Contacts of the strand formed by residues 44 - 50 (chain A) in PDB entry 2CHT
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.4 7.3 - - - +
43A VAL* 1.3 82.1 - - + +
45A MET* 1.3 64.8 + - - +
46A LEU* 5.5 7.4 - - + +
71A VAL* 4.9 0.4 - - - -
72A PRO* 3.2 17.5 - - - +
94A THR* 2.8 38.8 + - - +
5B GLY* 3.6 6.5 - - - -
44B GLN* 4.7 6.9 - - - +
46B LEU* 4.9 7.3 - - - +
92B MET* 3.5 37.3 - - + +
94B THR* 2.7 43.5 + - - +
44C GLN* 5.3 4.3 + - - +
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Residues in contact with MET 45 (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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28A LEU* 3.8 31.9 - - + -
42A VAL* 5.0 1.3 - - + -
44A GLN* 1.3 77.4 - - - +
46A LEU* 1.3 74.4 + - - +
47A LEU* 4.4 10.8 - - + -
62A VAL* 3.6 17.9 - - + -
68A TRP* 4.3 24.5 - - + -
71A VAL* 4.4 4.0 - - + -
72A PRO 2.8 6.3 + - - +
73A VAL* 3.1 31.0 - - + -
74A THR 2.9 23.4 + - - -
91A VAL* 4.6 3.1 - - + -
92A MET 3.4 13.0 - - - +
93A MET* 4.0 17.9 - - + -
92B MET* 5.0 2.0 - - - +
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Residues in contact with LEU 46 (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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44A GLN* 5.5 7.6 - - + +
45A MET* 1.3 78.2 - - - +
47A LEU* 1.3 62.4 + - - +
48A SER 4.3 0.7 - - - -
74A THR* 3.0 33.2 - - + +
76A MET* 3.9 26.2 - - + -
91A VAL* 3.2 6.8 - - - +
92A MET* 2.9 46.3 + - + +
46B LEU* 4.1 19.1 - - + -
76B MET* 4.4 2.9 - - + -
92B MET* 5.3 5.8 - - + -
44C GLN* 4.9 3.8 - - - +
46C LEU* 3.7 42.2 - - + -
76C MET* 5.7 0.2 - - + -
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Residues in contact with LEU 47 (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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24A THR* 4.0 20.0 - - + -
28A LEU* 4.7 2.0 - - + -
45A MET* 4.4 13.0 - - + -
46A LEU* 1.3 77.3 - - - +
48A SER* 1.3 58.7 + - - +
58A PRO* 3.9 17.2 - - + +
59A ALA* 3.3 36.8 - - + +
62A VAL* 4.2 16.8 - - + -
73A VAL* 4.6 7.6 - - + -
74A THR 2.9 8.6 + - - +
75A CYS* 2.9 33.5 - - - +
76A MET* 3.2 3.1 + - - -
89A ILE* 4.9 2.5 - - + -
90A ARG 3.4 5.2 - - - +
91A VAL* 3.7 28.7 - - + -
79B MET* 5.4 0.5 - - - +
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Residues in contact with SER 48 (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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46A LEU 4.3 0.4 - - - -
47A LEU* 1.3 71.3 - - - +
49A ALA* 1.3 59.4 + - - +
58A PRO* 5.4 1.1 - - - -
76A MET* 3.2 36.5 - - - +
78A GLU* 3.4 31.8 + - - +
88A CYS 3.9 0.9 - - - +
89A ILE* 3.4 5.1 - - - +
90A ARG* 2.8 45.0 + - - +
74C THR* 4.8 3.5 + - - +
75C CYS 4.5 2.6 + - - -
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Residues in contact with ALA 49 (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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20A ILE* 6.3 0.2 - - + -
47A LEU 4.3 0.6 + - - -
48A SER* 1.3 73.7 - - - +
50A THR* 1.3 68.2 + - - +
53A LEU* 4.1 17.3 - - + -
58A PRO* 4.4 10.3 - - + -
76A MET 3.4 6.7 + - - -
77A GLN* 3.4 6.8 - - - +
78A GLU* 3.1 22.5 + - - -
88A CYS 3.6 5.4 - - - -
89A ILE* 4.5 1.6 - - + +
79B MET* 3.7 34.8 - - + -
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Residues in contact with THR 50 (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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49A ALA* 1.3 75.7 - - - +
51A PRO* 1.4 66.2 - - + +
52A ASP* 2.8 35.7 + - - +
53A LEU* 3.0 20.3 + - - +
77A GLN* 4.5 0.6 - - - +
78A GLU* 4.1 12.3 - - + -
79A MET 5.5 1.3 - - - +
85A LEU 3.5 23.6 - - - +
87A LYS* 3.4 0.9 + - - -
88A CYS 3.0 28.4 + - - +
90A ARG* 3.7 18.8 - - - +
57C PHE* 6.1 0.4 - - + -
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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