Contacts of the strand formed by residues 38 - 42 (chain C) in PDB entry 3CMM
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 ASN 38 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLU* 5.6 2.8 - - - +
36C THR 4.5 2.2 + - - -
37C SER* 1.3 72.3 - - - +
39C VAL* 1.3 60.0 + - - +
61C LYS* 3.4 38.1 + - - +
62C SER* 2.8 26.6 + - - +
122C GLN 3.9 10.5 + - - +
123C PHE* 3.6 18.7 - - + +
124C GLN* 2.5 62.6 + - - +
125C VAL 3.3 6.4 + - - -
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C SER 4.3 2.7 - - - +
38C ASN* 1.3 78.2 - - - +
40C LEU* 1.3 67.2 + - - +
41C ILE* 4.4 7.0 - - + -
55C VAL* 4.4 1.1 - - + -
60C VAL* 4.2 25.6 - - + -
62C SER 3.2 11.1 + - - +
63C MET* 3.7 25.8 - - + +
64C THR* 2.8 28.8 + - - +
123C PHE* 4.1 4.1 - - - -
125C VAL* 3.6 15.7 - - + +
127C VAL* 4.7 3.1 - - + -
374C VAL* 4.1 30.5 - - + -
378C CYS* 4.3 6.3 - - - -
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 1.3 72.6 - - - +
41C ILE* 1.3 85.1 + - - +
42C LEU* 3.4 28.3 - - + -
64C THR* 3.3 25.4 - - + +
65C VAL 4.2 0.9 - - - +
66C PHE* 4.2 7.9 - - + -
111C LEU* 4.5 9.2 - - + -
120C LEU* 3.6 28.9 - - + -
123C PHE* 3.6 33.4 - - + -
125C VAL 3.0 10.9 + - - +
126C VAL* 3.6 7.2 - - + +
127C VAL* 2.8 29.5 + - - +
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Residues in contact with ILE 41 (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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39C VAL* 4.4 3.8 - - + -
40C LEU* 1.3 79.6 - - - +
42C LEU* 1.3 67.3 + - - +
43C GLY 3.6 20.0 + - - +
44C LEU* 4.0 10.0 - - + +
48C GLY* 4.0 10.3 - - - +
51C ILE* 3.8 17.9 - - + -
52C ALA* 3.7 26.0 - - + +
55C VAL* 5.0 0.7 - - + -
63C MET* 3.6 29.4 - - + -
64C THR 2.8 13.4 + - - +
65C VAL* 3.5 6.2 - - + +
66C PHE 2.9 26.7 + - - -
127C VAL* 3.6 22.2 - - + +
129C THR* 4.5 4.0 - - - +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LEU* 3.4 37.5 - - + -
41C ILE* 1.3 73.3 - - - +
43C GLY* 1.3 59.1 + - - +
66C PHE* 3.6 25.1 - - + +
114C LEU* 4.1 13.0 - - + -
120C LEU* 5.6 0.9 - - + -
126C VAL* 4.3 16.2 - - + -
127C VAL 2.8 18.3 + - - +
128C ALA* 4.3 9.9 - - + -
129C THR* 2.8 29.3 + - - +
131C THR* 4.6 2.9 - - - -
132C VAL* 4.0 17.1 - - + +
140C ILE* 3.9 29.2 - - + -
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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