Contacts of the strand formed by residues 145 - 149 (chain C) in PDB entry 1C2O
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 VAL 145 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C VAL* 4.1 4.3 - - + -
102C TRP 3.5 12.1 - - - +
103C THR* 3.9 13.2 - - + +
104C PRO* 4.9 0.7 - - + -
108C PRO* 4.5 5.4 - - + -
112C THR* 3.5 10.5 - - - +
113C PRO 3.4 6.6 + - - +
114C VAL* 3.1 36.5 - - + +
115C LEU 3.1 4.1 + - - -
144C ALA* 1.3 72.7 - - - +
146C LEU* 1.3 58.6 + - - +
147C VAL* 4.7 0.4 - - + -
187C ILE* 3.5 32.8 - - + -
190C PHE* 3.9 9.2 - - + +
191C GLY 3.8 10.8 - - - +
192C GLY* 3.7 22.9 - - - +
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Residues in contact with LEU 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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101C VAL* 3.3 4.7 - - - +
102C TRP* 2.9 64.4 + - + +
115C LEU* 3.5 19.1 - - + +
117C TRP* 5.0 2.5 - - + -
133C TYR 5.2 0.2 - - - +
135C GLY* 3.4 35.2 - - - +
138C LEU* 3.9 22.2 - - + -
139C ALA* 5.1 0.7 - - + -
144C ALA* 3.4 6.7 + - + +
145C VAL* 1.3 73.6 - - - +
147C VAL* 1.3 75.4 + - - +
148C SER* 4.3 4.7 - - - +
200C PHE* 4.8 6.3 - - + -
455C PHE* 3.9 20.6 - - + -
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Residues in contact with VAL 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 4.0 22.0 - - + -
100C ASN 3.1 17.5 - - - +
101C VAL* 4.1 4.0 - - + -
114C VAL* 5.1 1.8 - - + -
115C LEU 3.0 7.7 + - - +
116C ILE* 3.2 18.5 - - + +
117C TRP* 2.7 32.9 + - - +
145C VAL* 4.7 3.4 - - + +
146C LEU* 1.3 82.0 - - - +
148C SER* 1.3 59.9 + - - +
149C MET* 4.5 2.4 + - + +
179C ALA* 5.9 2.5 - - + +
182C TRP* 5.4 0.2 - - + -
183C VAL* 3.6 31.0 - - + -
187C ILE* 3.7 20.4 - - + -
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Residues in contact with SER 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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99C LEU* 4.3 1.3 - - - -
100C ASN* 2.8 45.6 + - - -
102C TRP* 3.5 19.2 - - - -
117C TRP* 3.8 28.9 - - - -
128C ALA* 3.2 22.1 + - - +
133C TYR 4.6 3.6 + - - -
146C LEU* 4.5 2.9 - - - -
147C VAL* 1.3 77.5 - - - +
149C MET* 1.3 59.2 + - - +
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Residues in contact with MET 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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37C PHE* 3.9 3.4 - - + -
98C TYR 3.7 2.7 - - - +
99C LEU* 3.6 23.6 - - + -
116C ILE* 4.6 5.6 - - + +
117C TRP 3.8 16.0 + - - +
118C ILE* 4.2 20.9 - - + -
119C TYR* 3.3 20.6 - - - -
128C ALA* 3.6 3.4 - - - +
147C VAL* 4.3 2.5 - - + +
148C SER* 1.3 71.7 - - - +
150C ASN* 1.3 76.4 + - - +
151C TYR* 4.5 2.7 - - + +
176C GLN* 3.3 49.4 - - + +
179C ALA* 3.7 24.2 - - + -
180C LEU* 4.4 10.3 - - + -
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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