 8.3 + - - -
137C TRP* 3.8 59.9 + - + +
140C PHE* 4.3 14.8 - - + -
141C ASP* 4.1 14.6 - - - +
173C TRP 3.8 16.2 + - - +
174C ARG* 4.7 3.3 - - - +
175C LEU* 1.3 76.4 - - - +
177C ARG* 1.3 101.4 + - + +
178C VAL 3.2 0.2 - - - -
179C SER* 3.8 9.6 - - - +
180C SER* 2.9 36.1 + - - -
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Residues in contact with ARG 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLU* 5.6 8.5 + - - +
66C LEU* 4.4 19.9 - - + +
67C VAL* 4.2 14.4 - - + +
70C VAL* 4.2 11.9 - - + -
102C PHE* 3.8 34.0 + - - -
105C ASP* 3.5 32.2 + - - +
106C ILE* 6.0 2.8 - - - +
109C THR* 5.6 1.2 - - - +
133C TYR* 5.2 4.9 + - - -
141C ASP* 5.3 4.8 - - - +
174C ARG* 3.7 14.6 + - - +
175C LEU 3.2 0.6 - - - -
176C ARG* 1.3 119.4 - - - +
178C VAL* 1.3 60.6 + - + +
180C SER* 3.8 7.3 + - - -
181C LEU* 3.6 19.1 + - - +
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Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C VAL* 4.0 27.1 - - + +
70C VAL* 3.7 26.9 - - + -
71C ILE* 4.5 10.5 - - + -
175C LEU* 3.1 11.9 + - + +
177C ARG* 1.3 78.7 - - - +
179C SER* 1.3 64.3 + - - +
180C SER 3.3 0.2 - - - -
181C LEU* 3.1 16.6 + - + +
182C PHE* 3.2 35.2 + - + -
701C 3PE 4.2 26.5 - - + -
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Residues in contact with SER 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C LEU 3.2 15.0 + - - -
176C ARG* 4.3 7.6 - - - -
177C ARG 3.6 0.2 - - - -
178C VAL* 1.3 77.1 - - - +
180C SER* 1.3 58.4 + - - +
181C LEU 3.2 0.6 + - - -
182C PHE* 3.7 5.6 + - - +
183C ALA* 3.5 18.7 + - - +
200C LYS* 5.6 1.6 - - - -
701C 3PE 3.8 43.9 + - - +
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Residues in contact with SER 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C ARG* 2.9 27.6 + - - -
177C ARG* 3.8 8.5 + - - -
178C VAL 3.3 0.2 - - - -
179C SER* 1.3 74.8 - - - +
181C LEU* 1.3 59.9 + - - +
183C ALA* 4.1 10.7 - - - +
184C ARG* 3.8 27.7 + - - +
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Residues in contact with LEU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLU 5.4 1.1 - - - +
64C MET* 4.2 27.1 - - + -
67C VAL* 3.7 32.1 - - + -
177C ARG 3.6 13.6 + - - +
178C VAL* 3.1 9.9 + - + +
180C SER* 1.3 79.0 + - - +
182C PHE* 1.3 71.7 + - + +
183C ALA 3.2 1.6 - - - -
184C ARG* 3.3 21.1 + - - +
185C LEU* 3.0 54.3 + - + +
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Residues in contact with PHE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C VAL* 3.2 40.1 + - + +
179C SER 3.7 5.6 + - - +
180C SER 3.6 0.2 - - - -
181C LEU* 1.3 86.9 - - + +
183C ALA* 1.3 61.6 + - - +
185C LEU* 4.3 3.0 - - + +
186C GLU* 3.3 31.3 + - - +
196C ILE* 4.3 28.7 - - + +
199C THR* 4.1 37.5 - - + -
200C LYS* 4.0 40.6 - - + -
203C SER* 4.5 9.6 - - - -
701C 3PE 4.3 13.7 - - + -
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Residues in contact with ALA 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C SER 3.5 13.7 + - - +
180C SER* 4.5 8.5 - - - +
181C LEU 3.2 0.6 - - - -
182C PHE* 1.3 80.1 - - - +
184C ARG* 1.3 56.4 + - - +
186C GLU* 3.9 10.7 + - - +
187C LYS* 2.7 37.8 + - - +
200C LYS* 5.9 2.0 - - - +
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Residues in contact with ARG 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ARG* 5.6 7.1 - - - +
63C GLU* 3.7 33.0 + - - +
64C MET* 5.7 4.6 - - - +
180C SER* 3.8 24.9 + - - +
181C LEU* 3.3 24.5 + - - +
182C PHE 3.3 0.2 - - - -
183C ALA* 1.3 78.2 - - - +
185C LEU* 1.3 74.4 + - + +
186C GLU 3.2 1.3 + - - -
187C LYS* 3.4 12.8 + - - +
188C ASP* 3.4 21.4 + - - +
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Residues in contact with LEU 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C MET* 6.1 4.9 - - + -
181C LEU* 3.0 41.5 + - + +
182C PHE* 4.5 5.4 - - + +
184C ARG* 1.3 85.5 - - + +
186C GLU* 1.3 63.5 + - - +
187C LYS 3.3 0.4 + - - -
188C ASP* 3.6 23.0 + - - +
191C PHE* 3.7 47.3 - - + +
192C ASN 4.6 1.0 - - - +
196C ILE* 4.0 34.5 - - + +
310D ARG* 4.2 1.2 + - - -
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Residues in contact with GLU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C PHE 3.3 19.8 + - - +
183C ALA* 4.1 9.7 - - - +
184C ARG 3.2 0.8 - - - -
185C LEU* 1.3 80.0 - - - +
187C LYS* 1.3 56.2 + - + +
192C ASN 5.6 0.4 - - - -
193C TYR* 3.9 26.1 + - + -
196C ILE* 3.8 17.2 - - + +
197C ARG* 2.8 41.4 + - - -
200C LYS* 4.0 11.5 + - - +
701C 3PE 5.4 3.8 - - - -
306D THR* 4.3 16.9 + - + +
310D ARG* 2.4 35.7 + - - +
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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