Contacts of the helix formed by residues 148 - 161 (chain C) in PDB entry 1XS2
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 ASP 148 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C GLN 3.3 1.8 + - - -
147C ALA* 1.3 87.0 - - - +
149C GLU* 1.3 65.9 + - + +
150C GLN* 3.3 8.2 + - - +
151C ALA* 2.6 40.4 + - - +
152C THR* 3.1 21.5 + - - -
175C TRP* 3.6 17.0 - - + -
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Residues in contact with GLU 149 (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 ASP* 1.3 75.2 - - - +
150C GLN* 1.3 61.4 + - - +
152C THR* 3.6 5.5 - - - -
153C VAL* 3.2 28.6 + - - +
175C TRP* 3.7 20.2 - - + -
178C GLN* 3.6 22.5 - - + +
179C PRO* 5.3 2.0 - - - -
181C ARG* 3.4 27.0 + - - -
182C ALA* 3.9 20.7 - - + +
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Residues in contact with GLN 150 (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 ASP* 3.3 7.8 + - - +
149C GLU* 1.3 77.1 - - - +
151C ALA* 1.3 61.2 + - - +
153C VAL* 3.2 17.1 + - - +
154C ASP* 2.9 61.2 + - - +
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Residues in contact with ALA 151 (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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146C GLN* 4.1 15.8 + - + +
147C ALA* 4.4 7.2 - - + +
148C ASP* 2.6 32.8 + - - +
150C GLN* 1.3 72.8 - - - +
152C THR* 1.3 57.2 + - - +
154C ASP* 3.5 11.0 + - - +
155C LEU* 3.0 29.1 + - - +
158C ARG* 4.1 3.0 + - - +
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Residues in contact with THR 152 (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 LEU* 5.1 0.4 - - + +
146C GLN* 3.1 28.1 + - + +
148C ASP 3.1 18.8 + - - -
149C GLU* 3.6 7.4 - - - -
151C ALA* 1.3 74.2 - - - +
153C VAL* 1.3 60.0 + - - +
155C LEU* 3.2 3.6 + - - +
156C VAL* 2.9 32.2 + - - +
169C LEU* 4.1 20.2 - - + -
175C TRP* 4.5 3.6 + - - -
179C PRO* 4.2 24.0 - - + +
183C THR* 3.5 21.5 - - - +
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Residues in contact with VAL 153 (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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149C GLU 3.2 15.5 + - - +
150C GLN* 3.2 23.6 + - - +
152C THR* 1.3 75.8 - - - +
154C ASP* 1.3 58.5 + - - +
156C VAL* 3.4 7.9 + - - +
157C ARG* 2.9 37.8 + - - +
182C ALA* 3.7 34.3 - - + +
183C THR* 3.8 9.0 - - - +
186C ALA* 3.8 23.6 - - + -
187C PHE* 4.1 9.3 - - + -
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Residues in contact with ASP 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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150C GLN* 2.9 55.2 + - - +
151C ALA* 3.6 7.9 - - - +
153C VAL* 1.3 76.1 - - - +
155C LEU* 1.3 63.5 + - - +
157C ARG* 3.1 22.6 + - - +
158C ARG* 3.1 39.9 + - - +
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Residues in contact with LEU 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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143C LEU* 4.0 29.6 - - + -
144C GLY 5.4 0.2 - - - +
146C GLN* 3.5 35.0 - - + +
151C ALA 3.0 17.9 + - - +
152C THR 3.7 4.3 - - - +
154C ASP* 1.3 76.6 - - - +
156C VAL* 1.3 60.0 + - - +
158C ARG* 3.1 30.3 - - - +
159C HIS* 2.8 45.7 + - + -
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Residues in contact with VAL 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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143C LEU* 3.7 13.2 - - + -
152C THR 2.9 18.7 + - - +
153C VAL* 3.6 6.5 - - - +
155C LEU* 1.3 74.7 - - - +
157C ARG* 1.3 59.1 + - - +
159C HIS* 3.0 6.7 + - - +
160C VAL* 2.9 37.8 + - + +
167C ILE* 3.9 12.5 - - + +
169C LEU* 3.7 30.5 - - + -
183C THR* 4.0 22.2 - - + +
187C PHE* 3.8 21.3 - - + -
190C ILE* 4.5 2.5 - - + -
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Residues in contact with ARG 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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153C VAL* 2.9 24.6 + - - +
154C ASP* 3.1 13.5 + - - +
156C VAL* 1.3 72.8 - - - +
158C ARG* 1.3 66.3 + - - +
160C VAL* 3.2 1.4 + - - +
161C GLU* 2.9 57.8 + - + +
186C ALA* 4.4 13.7 + - - +
187C PHE* 3.7 41.5 - - + -
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Residues in contact with ARG 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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146C GLN* 6.0 0.2 - - - +
151C ALA* 4.1 3.2 + - - +
154C ASP* 3.1 30.3 + - - +
155C LEU* 3.1 51.6 - - - +
157C ARG* 1.3 77.8 - - - +
159C HIS* 1.3 67.0 + - + +
161C GLU* 3.5 10.8 + - - +
162C GLN* 3.3 22.7 + - - +
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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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141C VAL* 3.8 40.6 - - + -
143C LEU* 3.5 24.2 - - + +
155C LEU* 2.8 38.0 + - + -
156C VAL* 3.0 8.2 + - - +
158C ARG* 1.3 79.7 - - + +
160C VAL* 1.3 63.6 - - - +
161C GLU 3.2 1.6 - - - -
162C GLN* 3.0 22.0 + - + +
163C GLY 3.4 4.9 + - - -
164C TYR* 3.4 22.6 + + + -
167C ILE* 3.9 6.5 - - + -
328C ARG* 3.9 22.5 + - - -
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Residues in contact with VAL 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 VAL* 2.9 36.2 + - + +
157C ARG 3.2 4.0 + - - +
159C HIS* 1.3 76.6 - - - +
161C GLU* 1.3 60.0 + - + +
163C GLY* 3.1 17.9 + - - +
164C TYR 4.8 8.7 - - - +
167C ILE* 4.2 15.9 - - + -
187C PHE* 4.2 22.9 - - + -
190C ILE* 4.2 25.1 - - + -
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Residues in contact with GLU 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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157C ARG* 2.9 48.6 + - + +
158C ARG* 3.7 8.2 - - - +
160C VAL* 1.3 80.7 - - + +
162C GLN* 1.3 66.3 + - - +
163C GLY 3.3 1.3 + - - -
187C PHE* 6.5 0.2 - - + -
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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