Contacts of the strand formed by residues 114 - 121 (chain E) in PDB entry 4BEI
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 114 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61E GLN* 3.5 7.5 + - - +
62E LEU* 2.7 50.0 + - + +
76E TYR* 3.7 24.7 - - + +
112E LEU* 3.9 22.9 - - + -
113E ASN* 1.3 80.5 - - - +
115E THR* 1.3 76.8 + - - +
116E ARG* 3.9 16.8 - - + +
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Residues in contact with THR 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E SER* 3.7 17.0 - - - +
60E SER 3.5 12.1 - - - +
61E GLN* 2.7 25.3 + - + +
114E VAL* 1.3 85.0 - - - +
116E ARG* 1.3 67.6 + - - +
117E GLY 5.0 0.2 - - - +
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Residues in contact with ARG 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E SER* 2.7 56.1 + - - +
62E LEU* 4.2 9.8 - - + +
76E TYR* 4.2 25.9 + - - -
77E TRP* 4.7 5.5 - - - +
78E LEU* 3.8 45.5 + - + +
90E ALA* 5.1 3.8 - - - +
91E LYS* 4.5 27.3 - - - +
114E VAL* 3.9 12.5 + - + +
115E THR* 1.3 81.1 - - - +
117E GLY* 1.3 61.7 + - - +
118E PHE* 4.7 2.1 - - - -
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Residues in contact with GLY 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E TYR* 3.2 27.1 + - - -
58E ILE 3.3 9.0 - - - -
59E SER* 4.0 3.8 - - - -
90E ALA* 4.8 4.0 - - - +
91E LYS* 6.0 0.5 - - - -
115E THR* 5.0 1.6 - - - +
116E ARG* 1.3 82.4 + - - +
118E PHE* 1.3 66.0 + - - +
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Residues in contact with PHE 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E LEU* 5.0 0.4 - - + -
57E TYR* 3.5 9.7 - - - -
58E ILE* 3.0 65.4 + - + +
60E SER* 4.6 8.3 - - - -
78E LEU* 4.3 10.3 - - + -
80E ILE* 3.8 20.6 - - + -
88E PHE* 5.0 1.6 - + - -
90E ALA* 3.6 38.8 - - + +
116E ARG 4.7 0.7 - - - -
117E GLY* 1.3 77.7 - - - +
119E TRP* 1.3 63.9 + - - +
120E VAL* 3.6 27.8 - - + -
131E VAL* 3.6 33.4 - - + -
149E PHE* 4.2 4.7 - + - -
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Residues in contact with TRP 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ASN 5.9 0.7 - - - -
55E GLY 5.2 0.9 - - - -
56E GLY* 3.4 37.0 - - - -
57E TYR* 3.8 33.2 - + + -
88E PHE* 4.6 0.3 - - - -
118E PHE* 1.3 76.8 - - - +
120E VAL* 1.3 65.9 + - - +
121E PRO* 4.5 12.8 - - + -
219F ARG* 2.6 37.6 + - - +
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Residues in contact with VAL 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E LEU* 3.7 19.1 - - + -
55E GLY* 3.2 2.4 - - - -
56E GLY 2.9 31.8 + - - +
58E ILE* 4.4 1.8 - - + -
88E PHE* 4.6 8.5 - - + -
118E PHE* 3.6 27.6 - - + +
119E TRP* 1.3 79.8 - - - +
121E PRO* 1.3 67.4 - - - +
124E MET* 4.4 11.2 - - + -
129E TYR* 4.8 6.7 - - + -
149E PHE* 3.8 24.2 - - + -
151E LYS* 3.9 24.7 - - + -
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Residues in contact with PRO 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E GLY* 4.2 0.4 - - - -
88E PHE* 5.9 0.2 - - + -
119E TRP* 4.7 14.1 - - + -
120E VAL* 1.3 91.6 - - - +
122E GLU* 1.3 65.9 + - - +
123E TYR* 3.3 47.3 - - + +
124E MET* 3.1 31.5 + - + +
151E LYS* 3.4 5.7 - - - -
201F GLU* 4.1 3.8 - - - +
219F ARG* 3.5 21.5 - - - +
221F LYS* 6.1 1.1 - - - +
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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