Contacts of the strand formed by residues 140 - 145 (chain A) in PDB entry 3C0M
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 MET 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ILE* 4.4 14.8 - - + +
117A SER* 3.8 18.4 - - - +
128A VAL* 3.8 16.6 - - + +
129A GLY* 3.7 38.1 - - - +
137A GLY* 4.2 4.0 - - - +
138A GLU 4.1 13.2 - - - +
139A ASP* 1.3 75.0 - - - +
141A ASP* 1.3 65.7 + - - +
142A VAL* 3.6 9.2 + - + +
151A ILE* 3.5 27.1 - - + +
152A ARG* 3.1 19.7 - - - +
153A GLY* 3.8 13.5 - - - +
168A THR 4.7 2.5 - - - +
170A ILE* 5.1 2.0 - - + -
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Residues in contact with ASP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ASP* 4.3 1.3 + - - +
140A MET* 1.3 76.1 - - - +
142A VAL* 1.3 61.9 + - - +
143A THR* 3.9 15.7 - - + +
150A VAL 3.6 1.2 - - - +
151A ILE* 3.5 5.2 - - - -
152A ARG* 2.8 35.2 + - + +
154A ASN* 2.8 40.4 + - - +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A VAL* 3.4 40.4 - - + +
107A HIS* 3.7 40.7 + - + +
113A ILE* 4.4 13.0 - - + -
140A MET 3.6 8.7 + - - +
141A ASP* 1.3 77.8 - - - +
143A THR* 1.3 61.3 + - - +
144A ARG 4.3 0.3 + - - -
149A TRP* 4.1 10.7 - - + -
150A VAL 3.5 7.0 - - - +
151A ILE* 4.5 10.3 - - + -
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Residues in contact with THR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ASP* 4.3 18.4 - - + -
142A VAL* 1.3 76.9 - - - +
144A ARG* 1.3 67.1 + - - +
145A ASP* 5.2 0.3 - - - +
149A TRP* 3.5 6.2 - - - +
150A VAL* 2.7 56.5 + - - +
152A ARG* 4.7 8.5 + - - +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 4.2 19.2 - - - +
102A GLN* 4.0 6.0 + - - +
142A VAL 4.3 0.4 + - - -
143A THR* 1.3 83.1 + - - +
145A ASP* 1.3 62.3 + - - +
146A GLY 3.1 28.0 + - - +
147A ASP* 3.1 19.6 + - - +
148A GLY 4.1 1.3 + - - -
149A TRP* 3.2 53.3 - - + +
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Residues in contact with ASP 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 5.2 0.7 - - - +
144A ARG* 1.3 76.7 - - - +
146A GLY* 1.3 66.4 + - - +
147A ASP 3.2 2.9 + - - -
148A GLY* 3.1 22.1 + - - +
150A VAL* 3.8 29.7 - - + +
171A LYS* 4.6 13.3 + - - -
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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