Contacts of the strand formed by residues 105 - 110 (chain B) in PDB entry 3AG2
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 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B HIS* 2.9 77.0 + + + +
103B GLN 4.2 7.0 - - - -
104B TRP* 1.3 81.1 - - - +
106B TRP* 1.3 74.3 + - - +
119B ASP* 3.4 32.6 + - + -
120B SER 3.4 13.0 - - - +
121B TYR* 3.2 49.1 - + + +
207B MET* 3.6 14.1 - - - +
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Residues in contact with TRP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B THR* 3.3 20.0 - - + +
100B MET 3.6 2.0 - - - -
101B GLY* 3.5 30.7 - - - -
105B TYR* 1.3 79.6 - - - +
107B SER* 1.3 57.6 + - - +
108B TYR* 3.5 24.9 - - + +
119B ASP 3.5 0.2 - - - -
120B SER* 2.7 42.4 + - - +
154B VAL* 4.7 0.2 - - + -
161B HIS* 3.6 15.0 - - + -
162B SER 3.5 36.3 - - - -
163B TRP* 3.6 25.4 - + + -
174B ALA* 4.0 9.9 - - + -
196B CYS* 4.2 5.6 - - + -
207B MET* 2.9 42.3 + - + +
208B PRO 3.5 21.5 - - - -
209B ILE* 3.7 11.8 - - + +
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B THR* 3.0 9.7 + - - -
100B MET* 2.9 45.9 + - - +
102B HIS* 3.0 26.7 + - - -
106B TRP* 1.3 74.2 - - - +
108B TYR* 1.3 64.3 + - - +
109B GLU* 4.8 4.5 + - - +
117B SER* 6.3 1.1 - - - -
118B PHE 3.3 7.4 - - - -
119B ASP* 3.4 22.0 - - - -
157B GLU* 5.2 0.5 + - - -
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 4.7 4.7 - - + -
98B LYS 3.3 5.6 - - - +
99B THR* 3.1 31.4 - - - -
106B TRP* 3.5 19.8 - - + +
107B SER* 1.3 74.1 - - - +
109B GLU* 1.3 62.7 + - - +
110B TYR* 4.0 9.9 - - + -
117B SER* 3.1 26.2 - - - -
118B PHE* 2.9 44.2 + + + -
120B SER* 3.5 25.0 + - - -
142B VAL* 3.2 38.2 - - + +
152B MET* 4.9 0.7 - - + -
163B TRP* 3.0 28.8 + + - -
208B PRO 5.0 0.2 + - - -
209B ILE* 3.8 11.8 - - - +
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Residues in contact with GLU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B THR 4.5 0.2 - - - +
97B VAL* 3.6 4.3 - - - +
98B LYS* 2.8 82.5 + - + +
100B MET* 3.7 26.7 - - + +
107B SER* 4.8 4.1 + - - +
108B TYR* 1.3 81.9 - - - +
110B TYR* 1.3 62.7 + - - +
111B THR* 3.9 7.8 + - + +
116B LEU 3.4 6.1 - - - +
117B SER* 3.9 11.7 - - - -
157B GLU* 4.7 4.5 - - - +
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Residues in contact with TYR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 4.8 5.4 - - + -
96B THR 4.4 7.6 - - - +
97B VAL* 3.7 35.9 - - + -
108B TYR* 4.0 6.7 - - + -
109B GLU* 1.3 79.3 - - - +
111B THR* 1.3 58.9 + - - +
112B ASP 3.7 2.6 + - - -
114B GLU* 3.1 13.3 + - - +
116B LEU* 2.8 45.7 + - + +
118B PHE* 3.6 25.6 - + - -
142B VAL* 3.3 19.4 - - - +
143B VAL 2.8 34.5 + - - -
144B LEU* 4.0 1.1 - - + -
219B PHE* 3.6 26.7 - + - -
222B TRP* 3.5 10.1 - + - -
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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