Contacts of the strand formed by residues 106 - 111 (chain G) in PDB entry 5TJ4
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 TYR 106 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79G ILE* 3.6 40.3 - - + +
80G THR 4.7 0.7 + - - -
81G PRO* 4.3 9.8 - - + -
85G PHE* 4.0 9.9 - + - -
89G LEU* 5.3 0.2 - - + -
94G TRP* 4.1 12.8 - + - -
105G ALA* 1.3 71.0 - - - +
107G PRO* 1.3 68.8 - - + +
108G ILE* 3.5 6.8 + - + +
263G SER* 3.2 3.3 - - - -
264G ALA* 2.7 43.4 + - + +
266G ILE* 4.2 7.9 - - + -
277G LYS* 3.3 17.2 - - + +
280G LEU* 3.4 30.1 - - + -
281G GLU* 2.8 41.4 + - + -
285G LEU* 4.1 26.7 - - + -
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Residues in contact with PRO 107 (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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89G LEU* 3.9 8.4 - - + +
93G THR* 3.5 51.4 - - - +
94G TRP* 3.5 30.5 - - + -
97G VAL* 3.8 8.7 - - + -
105G ALA 3.5 4.2 - - - +
106G TYR* 1.3 83.8 - - - +
108G ILE* 1.3 64.1 + - - +
261G VAL* 3.9 8.7 - - + -
262G LEU 4.0 0.4 - - - +
263G SER* 4.0 10.3 - - - +
285G LEU* 3.6 14.0 - - - +
303G ALA* 3.7 7.5 - - + +
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Residues in contact with ILE 108 (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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61G PHE* 3.9 19.7 - - + -
106G TYR* 3.5 17.9 - - + +
107G PRO* 1.3 78.2 - - - +
109G ALA* 1.3 65.9 + - + +
262G LEU* 2.8 35.0 + - + +
263G SER* 4.2 0.9 - - - -
264G ALA* 4.1 15.9 - - + +
280G LEU* 5.2 0.7 - - + -
284G LEU* 4.2 21.3 - - + -
285G LEU* 4.0 20.7 - - + +
290G LEU* 4.5 11.6 - - + +
299G LEU* 4.4 16.8 - - + -
302G VAL* 3.7 5.5 - - - +
303G ALA* 2.8 23.2 + - - +
304G LEU 4.4 0.9 + - - -
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Residues in contact with ALA 109 (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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108G ILE* 1.3 86.9 - - + +
110G VAL* 1.3 64.1 + - - +
111G GLU* 4.0 0.4 + - - -
261G VAL* 3.2 6.5 - - - +
262G LEU* 2.7 37.9 + - + +
299G LEU* 3.7 39.7 - - + +
301G ALA 3.6 10.8 - - - +
302G VAL* 3.8 5.8 - - + +
303G ALA* 3.9 3.5 - - - +
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Residues in contact with VAL 110 (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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90G TYR* 6.4 0.2 - - + -
92G PHE* 3.8 34.5 - - + -
93G THR* 4.1 13.2 - - + -
109G ALA* 1.3 74.8 - - - +
111G GLU* 1.3 63.5 + - - +
259G VAL* 3.7 25.8 - - + -
260G GLY 3.6 4.5 - - - +
261G VAL* 4.4 9.2 - - + +
299G LEU 4.4 0.9 - - - -
300G GLY* 3.7 4.0 - - - -
301G ALA* 2.7 46.0 + - + +
302G VAL 5.2 3.4 - - - +
320G THR* 4.6 4.4 - - + +
321G MET* 4.7 14.8 - - + -
324G ALA* 4.9 5.8 - - + -
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Residues in contact with GLU 111 (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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15G LYS* 3.4 17.1 + - - +
63G ALA* 4.2 6.6 - - - +
110G VAL* 1.3 75.4 - - - +
112G ALA* 1.3 65.0 + - - +
155G TYR* 3.9 5.2 + - - +
229G PRO* 4.5 8.3 - - + -
230G TRP* 3.7 26.5 - - + -
259G VAL* 3.5 3.4 - - - +
260G GLY* 2.9 44.5 + - - +
262G LEU* 3.8 23.2 - - - +
299G LEU 4.1 14.7 - - - +
320G THR* 4.8 0.7 - - - -
1Q GLC 3.1 36.2 + - - -
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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