Contacts of the strand formed by residues 118 - 125 (chain F) in PDB entry 1Q57
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 ILE 118 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68F VAL* 4.1 16.2 - - + +
69F TRP 5.9 1.3 - - - +
110F ASP* 3.6 23.1 - - - +
111F TYR 3.7 7.0 - - - +
112F ARG* 3.3 40.6 - - - +
117F ASN* 1.3 79.8 - - - +
119F VAL* 1.3 60.4 + - - +
120F SER 3.9 17.9 - - - +
121F GLN* 3.9 17.5 - - - +
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Residues in contact with VAL 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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68F VAL* 4.6 3.5 - - - +
111F TYR 2.9 5.7 + - - +
112F ARG 4.1 2.2 - - - -
113F ASP* 3.5 45.1 - - + +
117F ASN* 3.7 4.5 - - + +
118F ILE* 1.3 75.5 - - - +
120F SER* 1.3 63.0 + - - +
134F GLY* 3.7 3.9 - - - -
135F SER* 3.0 37.8 + - - +
137F LYS* 6.0 4.3 - - + -
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Residues in contact with SER 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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68F VAL* 4.3 1.8 - - - -
111F TYR* 3.0 39.5 + - - +
118F ILE* 3.6 7.4 - - - +
119F VAL* 1.3 86.4 - - - +
121F GLN* 1.3 66.1 + - - +
133F THR 3.2 15.0 - - - -
134F GLY* 4.0 2.7 - - - -
135F SER 3.7 13.4 + - - -
136F HIS* 3.0 31.4 + - - -
137F LYS 5.0 0.2 + - - -
140F ALA* 5.1 1.6 - - - +
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Residues in contact with GLN 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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68F VAL* 3.0 30.1 - - - +
69F TRP* 3.0 32.7 + - - +
97F TRP* 3.3 17.6 - - - -
108F VAL* 3.2 21.8 - - + -
109F ALA 3.3 4.9 - - - +
110F ASP* 3.1 26.1 + - - +
111F TYR* 4.8 2.0 - - - -
118F ILE* 3.9 6.6 - - - +
120F SER* 1.3 74.5 - - - +
122F LYS* 1.3 59.8 + - - +
123F VAL 3.9 0.2 - - - -
132F THR* 3.1 8.8 + - - -
133F THR* 2.7 56.6 + - + +
136F HIS* 5.3 1.1 + - - -
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Residues in contact with LYS 122 (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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107F GLN 3.6 2.8 - - - +
109F ALA* 2.8 35.3 + - - +
111F TYR* 3.9 19.1 + - + +
121F GLN* 1.3 74.6 - - - +
123F VAL* 1.3 61.6 + - - +
130F PHE* 3.2 41.8 - - + -
131F LYS 3.9 1.6 - - - -
132F THR* 4.6 11.2 - - - -
136F HIS* 4.3 17.3 - - + +
159F GLU* 2.9 41.2 + - - +
179F GLY 4.5 6.1 + - - +
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Residues in contact with VAL 123 (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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69F TRP* 3.7 24.5 - - + -
106F TYR* 3.3 36.3 - - + -
107F GLN 3.3 6.3 - - - +
108F VAL* 3.5 23.8 - - + -
122F LYS* 1.3 74.3 - - - +
124F ARG* 1.3 63.2 + - - +
130F PHE* 3.2 13.4 - - - -
131F LYS* 2.7 50.2 + - + +
133F THR* 3.6 22.0 - - + -
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Residues in contact with ARG 124 (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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96F TYR* 4.8 3.4 - - - +
105F MET* 4.1 13.3 + - - +
106F TYR* 3.0 15.2 - - - +
107F GLN* 2.7 81.7 + - + +
123F VAL* 1.3 75.8 - - - +
125F ASP* 1.3 74.9 + - - +
126F LYS* 3.1 38.2 + - - +
129F ASN 3.7 11.0 - - - +
130F PHE* 4.7 10.5 - - + +
131F LYS* 6.4 0.2 - - - -
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Residues in contact with ASP 125 (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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104F VAL* 4.3 4.0 - - + -
105F MET 4.7 2.2 - - - -
106F TYR* 3.9 25.0 + - + -
124F ARG* 1.3 85.7 + - - +
126F LYS* 1.3 92.3 + - - +
127F ASP* 3.5 11.6 + - - +
128F LYS* 3.0 9.7 + - - -
129F ASN* 2.9 45.0 + - - +
130F PHE* 5.2 0.4 - - - +
131F LYS* 6.0 2.1 - - - +
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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