Contacts of the strand formed by residues 40 - 43 (chain G) in PDB entry 5T0J
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 VAL 40 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38G THR* 4.0 17.3 - - + -
39G SER* 1.3 74.2 - - - +
41G ALA* 1.3 61.9 + - - +
42G VAL* 3.7 22.7 + - + +
49G VAL 3.9 1.6 - - - +
50G ILE* 3.6 6.7 - - - +
51G VAL* 3.2 44.5 + - + +
167G ALA* 3.8 13.9 - - + -
172G GLN* 4.4 4.0 - - + -
175G SER* 3.3 36.6 - - - +
179G LEU* 3.8 8.1 - - + -
201G CYS* 4.4 8.7 - - - -
205G VAL* 6.1 0.2 - - + -
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Residues in contact with ALA 41 (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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39G SER 4.0 1.2 + - - +
40G VAL* 1.3 72.5 - - - +
42G VAL* 1.3 64.1 + - - +
50G ILE* 3.7 19.3 - - + -
139G ILE* 4.1 18.4 - - + -
151G VAL* 3.6 23.1 - - + +
153G LYS* 4.9 1.1 - - - +
165G ALA* 3.7 1.2 - - - +
166G THR 3.3 38.7 + - - +
167G ALA* 3.9 6.8 - - - +
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Residues in contact with VAL 42 (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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40G VAL* 3.7 11.2 - - + -
41G ALA* 1.3 79.1 - - - +
43G ARG* 1.3 62.1 + - - +
44G GLY 4.3 0.2 - - - -
48G ALA* 3.4 3.4 - - - +
49G VAL* 2.9 37.2 + - + +
50G ILE* 4.5 1.0 - - - +
51G VAL* 6.3 0.4 - - + -
151G VAL* 4.5 1.3 - - - -
165G ALA* 4.1 17.0 - - + -
179G LEU* 3.6 31.4 - - + -
183G VAL* 4.3 7.6 - - + -
189G TRP* 3.5 34.3 - - + -
197G THR* 4.9 9.9 - - - +
201G CYS* 5.9 0.7 - - - -
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Residues in contact with ARG 43 (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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42G VAL* 1.3 82.5 - - - +
44G GLY* 1.3 73.1 + - - +
45G LYS 5.7 0.2 + - - -
47G CYS 3.3 11.4 - - - +
48G ALA* 3.7 12.1 - - + -
147G GLN 4.8 3.2 + - - -
149G PRO* 2.7 50.4 + - + -
150G GLN* 3.5 21.0 - - - +
151G VAL* 3.7 3.6 - - + -
163G PHE 4.1 5.9 + - - -
164G LYS* 3.2 65.2 + - - +
165G ALA* 4.4 2.0 - - - +
183G VAL* 5.4 4.2 - - - +
189G TRP* 4.4 3.3 - - - -
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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