Contacts of the helix formed by residues 157 - 167 (chain C) in PDB entry 3L73
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 ILE 157 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154C ILE* 3.6 21.5 - - + -
155C PRO 2.6 21.3 + - - +
156C TYR* 1.3 77.5 - - + +
158C GLY* 1.3 63.1 + - - +
160C THR* 4.1 9.6 - - + -
161C LEU* 3.2 26.8 + - + +
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Residues in contact with GLY 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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151C PHE 3.5 13.7 - - - -
152C SER* 3.8 8.3 - - - -
154C ILE* 3.2 25.2 + - - -
156C TYR 3.1 6.5 - - - +
157C ILE* 1.3 73.8 - - - +
159C HIS* 1.3 53.5 + - - +
160C THR 2.6 17.1 + - - -
161C LEU* 3.1 13.6 + - - +
162C VAL* 3.2 13.9 + - - +
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Residues in contact with HIS 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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152C SER* 3.8 36.1 + - - +
156C TYR 4.8 2.5 + - - +
158C GLY* 1.3 70.7 - - - +
160C THR* 1.3 58.7 + - - +
162C VAL* 4.0 4.0 - - - +
163C GLU* 3.3 36.3 + - - +
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Residues in contact with THR 160 (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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156C TYR 5.2 3.3 + - - -
157C ILE* 4.1 12.7 - - - +
158C GLY 2.6 6.5 + - - -
159C HIS* 1.3 72.9 - - - +
161C LEU* 1.3 68.9 + - - +
162C VAL 2.6 6.1 + - - -
163C GLU* 2.8 15.1 + - - +
164C TRP* 2.9 17.2 + - + +
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Residues in contact with LEU 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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151C PHE* 4.1 23.3 - - + -
154C ILE* 4.0 27.1 - - + -
157C ILE* 3.2 19.4 + - + +
158C GLY* 3.1 4.3 + - - +
160C THR* 1.3 81.1 - - - +
162C VAL* 1.3 59.6 + - - +
164C TRP* 3.6 24.4 - - + +
165C ALA* 3.2 22.6 + - + +
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Residues in contact with VAL 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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148C THR* 3.7 11.0 - - - +
149C ASN* 5.0 2.0 - - - +
151C PHE* 3.5 19.1 - - + -
152C SER* 3.2 38.6 - - - +
158C GLY 3.2 7.8 + - - +
159C HIS* 4.0 6.7 - - - +
160C THR 2.6 4.9 + - - -
161C LEU* 1.3 70.5 - - - +
163C GLU* 1.3 57.5 + - + +
164C TRP 2.9 4.3 - - - -
165C ALA* 3.0 20.9 + - - +
166C TRP* 3.0 55.9 + - + -
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Residues in contact with GLU 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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159C HIS* 3.3 23.9 + - - +
160C THR* 2.8 9.0 + - - +
162C VAL* 1.3 77.8 - - + +
164C TRP* 1.3 59.8 + - - +
166C TRP* 4.1 12.1 - - + +
167C GLY* 3.5 1.9 + - - -
168C GLY* 3.4 34.4 + - - +
169C PHE* 3.3 39.3 - - + +
63R SER* 4.9 0.9 - - - -
64R ALA* 4.7 6.4 + - - +
92R ARG* 5.1 2.4 + - - -
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Residues in contact with TRP 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 THR* 2.9 20.1 + - + +
161C LEU* 3.6 24.7 - - + +
163C GLU* 1.3 79.9 - - - +
165C ALA* 1.3 60.0 + - + +
167C GLY 3.3 1.4 + - - -
178C ARG* 2.6 30.5 + - - -
59R ILE* 3.1 52.6 + - + +
60R SER* 5.6 0.2 - - - -
62R LEU* 3.3 44.0 - - + +
63R SER* 3.8 28.0 - - - +
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Residues in contact with ALA 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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148C THR* 5.9 6.5 - - + -
151C PHE* 5.7 7.9 - - + -
161C LEU* 3.2 14.2 + - + +
162C VAL* 3.0 11.3 + - - +
164C TRP* 1.3 88.0 - - + +
166C TRP* 1.3 61.9 + - + +
175C THR* 4.2 4.5 - - - +
178C ARG* 3.0 28.4 + - - +
179C PHE* 4.9 7.1 - - + -
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Residues in contact with TRP 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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145C THR* 4.7 3.4 - - + -
148C THR* 2.7 37.0 + - + -
149C ASN* 3.8 33.4 - - - -
162C VAL* 3.0 41.6 + - + +
163C GLU* 4.4 5.8 - - + -
165C ALA* 1.3 80.1 - - + +
167C GLY* 1.3 62.0 + - - +
168C GLY 4.0 11.4 - - - +
169C PHE* 3.2 35.4 - - - -
170C SER* 3.9 14.7 - - - +
171C VAL* 3.4 25.5 - - + +
174C PRO* 3.7 3.6 - - - +
175C THR* 2.6 46.0 + - + +
178C ARG* 3.8 1.3 - - - -
179C PHE* 6.0 0.2 - + - -
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Residues in contact with GLY 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 GLU 3.5 4.9 + - - -
164C TRP 3.3 3.2 + - - -
165C ALA 3.3 0.2 - - - -
166C TRP* 1.3 80.2 - - - +
168C GLY* 1.3 57.5 + - - +
174C PRO* 3.7 17.6 - - - +
178C ARG* 3.3 30.0 - - - +
62R LEU 3.8 8.3 - - - -
63R SER 4.7 0.4 - - - -
64R ALA* 3.8 17.9 - - - +
65R SER 4.7 0.5 + - - -
68R VAL* 4.3 7.1 - - - +
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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