Contacts of the helix formed by residues 167 - 174 (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 167 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C PHE* 4.4 40.9 - - + -
163C GLY* 3.6 22.9 - - - +
164C PHE* 3.8 14.2 + - + +
165C ARG 3.2 0.4 - - - -
166C ILE* 1.3 81.2 - - + +
168C SER* 1.3 58.2 + - - +
169C MET 3.2 1.3 - - - -
170C LEU* 3.4 47.3 + - + +
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Residues in contact with SER 168 (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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77C CYS* 3.3 19.5 + - - -
80C GLN* 4.4 5.5 + - - -
148C PHE* 5.3 2.7 - - - +
149C GLN* 4.8 18.9 - - - +
164C PHE 4.1 2.1 + - - -
165C ARG* 3.2 21.4 + - - -
166C ILE 3.1 1.2 - - - -
167C LEU* 1.3 74.5 - - - +
169C MET* 1.3 57.5 + - - +
170C LEU 3.2 5.5 + - - -
171C ARG* 3.2 34.2 + - - +
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Residues in contact with MET 169 (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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77C CYS* 3.3 35.9 - - - +
78C PRO* 3.7 6.1 - - + -
81C PHE* 3.6 31.4 - - + -
165C ARG 4.6 1.6 - - - +
166C ILE* 2.9 28.3 + - + +
168C SER* 1.3 76.7 - - - +
170C LEU* 1.3 60.0 + - + +
171C ARG 3.1 5.8 - - - -
172C LEU* 3.1 41.0 + - + +
173C TRP* 4.4 1.9 + - - -
215C PHE* 3.6 30.3 - - + -
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Residues in contact with LEU 170 (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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143C CYS* 3.5 32.5 - - + +
144C SER* 3.1 23.3 + - - -
148C PHE* 5.0 6.5 - - + -
166C ILE 5.3 2.0 - - - +
167C LEU* 3.4 41.5 - - + +
168C SER 3.2 1.2 - - - -
169C MET* 1.3 76.9 - - + +
171C ARG* 1.3 55.7 + - - +
172C LEU 3.1 4.9 - - - -
173C TRP* 3.1 47.3 + - + +
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Residues in contact with ARG 171 (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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72C TYR* 5.7 0.4 - - - -
73C SER* 3.5 31.2 + - - +
74C ALA* 5.2 0.9 - - - +
76C ILE* 3.6 32.5 - - - +
77C CYS* 3.6 29.3 + - - +
80C GLN* 3.4 19.8 - - - +
95C ASP* 4.4 17.4 + - - +
98C VAL* 6.1 1.6 - - - +
99C ASN* 5.4 9.4 - - - +
144C SER* 4.3 5.4 - - - +
168C SER* 3.2 31.1 + - - +
169C MET 3.1 1.2 - - - -
170C LEU* 1.3 76.0 - - - +
172C LEU* 1.3 56.7 + - - +
173C TRP 3.3 1.1 - - - -
174C ARG* 3.3 48.6 - - - +
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Residues in contact with LEU 172 (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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74C ALA* 3.8 29.4 - - + +
77C CYS* 4.0 17.2 - - + -
78C PRO* 4.9 2.9 - - + -
169C MET* 3.1 30.4 + - + +
170C LEU 3.1 1.4 - - - -
171C ARG* 1.3 74.0 - - - +
173C TRP* 1.3 67.4 + - + +
174C ARG 3.2 2.2 - - - -
175C LEU* 3.4 30.1 - - + +
207C PHE* 3.7 35.7 - - + -
211C CYS* 4.7 12.3 - - - -
215C PHE* 5.7 0.9 - - + -
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Residues in contact with TRP 173 (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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139C ALA 5.5 0.7 - - - -
140C PHE* 3.2 70.1 - + + -
143C CYS* 4.4 19.3 - - + -
144C SER* 3.3 12.3 - - - +
169C MET 5.4 1.1 - - - -
170C LEU* 3.1 44.3 + - + +
172C LEU* 1.3 80.2 - - + +
174C ARG* 1.3 55.4 + - - +
175C LEU* 3.1 8.5 + - - -
176C ARG* 3.8 8.4 + - - +
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Residues in contact with ARG 174 (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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70C VAL* 3.3 27.2 - - + +
73C SER* 3.3 32.1 + - - +
98C VAL* 3.9 18.8 - - - +
99C ASN* 3.4 20.6 + - - +
102C PHE* 3.7 47.4 - - + +
144C SER* 2.4 38.3 + - - -
145C THR* 4.4 0.4 - - - +
170C LEU 4.4 0.8 + - - -
171C ARG* 3.3 38.3 + - - +
173C TRP* 1.3 74.4 - - - +
175C LEU* 1.3 58.3 + - + +
176C ARG* 3.2 10.3 + - - +
177C ARG* 3.7 13.5 + - - +
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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