Contacts of the strand formed by residues 44 - 50 (chain C) in PDB entry 2CHS
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 GLN 44 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A GLY* 3.9 6.6 - - - -
44A GLN* 5.2 5.2 - - - +
46A LEU* 5.2 3.8 - - - +
92A MET* 3.6 34.5 - - + +
94A THR* 2.7 37.7 + - - +
44B GLN* 4.6 6.6 - - - +
42C VAL* 3.4 8.4 - - - +
43C VAL* 1.3 85.4 - - + +
45C MET* 1.3 64.6 + - - +
46C LEU* 4.8 11.7 - - + +
72C PRO* 3.4 18.8 - - + +
93C MET* 3.7 1.2 - - - -
94C THR* 3.0 43.5 + - - +
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Residues in contact with MET 45 (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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92A MET* 3.9 1.7 - - - +
28C LEU* 3.7 25.8 - - + -
44C GLN* 1.3 74.6 - - - +
46C LEU* 1.3 70.6 + - - +
47C LEU* 4.0 10.1 - - + -
62C VAL* 3.9 18.8 - - + -
68C TRP* 3.3 39.3 - - + -
71C VAL* 3.7 13.7 - - + -
72C PRO 2.9 6.5 + - - +
73C VAL* 3.1 36.3 - - + -
74C THR 3.1 5.0 + - - -
91C VAL* 3.8 18.8 - - + -
92C MET 3.5 5.4 - - - +
93C MET* 4.1 16.6 - - + -
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Residues in contact with LEU 46 (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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46A LEU* 3.8 30.5 - - + -
76A MET* 4.7 3.1 - - + -
92A MET* 4.3 9.4 - - + -
44B GLN* 5.1 6.1 - - - +
46B LEU* 4.1 19.3 - - + -
44C GLN* 4.8 10.1 - - + +
45C MET* 1.3 80.7 - - - +
47C LEU* 1.3 62.7 + - - +
74C THR* 3.3 33.9 - - + +
76C MET* 3.9 28.4 - - + +
90C ARG 4.0 0.2 - - - +
91C VAL* 3.3 4.2 - - - +
92C MET* 2.9 44.0 + - + +
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Residues in contact with LEU 47 (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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24C THR* 3.9 24.2 - - + -
27C LEU* 5.8 1.3 - - + -
28C LEU* 5.2 2.5 - - + -
45C MET* 4.0 25.8 - - + -
46C LEU* 1.3 75.3 - - - +
48C SER* 1.3 60.1 + - - +
58C PRO* 4.1 8.5 - - + -
59C ALA* 4.3 23.1 - - + +
62C VAL* 4.4 8.1 - - + -
73C VAL* 4.8 6.7 - - + -
74C THR 3.2 5.6 + - - +
75C CYS* 3.0 41.6 - - - +
76C MET* 3.1 6.0 + - - +
89C ILE* 4.0 14.1 - - + -
90C ARG 3.2 8.5 - - - +
91C VAL* 3.8 23.1 - - + -
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Residues in contact with SER 48 (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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79A MET* 5.3 0.7 - - - -
74B THR* 4.9 2.8 + - - +
75B CYS 4.4 3.9 + - - -
47C LEU* 1.3 75.6 - - - +
49C ALA* 1.3 63.0 + - - +
58C PRO* 5.6 0.9 - - - -
75C CYS* 5.4 0.2 - - - -
76C MET* 3.1 36.1 - - - +
78C GLU* 3.7 29.1 + - - +
88C CYS 3.9 0.3 - - - +
89C ILE* 3.2 8.4 - - - +
90C ARG* 2.8 44.9 + - - +
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Residues in contact with ALA 49 (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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79A MET* 3.7 34.7 - - + +
48C SER* 1.3 77.7 - - - +
50C THR* 1.3 70.0 + - - +
51C PRO 3.8 0.2 - - - -
53C LEU* 4.1 17.9 - - + +
58C PRO* 4.8 2.9 - - + -
76C MET 3.2 5.3 + - - -
77C GLN* 3.7 6.8 - - - +
78C GLU* 3.0 22.8 + - - -
88C CYS 3.4 5.2 - - - -
89C ILE* 4.5 4.9 - - + -
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Residues in contact with THR 50 (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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57B PHE* 6.2 0.9 - - + -
49C ALA* 1.3 76.4 - - - +
51C PRO* 1.3 67.0 - - + +
52C ASP* 2.9 33.7 + - - -
53C LEU* 3.3 15.9 + - - +
78C GLU* 4.0 11.8 - - + +
79C MET 5.3 2.0 - - - +
84C GLY 5.9 0.4 - - - -
85C LEU 3.3 25.1 - - - +
86C LYS* 4.8 2.7 - - + -
87C LYS* 3.3 2.6 + - - -
88C CYS 3.0 25.4 + - - +
90C ARG* 3.8 20.4 - - - +
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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