Contacts of the helix formed by residues 160 - 170 (chain C) in PDB entry 1C7G
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 160 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158C ILE* 3.2 8.3 + - + +
159C ASP* 1.3 72.5 + - - +
161C ASN* 1.3 62.2 + - - +
163C LEU* 3.8 11.3 - - + +
164C ALA* 3.0 28.4 + - - +
196C ASN* 4.3 8.1 - - - +
199C ALA* 3.6 23.3 - - + -
200C VAL* 3.9 37.5 - - + +
203C MET* 3.8 29.0 - - + +
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Residues in contact with ASN 161 (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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159C ASP* 2.8 20.1 + - - +
160C LEU* 1.3 75.6 + - - +
162C LYS* 1.3 62.6 + - + +
164C ALA* 3.5 5.1 + - - +
165C THR* 2.9 34.9 + - - +
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Residues in contact with LYS 162 (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 ASP* 4.2 9.2 + - - +
140C ILE* 4.0 25.5 - - + +
141C VAL 3.2 27.2 + - - +
143C ASP* 3.0 35.4 + - - +
146C HIS* 5.1 5.3 - - - -
159C ASP* 3.0 30.8 + - + +
161C ASN* 1.3 81.5 - - + +
163C LEU* 1.3 56.8 + - - +
165C THR* 3.5 6.0 + - - +
166C LEU* 3.1 26.3 + - - +
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Residues in contact with LEU 163 (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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140C ILE* 4.0 24.4 - - + +
158C ILE* 4.5 3.8 - - + -
159C ASP 3.1 12.2 + - - +
160C LEU* 3.8 20.6 - - + +
162C LYS* 1.3 75.6 - - - +
164C ALA* 1.3 65.8 + - - +
166C LEU* 3.0 17.1 + - + +
167C ILE* 3.0 41.0 + - + +
175C ILE* 5.5 1.1 - - + -
178C ILE* 3.9 32.8 - - + -
200C VAL* 4.5 16.6 - - + +
203C MET* 4.0 25.8 - - + -
204C ALA 5.5 0.4 - - - +
209C ILE* 5.4 0.7 - - + -
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Residues in contact with ALA 164 (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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160C LEU 3.0 18.8 + - - +
161C ASN* 3.9 6.5 - - - +
163C LEU* 1.3 77.2 - - - +
165C THR* 1.3 57.4 + - - +
167C ILE* 3.4 7.6 + - - +
168C LYS* 3.0 31.2 + - - +
203C MET* 3.9 19.9 - - + -
207C TYR* 6.4 0.2 - - - -
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Residues in contact with THR 165 (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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161C ASN* 2.9 24.5 + - - +
162C LYS* 3.8 6.9 - - - +
164C ALA* 1.3 74.1 - - - +
166C LEU* 1.3 59.1 + - - +
168C LYS* 3.5 15.8 + - + +
169C GLU* 2.7 64.0 + - + +
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Residues in contact with LEU 166 (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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116C TYR* 4.9 7.6 - - + -
118C ALA* 3.5 33.0 - - + +
138C VAL* 4.2 30.1 - - + -
140C ILE* 4.7 1.8 - - + -
162C LYS 3.1 13.4 + - - +
163C LEU* 3.0 14.0 + - + +
165C THR* 1.3 75.8 - - - +
167C ILE* 1.3 64.8 + - - +
169C GLU* 4.8 2.0 - - - -
170C LYS* 2.9 51.7 + - + +
175C ILE* 4.1 23.5 - - + +
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Residues in contact with ILE 167 (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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163C LEU* 3.0 34.8 + - + +
164C ALA* 3.7 8.3 - - - +
165C THR 3.3 0.2 - - - -
166C LEU* 1.3 76.0 - - - +
168C LYS* 1.3 58.5 + - - +
171C GLY* 3.0 23.7 + - - -
172C ALA* 3.8 11.6 + - + +
175C ILE* 3.7 24.2 - - + -
203C MET* 4.2 12.3 - - + +
204C ALA* 5.5 0.9 - - - -
207C TYR* 3.7 52.0 - - + -
209C ILE* 3.6 17.7 - - + -
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Residues in contact with LYS 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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164C ALA* 3.0 22.2 + - - +
165C THR* 3.5 17.7 + - + +
167C ILE* 1.3 78.6 - - - +
169C GLU* 1.3 90.8 + - + +
170C LYS 3.5 0.5 + - - -
171C GLY* 4.3 2.4 + - - -
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Residues in contact with GLU 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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165C THR* 2.7 42.8 + - + +
166C LEU* 4.4 2.9 - - - +
168C LYS* 1.3 95.2 - - + +
170C LYS* 1.3 74.0 + - + +
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Residues in contact with LYS 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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116C TYR* 3.2 51.3 + - + -
138C VAL* 6.3 0.2 - - - -
166C LEU* 2.9 35.1 + - + +
169C GLU* 1.3 92.0 - - + +
171C GLY* 1.3 59.6 + - - +
173C GLU* 4.2 0.2 - - - +
174C ASN* 2.4 37.7 + - + +
175C ILE* 5.3 2.7 - - + -
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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