Contacts of the strand formed by residues 114 - 121 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61F GLN* 3.4 8.3 + - - +
62F LEU* 2.7 50.4 + - + +
64F ILE* 6.5 0.2 - - + -
76F TYR* 3.7 25.4 - - + +
112F LEU* 3.9 22.2 - - + -
113F ASN* 1.3 79.5 - - - +
115F THR* 1.3 77.8 + - - +
116F ARG* 3.8 16.8 - - + +
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Residues in contact with THR 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F SER* 3.7 17.0 - - - +
60F SER 3.5 12.1 - - - +
61F GLN* 2.7 25.4 + - + +
114F VAL* 1.3 85.0 - - - +
116F ARG* 1.3 66.7 + - - +
117F GLY 5.0 0.4 - - - +
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Residues in contact with ARG 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F SER* 2.6 56.8 + - - +
62F LEU* 4.2 9.9 - - + -
76F TYR* 4.0 26.3 + - - -
77F TRP* 4.5 5.5 - - - +
78F LEU* 3.8 45.7 + - + +
90F ALA* 5.3 3.4 - - - +
91F LYS* 4.6 25.9 - - - +
114F VAL* 3.8 13.4 + - + +
115F THR* 1.3 83.3 - - - +
117F GLY* 1.3 60.4 + - - +
118F PHE* 4.7 1.7 - - - -
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Residues in contact with GLY 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57F TYR* 3.2 26.7 + - - -
58F ILE 3.3 9.2 - - - -
59F SER* 4.0 4.5 - - - -
78F LEU* 6.1 0.2 - - - -
90F ALA* 4.8 4.0 - - - +
91F LYS* 5.9 0.7 - - - -
115F THR* 5.0 1.6 - - - +
116F ARG* 1.3 81.7 + - - +
118F PHE* 1.3 65.7 + - - +
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Residues in contact with PHE 118 (chain F).
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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219E ARG* 4.1 4.9 - - - +
46F LEU* 4.9 0.2 - - + -
57F TYR* 3.5 9.6 - - - -
58F ILE* 2.9 66.5 + - + +
60F SER* 4.6 8.5 - - - -
78F LEU* 4.4 9.4 - - + -
80F ILE* 3.9 19.5 - - + -
88F PHE* 5.0 0.2 - + - -
90F ALA* 3.6 37.5 - - + +
116F ARG 4.7 0.4 - - - -
117F GLY* 1.3 79.2 - - - +
119F TRP* 1.3 63.9 + - - +
120F VAL* 3.6 28.5 - - + -
131F VAL* 3.6 33.0 - - + -
149F PHE* 4.2 4.7 - + - -
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Residues in contact with TRP 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E ARG* 2.4 39.9 + - - +
54F ASN 5.9 0.9 - - - -
55F GLY 5.1 1.1 - - - -
56F GLY* 3.4 36.6 - - - -
57F TYR* 3.8 33.0 - + + -
118F PHE* 1.3 75.9 - - - +
120F VAL* 1.3 65.3 + - - +
121F PRO* 4.5 13.9 - - + -
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Residues in contact with VAL 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E ARG* 4.3 0.4 - - - +
51F LEU* 3.7 19.7 - - + -
55F GLY* 3.2 2.4 - - - -
56F GLY 2.9 32.5 + - - +
58F ILE* 4.4 1.1 - - + -
88F PHE* 4.6 8.1 - - + -
118F PHE* 3.6 27.6 - - + +
119F TRP* 1.3 78.0 - - - +
121F PRO* 1.3 68.5 - - - +
124F MET* 4.4 11.4 - - + -
129F TYR* 4.8 7.0 - - + -
149F PHE* 3.9 23.1 - - + -
151F LYS* 3.9 24.7 - - + -
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Residues in contact with PRO 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E GLU* 3.9 7.9 - - - +
219E ARG* 3.5 18.8 - - - +
221E LYS* 5.6 2.9 - - - +
54F ASN 5.3 0.2 - - - +
55F GLY* 4.2 0.4 - - - -
119F TRP* 3.7 15.5 - - + +
120F VAL* 1.3 91.4 - - - +
122F GLU* 1.3 65.5 + - - +
123F TYR* 3.2 46.2 - - + +
124F MET* 3.1 31.2 + - + +
151F LYS* 3.4 5.2 - - - -
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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