Contacts of the strand formed by residues 150 - 156 (chain A) in PDB entry 3EOV
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 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A PHE* 4.3 4.4 - - + -
52A ALA* 4.9 3.5 - - - +
110A ASN* 4.7 2.6 + - - +
113A VAL* 3.5 54.2 + - + +
114A LYS 3.8 10.8 - - - +
115A HIS* 3.6 36.1 - - + +
116A PHE* 4.2 7.0 - - + -
119A ALA* 3.8 23.1 - - + -
120A LEU 3.3 15.7 - - - +
121A SER* 4.1 0.9 - - - -
148A HIS 3.2 1.0 + - - +
149A VAL* 1.3 77.6 - - - +
151A PHE* 1.3 59.1 + - - +
152A GLY 4.2 5.4 - - - +
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Residues in contact with PHE 151 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.8 14.8 - - + +
48A PHE* 3.2 28.1 + - - -
52A ALA* 4.4 8.3 - - + -
55A THR* 3.7 26.2 - - + -
56A THR* 3.9 14.2 - - + +
59A PHE* 3.4 54.5 - + + -
120A LEU* 2.8 30.9 + - + -
121A SER 3.6 16.8 - - - -
122A MET* 3.5 25.1 - - + -
134A PHE* 4.3 1.3 - - + -
149A VAL* 3.3 13.0 - - + +
150A VAL* 1.3 74.6 - - - +
152A GLY* 1.3 55.4 + - - +
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Residues in contact with GLY 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLY 3.1 14.1 - - - -
47A LEU* 4.7 1.1 - - - -
48A PHE* 3.4 23.3 - - - -
116A PHE* 4.0 0.3 - - - -
119A ALA* 3.4 6.8 - - - +
120A LEU* 2.8 32.3 + - - +
150A VAL* 4.2 0.3 - - - +
151A PHE* 1.3 80.2 - - - +
153A LYS* 1.3 62.4 + - - +
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Residues in contact with LYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLU* 5.5 6.3 - - + -
23A PRO 5.6 1.1 - - - +
25A VAL* 4.7 5.6 - - + -
45A ILE* 3.5 5.8 - - - +
46A GLY 2.8 31.8 + - - +
48A PHE* 3.8 21.8 - - + -
116A PHE* 3.8 21.4 - - + -
118A GLY 3.1 12.3 - - - +
119A ALA* 4.3 0.2 - - - +
120A LEU* 4.4 2.6 - - - +
152A GLY* 1.3 76.2 - - - +
154A VAL* 1.3 70.3 + - - +
155A LEU* 3.3 26.1 + - + +
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 4.1 17.9 - - + -
44A THR 3.6 5.4 - - - +
45A ILE* 4.5 2.2 - - + +
118A GLY* 2.7 21.0 + - - +
120A LEU* 4.3 9.2 - - + -
136A ILE* 3.9 24.7 - - + -
153A LYS* 1.3 78.6 - - - +
155A LEU* 1.3 62.1 + - - +
156A ASP 3.5 29.4 - - - +
157A GLY 4.0 2.2 - - - -
158A MET* 3.8 34.8 - - + +
161A VAL* 4.6 1.6 - - + -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A VAL* 4.3 15.7 - - + -
28A LYS* 4.0 33.9 - - + -
44A THR* 2.8 18.1 + - + +
45A ILE 4.2 1.8 - - - -
46A GLY* 3.6 27.8 - - - +
153A LYS* 4.0 31.4 - - + +
154A VAL* 1.3 72.9 - - - +
156A ASP* 1.3 63.7 + - + +
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Residues in contact with ASP 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG 4.4 2.7 - - - +
44A THR* 2.7 49.2 + - + +
154A VAL* 3.4 7.2 - - - +
155A LEU* 1.3 84.2 - - + +
157A GLY* 1.3 63.9 + - - +
158A MET* 3.4 3.4 - - - +
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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