Contacts of the strand formed by residues 140 - 145 (chain C) in PDB entry 2CMH
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 TYR 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C GLU* 3.4 13.9 - - + +
76C VAL 3.4 35.0 - - - -
77C LEU* 3.8 10.2 - - + +
98C ASP* 2.6 34.1 + - + -
135C LEU* 3.8 14.7 - - - +
136C ASP 4.3 4.3 + - - -
138C LYS* 3.6 35.2 + - + +
139C LYS* 1.3 74.8 - - - +
141C ASP* 1.3 63.9 + - - +
142C LEU 4.1 2.7 - - - +
143C ILE* 3.4 26.5 - - + -
160C MET* 3.0 39.1 + - + +
161C LEU* 3.9 5.5 - - - +
162C LYS* 3.0 30.0 + - - +
165C GLY* 4.4 0.3 - - - -
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Residues in contact with ASP 141 (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 LYS* 2.8 43.1 + - - +
72C GLU* 3.6 21.9 - - - +
73C LEU* 3.9 8.7 - - + -
74C LYS* 2.8 25.8 + - - +
75C GLU 2.9 18.4 + - - +
140C TYR* 1.3 73.7 - - - +
142C LEU* 1.3 59.0 + - - +
161C LEU* 4.8 0.7 - - - -
162C LYS* 2.6 43.0 + - - +
164C ASP* 5.5 0.7 - - - +
165C GLY* 4.7 0.2 - - - -
166C VAL 3.2 13.0 + - - -
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Residues in contact with LEU 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C GLY* 3.7 28.5 - - - +
67C GLY 4.0 3.1 - - - +
70C LYS* 4.3 7.9 - - + -
73C LEU* 4.2 20.0 - - + -
75C GLU 3.6 1.4 + - - -
76C VAL* 3.4 9.3 - - + +
77C LEU 3.0 22.9 + - - -
90C LEU* 4.1 10.8 - - + -
140C TYR* 3.5 0.8 - - - +
141C ASP* 1.3 82.8 - - - +
143C ILE* 1.3 67.0 + - - +
144C PHE* 3.5 31.2 - - + -
166C VAL* 3.3 10.5 - - + +
168C ILE* 3.1 36.3 - - + -
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Residues in contact with ILE 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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77C LEU* 3.2 48.2 - - + +
79C VAL* 5.2 0.7 - - + -
140C TYR* 3.4 27.1 - - + -
142C LEU* 1.3 73.8 - - - +
144C PHE* 1.3 70.4 + - - +
157C LEU* 4.3 23.8 - - + +
160C MET* 4.4 4.5 - - + +
161C LEU* 3.1 25.8 - - + -
166C VAL 2.9 6.8 + - - +
167C PHE* 3.3 27.7 - - + -
168C ILE 3.0 25.5 + - - -
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Residues in contact with PHE 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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62C LEU* 3.4 49.6 - - + -
63C ALA* 4.2 7.0 - - - -
76C VAL* 4.1 14.4 - - + -
77C LEU 2.7 13.2 + - - +
78C ILE* 3.5 8.0 - - + +
79C VAL* 3.0 30.8 + - - +
86C LEU* 3.6 29.4 - - + -
90C LEU* 3.9 13.7 - - + -
142C LEU* 3.5 39.9 - - + -
143C ILE* 1.3 80.8 - - - +
145C CYS* 1.3 60.0 + - - +
146C LEU* 4.0 5.4 - - + -
168C ILE* 3.4 25.6 - - + -
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Residues in contact with CYS 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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79C VAL* 3.6 3.8 - - - -
80C ASP* 3.5 22.2 - - - -
144C PHE* 1.3 71.7 - - - +
146C LEU* 1.3 62.7 + - - +
147C GLN 3.3 24.7 + - - -
149C PRO* 3.4 23.8 - - - -
157C LEU* 4.3 11.9 - - + -
167C PHE* 3.6 23.3 - - + -
168C ILE 3.1 6.9 + - - +
169C SER* 3.4 8.6 - - - -
170C VAL* 3.3 25.1 + - - +
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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