Contacts of the strand formed by residues 148 - 152 (chain A) in PDB entry 3EBL
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 148 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ILE* 3.9 21.5 - - + -
81A TYR 3.4 11.0 - - - +
82A ARG* 4.1 9.9 - - + -
113A PHE* 3.6 25.6 - - + -
114A PRO 2.9 7.3 + - - +
115A VAL* 3.2 6.6 - - + -
116A ILE* 2.8 32.7 + - - +
145A SER* 4.5 0.4 + - - -
147A GLY* 1.3 79.9 - - - +
149A VAL* 1.3 63.9 + - - +
150A VAL* 4.3 1.3 - - + -
181A PHE* 3.8 24.9 - - + -
182A MET* 4.0 19.7 - - + -
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Residues in contact with VAL 149 (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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79A ARG 3.5 1.6 - - - +
80A ILE* 3.3 4.5 - - - +
81A TYR* 2.8 42.1 + - + +
116A ILE* 3.3 20.6 - - + +
118A PHE* 4.3 10.8 - - + -
138A CYS* 3.7 35.2 - - + +
141A PHE* 3.7 26.7 - - + -
142A VAL* 3.6 25.5 - - + +
145A SER* 5.1 0.4 - - - +
148A VAL* 1.3 77.6 - - - +
150A VAL* 1.3 65.6 + - - +
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Residues in contact with VAL 150 (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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78A VAL* 3.7 36.3 - - + -
79A ARG 3.5 2.7 - - - -
80A ILE* 4.2 7.4 - - + -
115A VAL* 4.1 13.9 - - + -
116A ILE 2.8 10.6 + - - +
117A ILE* 3.3 10.1 - - + +
118A PHE 2.7 30.2 + - - +
148A VAL* 4.3 2.2 - - + -
149A VAL* 1.3 77.8 - - - +
151A SER* 1.3 57.6 + - - +
152A VAL* 3.8 5.9 + - + -
172A ALA* 5.5 0.9 - - + -
175A TRP* 4.5 2.9 - - + -
176A VAL* 4.1 21.5 - - + -
182A MET* 3.7 29.8 - - + -
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Residues in contact with SER 151 (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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78A VAL* 3.2 4.8 - - - -
79A ARG* 2.8 41.9 + - - -
81A TYR* 3.9 9.2 - - - -
118A PHE* 3.4 23.7 + - - -
120A HIS* 5.2 2.1 + - - +
129A ALA* 3.5 27.6 + - - +
134A TYR* 5.4 0.9 - - - +
138A CYS* 3.8 23.0 - - - -
149A VAL 4.0 0.6 - - - -
150A VAL* 1.3 71.5 - - - +
152A VAL* 1.3 63.6 + - - +
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Residues in contact with VAL 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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76A LEU* 4.0 17.9 - - + -
77A GLU 4.2 1.8 - - - -
78A VAL* 4.1 10.8 - - + -
117A ILE* 3.7 21.8 - - + -
118A PHE 2.9 11.5 + - - +
119A PHE* 3.8 23.1 - - + -
120A HIS* 3.8 12.0 + - - -
129A ALA* 4.4 2.2 - - - +
150A VAL* 4.0 3.6 - - + +
151A SER* 1.3 76.0 + - - +
153A ASN* 1.3 61.7 + - - +
154A TYR* 3.0 28.9 + - + +
168A ASP 4.3 5.4 - - - +
172A ALA* 3.6 32.3 - - + -
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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