Contacts of the strand formed by residues 148 - 154 (chain B) in PDB entry 2ETK
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 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PHE 4.9 2.0 - - - -
88B GLY* 5.6 2.2 - - - -
106B LEU* 4.3 19.7 - - + -
107B LEU 3.2 11.0 - - - +
108B SER* 3.5 40.2 - - - -
109B LYS* 2.9 17.7 + - - -
144B GLN* 3.5 0.2 - - - -
145B ASP* 2.9 20.7 + - - -
147B ARG* 1.3 110.0 + - + +
149B LEU* 1.3 62.2 + - - +
150B TYR* 3.3 35.3 - - + +
378B GLU* 3.2 38.3 + - + +
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Residues in contact with LEU 149 (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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105B LYS 3.3 6.1 - - - +
106B LEU* 3.3 3.8 - - - -
107B LEU* 2.9 42.3 + - + +
109B LYS* 3.5 25.6 - - - +
112B MET* 3.7 26.9 - - + -
121B PHE* 3.9 24.0 - - + -
143B PHE 3.9 1.6 - - - -
144B GLN* 3.9 6.1 - - + +
148B TYR* 1.3 74.3 - - - +
150B TYR* 1.3 62.4 + - - +
151B MET* 5.6 0.2 - - - -
394B PHE* 3.9 23.8 - - + -
397B PHE* 3.6 37.9 - - + -
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Residues in contact with TYR 150 (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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73B ALA* 3.7 22.3 - - + +
104B MET* 3.7 29.6 - - + -
105B LYS 3.4 3.6 - - - -
106B LEU* 3.7 28.7 - - + +
141B TYR 3.9 0.7 - - - +
142B ALA* 3.2 8.3 - - - +
143B PHE* 2.8 73.7 + + + +
144B GLN* 4.0 1.1 - - - -
145B ASP* 3.0 31.0 + - - -
148B TYR* 3.3 37.7 - - + +
149B LEU* 1.3 76.2 - - - +
151B MET* 1.3 63.5 + - - +
152B VAL 4.0 0.7 - - - -
397B PHE* 3.8 1.6 - - - -
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Residues in contact with MET 151 (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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103B ALA 3.4 2.9 - - - +
104B MET* 4.3 0.2 - - - -
105B LYS* 3.0 63.0 + - + +
107B LEU* 3.8 22.2 - - + -
121B PHE* 5.1 2.5 - - + +
124B GLU* 3.5 29.2 - - - +
125B ARG 4.9 4.9 - - - -
128B MET* 3.7 20.6 - - + -
139B LEU* 4.2 18.6 - - + -
141B TYR 3.9 2.5 - - - -
142B ALA* 4.8 0.4 - - + -
150B TYR* 1.3 71.0 - - - +
152B VAL* 1.3 61.5 + - - +
153B MET* 3.2 16.0 + - + +
397B PHE* 3.6 30.7 - - + -
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Residues in contact with VAL 152 (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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76B TYR* 3.4 35.9 - - + +
102B TYR* 3.5 39.3 - - + -
103B ALA 4.0 2.2 - - - -
104B MET* 4.1 13.7 - - + +
139B LEU* 3.4 1.9 - - - +
140B PHE* 2.8 28.1 + - + +
141B TYR* 2.7 34.0 + - + +
143B PHE* 3.8 20.0 - - + -
151B MET* 1.3 69.9 - - - +
153B MET* 1.3 58.3 + - - +
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Residues in contact with MET 153 (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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90B VAL* 4.5 2.5 - - + -
102B TYR* 3.4 10.6 - - - +
103B ALA 3.0 43.5 + - - +
105B LYS* 3.7 32.5 - - + +
124B GLU* 5.2 1.3 - - - +
128B MET* 3.7 40.8 - - + +
137B VAL* 3.9 9.6 - - + -
138B GLN 3.3 11.4 - - - +
139B LEU* 4.6 3.1 - - + -
140B PHE* 4.0 4.0 - - - -
151B MET* 3.8 9.2 - - + +
152B VAL* 1.3 74.5 - - - +
154B GLU* 1.3 64.9 + - - +
216B ASP* 5.7 2.2 - - - -
416B HFS 3.7 38.1 - - + +
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Residues in contact with GLU 154 (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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101B VAL 5.5 0.2 - - - -
102B TYR* 4.9 2.2 - - - -
103B ALA 4.4 0.2 - - - -
136B VAL 3.8 0.3 - - - +
137B VAL* 3.9 6.7 - - + -
138B GLN* 3.1 41.8 + - - +
140B PHE* 3.5 24.8 - - + -
153B MET* 1.3 73.8 - - - +
155B TYR* 1.3 55.0 + - - +
156B MET* 3.4 26.1 + - + +
213B LYS* 3.5 28.5 + - - +
416B HFS 2.8 30.7 + - - -
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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