Contacts of the strand formed by residues 120 - 127 (chain C) in PDB entry 1F15
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 THR 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C ASP 5.4 1.1 - - - +
119C SER* 1.3 79.3 - - - +
121C VAL* 1.3 65.7 + - - +
122C TRP* 4.7 3.3 - - - -
152C VAL* 5.7 1.8 - - - -
153C TYR 3.2 11.4 - - - -
154C GLN* 3.5 34.1 - - + +
155C TYR* 4.4 3.1 - - + +
189C SER* 3.9 2.6 + - - -
190C LYS* 3.0 47.9 + - - +
191C ASP* 3.5 27.0 + - - +
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Residues in contact with VAL 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C VAL* 5.0 0.4 - - + -
117C PHE* 4.7 9.9 - - + -
119C SER* 5.2 0.7 - - - -
120C THR* 1.3 81.6 - - - +
122C TRP* 1.3 66.5 + - - +
123C VAL* 3.8 20.2 - - + -
151C LEU 4.0 0.2 - - - +
152C VAL* 3.5 4.5 - - - +
153C TYR* 2.9 49.6 + - + +
187C VAL* 4.0 10.3 - - + -
188C TYR 3.3 12.8 - - - +
189C SER* 4.7 5.6 - - - +
194C LEU* 4.2 28.0 - - + -
199C LEU* 4.3 17.7 - - + -
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Residues in contact with TRP 122 (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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58B PHE* 6.2 2.5 - + - -
113B PRO* 3.6 22.9 - - + -
114B LEU 3.7 2.7 - - - -
115B PRO* 3.5 42.4 - - + -
160B VAL* 3.8 28.3 - - + -
120C THR* 4.7 1.5 + - - -
121C VAL* 1.3 82.7 - - - +
123C VAL* 1.3 59.7 + - - +
143C PHE* 3.3 51.5 - + + -
150C VAL* 4.5 11.2 - - + -
151C LEU 3.4 5.8 - - - +
152C VAL* 3.8 22.5 - - + +
186C LEU 3.7 0.2 - - - +
188C TYR* 3.0 37.2 + + + +
190C LYS* 3.7 35.7 - - + +
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Residues in contact with VAL 123 (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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109C ILE* 4.0 27.6 - - + -
111C VAL* 4.2 16.4 - - + -
121C VAL* 3.8 23.8 - - + -
122C TRP* 1.3 76.5 - - - +
124C THR* 1.3 67.9 + - - +
143C PHE* 4.2 0.6 - - - -
150C VAL* 3.7 1.7 - - - -
151C LEU* 2.9 44.0 + - + +
166C LEU* 3.5 11.8 - - + +
185C VAL* 4.5 4.3 - - + -
186C LEU 3.3 10.5 - - - +
187C VAL* 4.1 15.0 - - + -
199C LEU* 5.9 0.2 - - + -
201C LEU* 4.5 5.6 - - + -
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Residues in contact with THR 124 (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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123C VAL* 1.3 78.4 + - - +
125C VAL* 1.3 72.3 + - - +
126C ARG* 5.0 1.8 - - - +
142C MET* 5.1 3.4 + - - +
143C PHE* 3.2 25.5 - - - -
148C SER* 2.9 34.7 + - - +
149C PRO* 2.7 26.9 - - + +
150C VAL* 3.9 2.8 - - + +
166C LEU* 4.1 5.8 - - - -
185C VAL* 3.2 6.2 - - - +
186C LEU* 2.8 40.5 + - - +
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Residues in contact with VAL 125 (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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90C LEU* 5.1 4.3 - - + -
107C LEU* 4.0 17.7 - - + -
109C ILE* 3.3 40.8 - - + -
124C THR* 1.3 76.5 - - - +
126C ARG* 1.3 67.1 + - - +
148C SER* 3.4 9.0 - - - -
149C PRO* 5.6 0.2 - - + -
166C LEU* 4.3 5.6 - - + -
168C TYR* 3.2 43.5 - - + -
183C TYR* 5.6 1.3 - - + -
184C ALA 2.9 16.8 - - - +
185C VAL* 3.5 11.9 - - + +
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Residues in contact with ARG 126 (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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124C THR* 5.0 1.3 - - + +
125C VAL* 1.3 77.3 - - - +
127C LYS* 1.3 69.3 + - - +
128C VAL* 3.3 11.8 + - + +
142C MET* 3.0 48.9 + - + +
145C ASP* 2.6 43.0 + - - -
147C ALA* 2.9 23.8 - - - +
148C SER* 2.9 28.8 + - - +
168C TYR* 4.1 8.1 - - + +
183C TYR* 3.4 11.8 - - - -
184C ALA 2.8 26.9 + - - +
186C LEU* 4.4 10.1 - - + -
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Residues in contact with LYS 127 (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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97A THR 4.6 6.3 + - - -
98A GLU* 5.0 11.7 - - - +
100A ASP* 4.0 19.4 + - - +
126C ARG* 1.3 79.4 - - - +
128C VAL* 1.3 66.9 + - - +
129C PRO* 3.7 12.5 - - + +
142C MET* 4.9 1.0 - - - +
168C TYR* 5.5 0.4 + - - -
179C ASP* 5.6 0.2 - - + -
182C LYS* 3.4 45.6 - - + +
183C TYR* 3.3 46.2 - - + -
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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