Contacts of the strand formed by residues 104 - 110 (chain B) in PDB entry 2EZT
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 104 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ALA 5.2 1.1 - - - +
66B ALA* 3.8 32.8 - - + +
67B ALA* 3.8 9.9 - - - +
70B ALA* 4.7 0.2 - - + -
76B ILE* 4.0 4.5 - - - +
77B GLY 3.2 9.9 - - - +
79B CYS* 4.2 2.0 - - - -
94B LEU* 4.1 22.9 - - + -
97B ALA* 3.7 28.0 - - + -
102B VAL* 3.4 3.1 + - + +
103B PRO* 1.3 80.2 - - - +
105B LEU* 1.3 68.3 + - - +
157B ALA* 3.9 2.6 - - - +
162B GLY 3.1 7.4 + - - +
163B VAL* 3.3 5.5 - - + +
164B ALA* 2.8 32.2 + - - +
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Residues in contact with LEU 105 (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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21B LEU* 3.6 31.4 - - + -
76B ILE* 3.8 15.6 - - + +
77B GLY 2.9 6.3 + - - +
78B VAL* 3.4 19.3 - - + -
79B CYS 3.0 26.0 + - - +
104B VAL* 1.3 76.0 - - - +
106B ALA* 1.3 63.2 + - - +
107B LEU* 3.9 28.3 - - + -
150B ILE* 4.2 6.3 - - + +
153B ALA* 3.6 32.3 - - + -
154B ILE* 4.0 12.3 - - + -
164B ALA* 3.5 9.6 - - + +
166B VAL* 4.4 4.7 - - + -
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Residues in contact with ALA 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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79B CYS* 3.4 12.1 - - - +
90B LEU* 4.4 8.3 - - + -
94B LEU* 3.8 38.4 - - + -
105B LEU* 1.3 74.9 - - - +
107B LEU* 1.3 65.2 + - - +
108B ILE* 4.6 2.5 - - + -
163B VAL* 4.7 0.2 - - + -
164B ALA 2.9 12.2 + - - +
165B VAL* 3.4 10.6 - - + +
166B VAL 3.1 24.1 + - - -
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Residues in contact with LEU 107 (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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17B VAL* 5.0 7.2 - - + -
18B ILE* 6.3 0.4 - - + -
21B LEU* 5.3 7.6 - - + -
29B LEU* 5.6 3.8 - - + -
37B ILE* 4.5 5.2 - - + -
40B ILE* 4.6 22.0 - - + -
78B VAL* 5.2 6.7 - - + -
79B CYS 3.0 11.4 + - - +
80B PHE* 3.0 19.5 - - + +
81B GLY 3.0 25.3 + - - +
105B LEU* 3.9 27.4 - - + -
106B ALA* 1.3 79.7 - - - +
108B ILE* 1.3 63.6 + - - +
150B ILE* 3.7 29.4 - - + -
166B VAL* 3.4 7.4 - - + +
168B ILE* 4.0 21.3 - - + -
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Residues in contact with ILE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 4.3 3.4 - - - -
81B GLY 3.4 5.4 - - - +
82B SER 4.4 1.8 - - - +
87B GLY* 4.1 6.7 - - - -
90B LEU* 3.4 33.2 - - + -
106B ALA* 4.6 2.9 - - + -
107B LEU* 1.3 76.5 - - - +
109B GLY* 1.3 73.1 + - - +
126B GLU* 3.4 20.6 - - - +
130B TYR* 3.8 34.1 - - + +
165B VAL* 3.5 28.5 - - + -
166B VAL 2.8 10.8 + - - +
167B GLN* 3.3 11.6 - - + -
168B ILE* 2.8 34.2 + - - +
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Residues in contact with GLY 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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36B SER* 3.3 17.9 - - - -
37B ILE* 3.8 10.9 - - - +
81B GLY 2.8 15.7 + - - -
82B SER 4.0 0.2 - - - -
83B ALA* 3.3 24.3 - - - -
108B ILE* 1.3 76.3 - - - +
110B GLN* 1.3 52.2 + - - -
126B GLU* 2.5 26.7 - - - +
168B ILE* 4.2 2.0 - - - -
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Residues in contact with GLN 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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36B SER* 3.3 13.9 + - - +
83B ALA* 4.0 6.2 - - - +
109B GLY* 1.3 73.9 - - - +
111B PHE* 1.3 86.9 + - - +
116B MET* 3.8 34.4 - - + +
123B GLU* 4.2 9.4 + - - +
124B MET 2.9 29.4 + - - +
125B ASN* 4.8 0.8 - - - +
126B GLU* 3.4 26.7 + - - +
139B THR* 5.2 5.1 + - + +
167B GLN* 4.8 3.5 - - + +
168B ILE 3.2 23.2 + - - +
169B PRO* 4.3 2.9 - - + -
170B VAL* 2.9 28.2 + - - +
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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