Contacts of the strand formed by residues 148 - 153 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C ILE* 3.9 17.9 - - + -
81C TYR 3.5 11.7 - - - +
82C ARG* 3.7 20.2 - - + -
113C PHE* 3.5 28.3 - - + -
114C PRO 3.0 6.1 + - - +
115C VAL* 3.3 5.3 - - + +
116C ILE* 2.7 32.9 + - - +
145C SER* 4.5 0.4 + - - -
147C GLY* 1.3 77.6 - - - +
149C VAL* 1.3 63.2 + - - +
150C VAL* 4.2 2.5 - - + -
181C PHE 5.8 0.4 - - - +
182C MET* 3.7 28.0 - - + -
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ARG 3.5 1.4 - - - +
80C ILE* 3.3 4.5 - - - -
81C TYR* 2.8 44.9 + - + +
116C ILE* 3.2 22.7 - - + +
118C PHE* 4.1 11.9 - - + -
138C CYS* 3.7 33.2 - - + +
141C PHE* 3.8 26.2 - - + -
142C VAL* 3.8 20.4 - - + +
145C SER* 5.1 0.7 - - - +
148C VAL* 1.3 76.9 - - - +
150C VAL* 1.3 67.3 + - - +
151C SER 3.9 0.4 - - - -
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Residues in contact with VAL 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C VAL* 3.7 37.5 - - + -
79C ARG 3.6 2.5 - - - -
80C ILE* 4.0 15.3 - - + -
115C VAL* 4.3 6.1 - - + -
116C ILE 2.7 11.8 + - - +
117C ILE* 3.3 10.2 - - + +
118C PHE 2.9 21.6 + - - -
148C VAL* 4.3 5.6 - - + -
149C VAL* 1.3 77.2 - - - +
151C SER* 1.3 58.2 + - - +
152C VAL* 3.7 6.1 + - + -
172C ALA* 5.5 1.3 - - + -
175C TRP* 4.4 3.6 - - + -
176C VAL* 4.0 30.3 - - + -
182C MET* 4.1 15.7 - - + -
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Residues in contact with SER 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C VAL* 3.1 5.6 - - - -
79C ARG 2.8 42.0 + - - -
81C TYR* 3.9 7.6 - - - -
118C PHE* 3.5 23.0 + - - +
120C HIS* 5.2 2.1 + - - +
129C ALA* 3.4 27.9 + - - +
134C TYR* 5.4 1.0 - - - +
138C CYS* 3.8 24.1 - - - -
149C VAL 3.9 0.8 - - - -
150C VAL* 1.3 72.6 - - - +
152C VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C LEU* 4.1 16.8 - - + -
77C GLU 4.0 4.0 - - - +
78C VAL* 4.1 9.0 - - + -
117C ILE* 3.8 15.7 - - + -
118C PHE 3.0 9.2 + - - +
119C PHE* 3.7 31.0 - - + -
120C HIS* 3.8 18.4 + - - -
129C ALA* 4.4 1.9 - - - +
150C VAL* 3.9 3.8 - - + +
151C SER* 1.3 74.4 + - - +
153C ASN* 1.3 61.6 + - - +
154C TYR* 3.2 23.1 + - + +
168C ASP 4.2 4.7 - - - +
172C ALA* 3.5 32.1 - - + -
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Residues in contact with ASN 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ASP* 5.6 0.6 + - - -
75C GLY 5.5 0.7 - - - +
76C LEU* 3.5 14.9 - - - +
77C GLU* 2.9 51.4 + - + +
78C VAL* 4.4 4.2 - - - +
79C ARG* 5.4 1.0 - - - +
120C HIS* 4.9 2.7 - - - -
128C SER* 3.4 16.1 + - - -
129C ALA* 3.0 42.2 + - - +
130C SER* 4.4 1.6 + - - +
152C VAL* 1.3 68.0 - - - +
154C TYR* 1.3 67.2 + - - +
155C ARG* 3.8 1.2 + - - +
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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