Contacts of the helix formed by residues 153 - 159 (chain C) in PDB entry 1C2O
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 VAL 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C CYS* 4.6 7.2 - - + +
70C TYR 3.7 18.6 - - - +
71C GLN* 3.8 13.9 - - + +
119C TYR* 4.2 11.2 - - + +
123C PHE* 3.4 16.6 - - - +
124C TYR 3.5 17.5 - - - +
125C SER* 3.1 28.9 - - - +
126C GLY 4.9 0.4 - - - +
151C TYR* 3.3 16.7 + - + +
152C ARG* 1.3 73.9 - - - +
154C GLY* 1.3 65.1 + - - +
156C PHE* 3.6 12.6 + - - +
157C GLY* 2.9 16.0 + - - -
158C PHE* 4.3 2.9 - - - -
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Residues in contact with GLY 154 (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 TYR 5.5 0.9 - - - -
71C GLN* 6.5 0.2 - - - -
123C PHE 2.8 16.2 + - - -
124C TYR* 3.6 3.7 - - - +
153C VAL* 1.3 75.2 - - - +
155C THR* 1.3 57.5 + - - -
156C PHE* 5.0 2.5 - - - -
157C GLY 3.0 0.7 + - - -
158C PHE* 2.7 30.3 + - - +
285C GLU* 3.7 23.1 - - - -
299C PHE* 3.6 12.4 - - - +
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Residues in contact with THR 155 (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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47C PHE* 3.6 9.2 - - - -
154C GLY* 1.3 71.2 - - - -
156C PHE* 1.3 74.3 + - - +
159C LEU* 2.7 61.1 + - + +
251C LEU* 3.9 15.9 - - + -
281C LEU* 3.8 27.3 - - + +
282C VAL* 4.8 0.9 + - - +
285C GLU* 4.6 7.7 + - + +
299C PHE* 3.8 27.9 - - + +
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Residues in contact with PHE 156 (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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46C ARG* 3.8 25.1 - - + -
47C PHE* 4.3 14.1 + + - -
70C TYR* 3.4 52.0 - + + +
94C GLU* 3.6 22.4 - - + +
152C ARG* 3.8 24.5 + - + -
153C VAL 3.7 8.3 - - - +
154C GLY* 3.2 2.2 - - - -
155C THR* 1.3 93.7 - - - +
157C GLY* 1.3 57.9 + - - +
171C VAL* 3.4 15.1 - - - +
278C ALA* 3.7 34.5 - - + -
281C LEU* 4.0 10.3 - - + -
282C VAL* 4.0 9.0 - - + -
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Residues in contact with GLY 157 (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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152C ARG* 3.0 32.7 - - - +
153C VAL 2.9 11.1 + - - -
154C GLY 3.6 1.6 - - - -
156C PHE* 1.3 80.0 - - - +
158C PHE* 1.4 64.1 + - - +
169C GLY* 5.3 0.2 - - - -
171C VAL* 3.2 14.0 + - - +
172C GLY 2.9 24.0 + - - -
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Residues in contact with PHE 158 (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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123C PHE* 3.5 47.3 - + - -
151C TYR* 4.7 5.4 - + - -
152C ARG 3.6 16.4 - - - -
153C VAL* 4.3 1.8 - - - -
154C GLY 2.7 14.5 + - - +
157C GLY* 1.4 81.7 - - - +
159C LEU* 1.3 66.6 - - - +
160C ALA* 2.9 12.6 + - - +
169C GLY* 4.4 2.2 - - - -
170C ASN* 3.9 14.9 + - - +
172C GLY* 4.0 13.2 - - - -
173C LEU* 4.0 19.3 - - + -
299C PHE* 3.7 11.9 - - - -
300C VAL* 3.5 29.7 - - - +
301C PRO* 3.4 35.7 - - + -
302C VAL* 5.6 0.9 - - - +
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Residues in contact with LEU 159 (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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47C PHE* 4.2 20.1 - - + +
155C THR* 2.7 54.9 + - + +
157C GLY 4.0 0.4 - - - -
158C PHE* 1.3 71.2 - - - +
160C ALA* 1.3 65.3 + - - +
161C LEU* 4.0 15.5 - - + -
167C ALA* 4.2 18.8 - - + +
169C GLY* 4.4 4.7 + - - -
248C ALA* 4.0 20.4 - - + -
251C LEU* 4.0 17.3 - - + -
273C LEU* 4.1 22.2 - - + -
299C PHE* 3.6 20.6 - - + -
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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