Contacts of the strand formed by residues 44 - 50 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42G VAL* 3.3 10.2 - - - +
43G VAL* 1.3 79.6 + - - +
45G MET* 1.3 67.6 + - - +
46G LEU* 5.3 5.2 - - + +
71G VAL* 5.1 0.2 - - - -
72G PRO* 3.2 19.7 - - + +
94G THR* 3.0 40.7 + - - +
5H GLY* 3.4 14.1 - - - -
44H GLN* 4.7 8.0 - - - +
46H LEU* 5.1 5.2 - - - +
92H MET* 3.9 25.2 - - + +
94H THR* 2.7 45.4 + - - +
44I GLN* 4.9 4.9 - - - +
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Residues in contact with MET 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G LEU* 3.9 15.7 - - + -
42G VAL* 4.7 0.2 - - + -
44G GLN* 1.3 79.2 - - - +
46G LEU* 1.3 68.7 + - - +
47G LEU* 4.1 7.2 - - + -
62G VAL* 3.9 19.1 - - + -
68G TRP* 4.3 2.2 - - + -
71G VAL* 3.9 15.9 - - + -
72G PRO 2.8 8.9 + - - +
73G VAL* 3.2 49.4 - - + +
74G THR 3.2 6.2 + - - +
91G VAL* 3.9 27.6 - - + -
92G MET 3.2 7.9 - - - +
93G MET* 3.5 34.5 - - + -
92H MET* 4.0 1.4 - - - +
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Residues in contact with LEU 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G GLN* 5.3 6.3 - - + +
45G MET* 1.3 76.2 - - - +
47G LEU* 1.3 65.2 + - - +
74G THR* 3.5 29.6 - - + +
76G MET* 3.7 29.8 - - + -
91G VAL* 3.3 5.2 - - - +
92G MET* 2.8 47.8 + - + +
46H LEU* 3.9 19.1 - - + -
76H MET* 4.9 0.7 - - + -
92H MET* 4.6 8.3 - - + -
44I GLN* 5.3 3.4 - - - +
46I LEU* 3.6 38.6 - - + -
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Residues in contact with LEU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G THR* 4.1 26.2 - - + -
27G LEU* 6.3 0.7 - - + -
28G LEU* 5.0 5.6 - - + -
45G MET* 4.1 11.4 - - + -
46G LEU* 1.3 77.4 - - - +
48G SER* 1.3 60.8 + - - +
58G PRO* 4.6 9.9 - - + -
59G ALA* 3.6 33.2 - - + +
62G VAL* 4.4 5.4 - - + -
73G VAL* 4.1 20.4 - - + -
74G THR 3.1 7.7 + - - +
75G CYS* 3.0 16.3 - - - +
76G MET* 2.9 26.8 + - - +
89G ILE* 4.7 5.2 - - + -
90G ARG 3.3 10.5 - - - +
91G VAL* 4.1 18.4 - - + -
79H MET* 6.1 0.2 - - - -
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Residues in contact with SER 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47G LEU* 1.3 77.6 - - - +
49G ALA* 1.3 60.4 + - - +
58G PRO* 5.4 1.6 - - - -
75G CYS* 5.5 0.4 - - - -
76G MET* 3.2 40.1 - - - +
78G GLU* 4.3 14.9 - - - +
88G CYS 3.8 0.3 - - - +
89G ILE* 3.2 8.2 - - - +
90G ARG* 3.0 55.5 + - - +
79H MET* 5.2 0.7 - - - -
74I THR* 4.8 0.2 + - - -
75I CYS 4.9 0.9 + - - -
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Residues in contact with ALA 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G SER* 1.3 74.4 - - - +
50G THR* 1.3 66.5 + - - +
53G LEU* 3.7 21.8 - - + +
58G PRO* 4.5 2.9 - - + -
76G MET 3.5 5.1 + - - -
77G GLN* 3.8 5.0 - - - +
78G GLU* 3.1 24.0 + - - -
88G CYS 3.4 7.2 - - - -
89G ILE* 4.5 6.1 - - + -
79H MET* 3.6 35.4 - - + -
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Residues in contact with THR 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G ALA* 1.3 78.6 - - - +
51G PRO* 1.3 70.4 - - + +
52G ASP* 2.6 36.7 + - - -
53G LEU* 3.0 18.6 + - - +
77G GLN* 4.5 2.6 - - - +
78G GLU* 4.1 9.9 - - + -
79G MET 4.8 2.7 - - - +
84G GLY* 6.4 0.2 - - - -
85G LEU 3.5 22.4 - - - +
86G LYS* 4.8 0.4 - - - -
87G LYS* 3.2 1.5 + - - -
88G CYS* 3.0 24.2 + - + +
90G ARG* 3.8 22.0 - - - +
79H MET* 6.0 0.5 - - - +
57I PHE* 6.4 0.7 - - + -
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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