Contacts of the helix formed by residues 154 - 163 (chain C) in PDB entry 4XQ2
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 154 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C LEU 4.5 3.2 + - - +
128C ILE* 6.1 1.6 - - + -
152C VAL 4.3 0.4 + - - -
153C VAL* 1.3 71.2 - - - +
155C VAL* 1.3 58.8 + - - +
156C ALA* 3.2 12.0 + - - +
157C GLU* 3.1 33.9 + - + +
158C VAL* 2.9 31.3 + - + +
160C ARG* 5.5 1.6 + - - -
186C LEU* 6.1 0.2 - - - +
287C VAL* 3.7 33.2 - - + +
291C GLN* 4.2 3.0 - - - +
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Residues in contact with VAL 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C ILE* 4.4 13.0 - - + +
144C THR* 4.0 15.7 - - + -
153C VAL 3.1 10.7 + - - +
154C ASP* 1.3 68.7 - - - +
156C ALA* 1.3 57.4 + - - +
158C VAL* 4.1 0.2 - - - +
159C SER* 2.7 44.1 + - - +
171C VAL* 3.8 34.1 - - + -
181C GLN* 5.0 1.8 - - - +
183C PRO* 4.3 1.8 - - + +
186C LEU* 3.9 28.3 - - + +
188C ALA* 4.0 15.5 - - + -
291C GLN* 3.2 15.3 + - - +
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Residues in contact with ALA 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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154C ASP* 3.2 8.1 + - - +
155C VAL* 1.3 78.1 - - - +
157C GLU* 1.3 52.8 + - - +
159C SER* 3.5 1.8 - - - -
160C ARG* 2.6 56.9 + - + +
186C LEU* 3.1 33.9 + - + +
187C GLY* 5.3 0.2 - - - -
291C GLN* 4.8 0.8 + - - -
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Residues in contact with GLU 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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125C PRO* 5.7 4.9 - - - +
128C ILE* 4.5 18.2 - - + +
154C ASP* 3.1 28.7 + - + +
156C ALA* 1.3 75.4 - - - +
158C VAL* 1.3 68.7 + - - +
160C ARG* 2.9 33.1 + - - +
161C ARG* 2.7 64.1 + - + +
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Residues in contact with VAL 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 4.2 10.8 - - + +
128C ILE* 3.6 35.7 - - + -
132C LEU* 4.0 11.1 - - + +
140C VAL* 3.9 20.4 - - + -
142C ILE* 3.7 25.8 - - + -
153C VAL* 3.8 17.0 - - + -
154C ASP 2.9 24.4 + - - +
157C GLU* 1.3 73.1 - - - +
159C SER* 1.3 57.5 + - - +
161C ARG* 3.3 6.1 + - - -
162C ALA* 3.0 25.2 + - + +
169C VAL* 5.3 0.7 - - + -
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Residues in contact with SER 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C VAL* 2.7 24.9 + - - +
156C ALA 3.8 2.9 - - - -
158C VAL* 1.3 69.4 - - - +
160C ARG* 1.3 57.3 + - - +
161C ARG 3.1 7.9 + - - -
162C ALA 4.3 0.2 - - - +
163C HIS* 3.0 35.4 + - - +
169C VAL* 3.2 37.3 - - - +
187C GLY* 3.5 28.9 + - - -
188C ALA* 3.8 4.2 - - - -
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Residues in contact with ARG 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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154C ASP* 5.5 1.6 + - - -
156C ALA* 2.6 32.9 + - + +
157C GLU* 2.9 32.3 + - - +
159C SER* 1.3 73.2 - - - +
161C ARG* 1.3 97.7 + - - +
163C HIS* 4.9 1.3 - - - -
164C GLU* 3.5 16.9 - - - +
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Residues in contact with ARG 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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128C ILE* 4.2 16.4 - - + -
129C ALA* 6.0 4.3 - - - -
132C LEU* 3.5 18.3 - - + +
157C GLU* 2.7 55.2 + - - +
158C VAL 4.3 0.2 - - - +
159C SER 3.1 0.2 - - - -
160C ARG* 1.3 130.5 + - - +
162C ALA* 1.3 65.2 + - - +
163C HIS 3.3 1.6 - - - -
164C GLU* 3.3 30.4 + - - +
165C ARG* 3.6 12.3 + - - +
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Residues in contact with ALA 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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132C LEU* 3.8 9.1 - - + +
140C VAL* 3.8 23.8 - - + -
158C VAL 3.0 17.4 + - - +
159C SER* 4.5 0.2 - - - -
161C ARG* 1.3 73.7 - - - +
163C HIS* 1.3 59.1 + - - +
164C GLU 3.0 4.7 - - - -
165C ARG* 2.9 21.7 + - - +
167C ALA* 3.1 26.0 + - + +
169C VAL* 3.6 26.0 - - + -
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Residues in contact with HIS 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 SER* 3.0 27.7 + - - +
160C ARG* 5.5 0.9 - - - -
161C ARG 3.3 0.2 - - - -
162C ALA* 1.3 74.6 - - - +
164C GLU* 1.3 61.0 + - + +
166C GLY* 4.0 8.0 + - - +
167C ALA 3.1 27.0 + - - +
168C ARG* 4.8 0.2 - - - -
169C VAL* 3.8 4.3 - - + +
187C GLY 3.1 27.5 + - - -
189C ASP* 2.4 34.7 + - - -
213C ARG* 5.7 1.1 - - - -
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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