Contacts of the strand formed by residues 142 - 150 (chain C) in PDB entry 1O95
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 HIS 142 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C ILE* 3.6 27.8 - - + +
135C ALA* 3.8 26.6 - - + +
140C TRP 3.0 16.9 + - - -
141C PRO* 1.3 75.9 - - - +
143C ALA* 1.4 60.1 + - - +
174C ILE* 3.4 12.8 - - - +
179C VAL 3.2 13.0 - - - +
72D PRO* 3.8 25.1 - - + +
73D ASP* 4.7 9.3 + - - +
76D GLU* 3.8 22.7 + - - -
101D GLY 3.3 26.3 + - - -
102D TYR* 4.7 0.6 - - - +
105D SER* 4.2 8.3 + - - -
109D LYS* 5.4 2.7 - - - -
182D ARG* 4.6 9.2 - - - -
183D SER* 4.9 4.7 + - - -
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Residues in contact with ALA 143 (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 ILE* 4.5 5.5 - - - +
142C HIS* 1.4 75.0 - - - +
144C ALA* 1.3 61.1 + - - +
146C VAL* 4.2 2.0 - - - +
160C ILE* 3.2 34.3 - - + -
162C ARG* 5.1 7.0 - - - -
172C VAL* 5.6 3.6 - - + -
174C ILE* 3.7 7.5 - - + +
179C VAL 3.5 5.1 + - - +
180C LEU* 3.6 14.5 - - + +
181C THR* 3.2 22.2 + - - +
72D PRO* 5.1 7.0 - - + -
101D GLY 5.6 0.2 - - - -
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Residues in contact with ALA 144 (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 ILE* 4.5 5.4 - - + -
143C ALA* 1.3 76.4 - - - +
145C VAL* 1.3 82.9 + - + +
146C VAL* 3.7 0.8 - - - +
162C ARG* 3.8 17.8 + - - +
181C THR* 3.3 11.0 - - + +
72D PRO* 6.0 0.2 - - - +
97D VAL* 4.5 2.7 - - - +
100D LEU* 3.7 15.0 - - + +
101D GLY* 3.5 31.2 - - - +
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Residues in contact with VAL 145 (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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120C VAL* 3.7 9.9 - - + -
144C ALA* 1.3 87.2 - - + +
146C VAL* 1.3 61.3 + - - +
162C ARG* 3.2 5.9 - - - -
163C GLU* 3.2 35.5 + - - +
181C THR* 2.9 15.7 + - - -
183C GLN* 3.6 27.8 - - + +
97D VAL* 3.3 36.8 - - + -
100D LEU* 4.0 25.4 - - + -
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Residues in contact with VAL 146 (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 ALA 4.2 7.6 - - - +
144C ALA 4.5 0.9 - - - -
145C VAL* 1.3 73.8 - - - +
147C ALA* 1.3 61.8 + - - +
148C ASP 3.4 28.3 - - - +
149C LEU* 4.6 2.2 - - + +
160C ILE* 4.0 24.7 - - + -
161C ARG 3.9 2.5 - - - +
180C LEU* 4.1 31.6 - - + -
181C THR 2.9 17.9 + - - +
182C ILE* 3.8 10.5 - - + -
183C GLN* 3.1 20.9 + - - +
186C ILE* 3.4 15.8 - - + +
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Residues in contact with ALA 147 (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 VAL 3.5 0.6 + - - -
146C VAL* 1.3 75.7 - - - +
148C ASP* 1.3 63.6 + - - +
161C ARG* 2.8 15.1 + - + +
163C GLU* 3.9 36.3 - - + +
169C LEU* 5.2 8.2 - - + +
183C GLN* 4.9 4.9 - - + -
184C LEU 5.5 1.3 - - - +
185C GLY 5.4 1.6 - - - +
186C ILE* 3.8 21.3 - - + +
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Residues in contact with ASP 148 (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 VAL* 3.4 10.9 - - - +
147C ALA* 1.3 82.6 - - - +
149C LEU* 1.3 74.7 + - - +
150C GLN* 3.8 19.1 + - - +
159C VAL 4.4 1.6 - - - +
160C ILE* 3.1 8.1 - - - -
161C ARG* 3.1 56.1 + - + +
169C LEU* 6.4 0.2 - - + -
186C ILE* 4.1 6.3 - - - -
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Residues in contact with LEU 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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45C GLU* 3.4 36.7 + - + +
48C LYS* 5.3 2.3 + - - -
49C ILE* 4.3 9.9 - - + -
115C MET* 5.2 2.7 - - + -
117C PHE* 3.6 35.7 - - + -
146C VAL* 4.9 3.6 - - + -
148C ASP* 1.3 84.5 - - - +
150C GLN* 1.3 64.5 + - - +
151C TYR* 4.1 11.9 - - + -
158C ALA* 4.4 18.2 - - + -
159C VAL 4.1 0.2 - - - -
160C ILE* 3.4 27.4 - - + -
180C LEU* 3.6 12.8 - - + -
182C ILE* 5.5 2.5 - - + -
186C ILE* 4.5 0.4 - - + +
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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* 3.8 17.1 - - - +
149C LEU* 1.3 70.6 - - - +
151C TYR* 1.3 59.2 + - - +
158C ALA* 3.3 7.8 - - - +
159C VAL* 3.2 63.8 + - - +
161C ARG* 5.3 4.7 + - - +
171C GLU* 4.2 12.2 + - - +
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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