Contacts of the strand formed by residues 113 - 117 (chain F) in PDB entry 3EXG
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 113 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76F PRO 3.1 10.9 + - - +
77F ILE* 3.5 8.4 - - + -
78F CYS* 2.6 31.7 + - - +
112F ILE* 1.3 84.4 - - - +
114F PHE* 1.3 75.6 + - - +
115F ARG* 3.7 11.6 + - + -
157F ILE* 4.5 4.9 - - + -
160F ALA* 3.3 38.4 - - + +
161F ILE* 3.9 11.7 - - + +
167F VAL* 3.4 9.2 - - + +
169F VAL* 4.0 18.6 - - + -
1008F K 3.6 4.0 - - - -
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Residues in contact with PHE 114 (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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63F ALA* 4.4 8.1 - - + -
67F VAL* 3.9 13.7 - - + -
78F CYS* 3.4 25.4 - - + +
80F PHE* 3.8 20.6 - + + -
83F PHE* 4.0 17.1 - - + -
93F VAL* 3.6 42.8 - - + -
97F ALA* 4.6 2.5 - - + -
112F ILE* 3.3 45.5 - - + -
113F VAL* 1.3 77.3 - - - +
115F ARG* 1.3 60.3 + - - +
166F PRO* 4.6 6.3 - - + -
167F VAL 3.0 12.7 + - - +
168F VAL* 3.2 11.0 - - + -
169F VAL 2.8 26.2 + - - +
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Residues in contact with ARG 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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9F ILE* 4.4 2.1 - - - +
13F MET* 4.0 24.5 - - - +
25F LEU* 4.2 4.9 - - - +
39F VAL* 3.9 19.7 - - - +
77F ILE* 3.7 25.4 - - + -
78F CYS 3.1 5.3 + - - +
79F GLU* 2.9 56.8 + - - +
80F PHE* 2.9 26.2 + - - +
83F PHE* 3.7 6.7 - - - -
113F VAL* 4.3 1.8 - - + -
114F PHE* 1.3 75.3 - - - +
116F GLY* 1.3 58.3 + - - +
117F PRO* 5.2 0.4 - - - +
157F ILE* 3.5 21.1 - - + -
169F VAL* 3.5 22.0 - - + -
171F GLU* 2.4 44.9 + - - +
176F TYR* 3.9 5.9 + - - -
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Residues in contact with GLY 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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79F GLU* 4.4 0.4 - - - -
80F PHE 3.4 11.0 - - - -
83F PHE* 3.6 10.0 - - - -
115F ARG* 1.3 82.9 - - - +
117F PRO* 1.3 78.7 - - - +
169F VAL 3.5 3.3 + - - +
171F GLU* 3.0 31.9 + - - -
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Residues in contact with PRO 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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37F TYR* 3.8 20.4 - - + +
79F GLU* 5.4 2.0 - - - +
80F PHE 3.7 1.8 - - - +
81F MET 3.1 28.5 - - - +
82F THR* 3.6 9.0 - - + -
83F PHE* 3.0 25.1 + - - -
115F ARG* 5.2 2.0 - - - +
116F GLY* 1.3 87.3 - - - +
118F ASN* 1.3 59.9 + - - +
171F GLU 3.3 10.5 - - - +
173F GLU* 3.6 29.4 - - + +
176F TYR* 3.4 18.3 - - + +
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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