Contacts of the strand formed by residues 45 - 49 (chain G) in PDB entry 5A0Q
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 45 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38G GLY* 4.5 2.2 - - - -
39G ILE 3.4 21.1 - - - +
40G ARG* 4.1 4.3 - - - -
44G GLY* 1.3 77.7 - - - +
46G VAL* 1.4 63.8 + - - +
47G PHE* 3.2 37.0 - - + +
138G GLY* 4.7 1.8 - - - -
139G SER 4.5 5.4 - - - +
146G ALA* 4.0 10.5 - - + -
147G GLN 3.4 31.6 - - - +
148G LEU* 3.8 31.2 - - + -
186G CYS* 5.2 0.4 - - - -
216G VAL* 3.8 13.9 + - + +
217G GLY 4.5 2.6 - - - +
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Residues in contact with VAL 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G GLY* 3.3 3.2 - - - -
39G ILE 3.3 24.1 + - - -
41G CYS* 5.9 0.7 - - + -
44G GLY 4.1 0.4 - - - -
45G VAL* 1.4 68.6 - - - +
47G PHE* 1.3 66.7 + - - +
186G CYS* 3.5 23.6 - - - +
189G ILE* 3.8 22.9 - - + -
190G VAL* 4.0 9.4 - - - +
193G VAL* 3.6 24.6 - - + +
213G LEU* 4.3 5.8 - - + -
214G SER 3.1 15.0 - - - +
215G TRP* 3.2 32.5 - - + +
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Residues in contact with PHE 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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38G GLY* 3.9 7.6 - - - -
45G VAL* 3.2 20.4 - - + -
46G VAL* 1.3 77.8 - - - +
48G GLY* 1.3 59.4 + - - +
66G LEU* 5.0 6.1 - - + -
74G GLY* 3.3 32.8 - - - -
75G MET 4.0 1.8 - - - -
76G ALA* 3.8 23.8 - - + -
136G MET* 3.3 32.3 - - + -
137G LEU 4.0 0.4 - - - -
138G GLY* 3.4 24.0 - - - -
148G LEU* 5.4 0.2 - - + -
213G LEU* 3.4 2.0 - - - -
214G SER* 2.8 46.2 + - - +
216G VAL* 3.2 27.6 - - + -
224G HIS* 4.0 4.9 - + - -
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Residues in contact with GLY 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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37G ILE 2.7 37.8 + - - -
47G PHE* 1.3 75.4 - - - +
49G VAL* 1.3 68.5 + - - +
66G LEU* 5.2 0.7 - - - -
193G VAL* 3.5 13.7 - - - -
197G ILE* 4.1 4.9 - - - -
212G GLU 3.3 15.3 - - - -
213G LEU* 4.0 1.1 - - - -
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Residues in contact with VAL 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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34G SER* 4.7 3.1 - - - +
35G THR 3.7 4.0 - - - +
36G ALA* 3.5 31.0 - - + +
48G GLY* 1.3 82.7 - - - +
50G GLU* 1.3 75.5 + - - +
66G LEU* 4.2 11.6 - - + +
76G ALA* 3.5 23.8 - - + -
77G VAL 4.3 10.8 - - - +
197G ILE* 4.1 2.0 - - - +
210G GLU 4.5 0.7 - - - +
212G GLU* 3.1 46.0 + - - +
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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