Contacts of the strand formed by residues 44 - 50 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLN* 5.2 4.0 - - - +
42B VAL* 3.4 7.8 - - - +
43B VAL* 1.3 83.0 - - + +
45B MET* 1.3 64.2 + - - +
46B LEU* 5.0 12.6 - - + +
72B PRO* 3.4 15.5 - - + +
92B MET 5.9 0.2 - - - +
93B MET* 3.9 0.2 - - - -
94B THR* 3.0 42.3 + - - +
5C GLY* 3.8 14.3 - - - -
44C GLN* 4.6 7.1 - - - +
46C LEU* 5.1 3.8 - - - +
92C MET* 3.8 31.1 - - + +
94C THR* 2.7 41.1 + - - +
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Residues in contact with MET 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.6 27.8 - - + -
42B VAL* 4.3 4.0 - - + -
44B GLN* 1.3 76.7 - - - +
46B LEU* 1.3 71.6 - - - +
47B LEU* 4.3 7.4 - - + -
62B VAL* 4.3 11.0 - - + -
68B TRP* 3.4 35.7 - - + -
71B VAL* 4.4 4.5 - - + -
72B PRO 3.0 5.1 + - - +
73B VAL* 3.2 44.1 - - + +
74B THR* 3.2 5.0 + - - +
91B VAL* 3.6 20.4 - - + -
92B MET 3.3 5.8 - - - +
93B MET* 3.8 20.4 - - + -
92C MET* 5.2 1.0 - - - +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLN* 5.0 4.0 - - - +
46A LEU* 4.1 26.0 - - + -
44B GLN* 5.0 10.1 - - + +
45B MET* 1.3 78.0 - - - +
47B LEU* 1.3 63.0 + - - +
48B SER 4.3 0.2 - - - -
74B THR* 3.3 34.1 - - + +
76B MET* 4.3 23.6 - - + +
90B ARG 3.9 0.2 - - - +
91B VAL* 3.3 5.2 - - - +
92B MET* 2.8 49.5 + - + +
46C LEU* 4.1 29.4 - - + -
76C MET* 4.6 0.9 - - + -
92C MET* 5.0 8.5 - - + -
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Residues in contact with LEU 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B THR* 4.4 18.4 - - + -
27B LEU* 6.1 0.9 - - + -
28B LEU* 5.1 2.7 - - + -
45B MET* 4.6 11.9 - - + -
46B LEU* 1.3 75.1 - - - +
48B SER* 1.3 59.3 + - - +
58B PRO* 3.9 14.8 - - + +
59B ALA* 3.5 37.7 - - + +
62B VAL* 4.5 14.8 - - + -
73B VAL* 4.8 5.8 - - + -
74B THR 3.0 10.4 + - - +
75B CYS* 3.1 13.7 - - - +
76B MET* 3.0 24.5 + - - +
89B ILE* 4.8 4.3 - - + -
90B ARG 3.4 5.2 - - - +
91B VAL* 3.7 28.3 - - + -
79C MET* 5.3 0.2 - - - +
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A THR* 4.8 1.7 + - - +
75A CYS 4.6 2.3 + - - -
46B LEU 4.3 0.2 - - - -
47B LEU* 1.3 74.7 - - - +
49B ALA* 1.3 59.7 + - - +
58B PRO* 5.4 1.1 - - - -
76B MET* 3.1 36.7 - - - +
78B GLU* 4.0 22.5 + - - +
88B CYS 3.8 0.6 - - - +
89B ILE* 3.2 7.9 - - - +
90B ARG* 2.8 54.6 + - - +
79C MET* 5.2 1.3 - - - -
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B SER* 1.3 75.6 - - - +
50B THR* 1.3 73.2 + - - +
51B PRO 3.6 0.3 - - - -
53B LEU* 3.9 19.5 - - + -
58B PRO* 4.6 2.7 - - + -
76B MET 3.3 6.3 + - - -
77B GLN* 3.7 6.9 - - - +
78B GLU* 3.0 21.6 + - - -
88B CYS 3.3 5.6 - - - +
89B ILE* 4.5 5.6 - - + -
79C MET* 3.8 32.3 - - + +
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Residues in contact with THR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PHE* 6.2 0.9 - - + -
49B ALA* 1.3 82.4 - - - +
51B PRO* 1.3 66.4 - - + +
52B ASP* 2.7 35.7 + - - +
53B LEU* 3.3 13.3 + - - +
78B GLU* 4.0 10.5 - - + +
79B MET 5.4 2.0 - - - +
84B GLY 6.1 0.2 - - - -
85B LEU 3.5 21.3 - - - +
86B LYS* 5.1 0.7 - - - -
87B LYS* 3.2 1.6 + - - -
88B CYS* 2.9 26.9 + - + +
90B ARG* 3.9 21.1 - - - +
79C MET* 6.1 0.3 - - - +
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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