Contacts of the helix formed by residues 118 - 130 (chain F) in PDB entry 7CR3
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 118 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A TYR* 3.4 29.8 - - + +
365A ARG* 5.0 3.3 + - - +
111F THR* 3.5 4.4 - - - +
117F LEU* 1.3 77.5 - - - +
119F ASP* 1.3 64.4 + - - +
120F GLU* 3.9 13.7 + - - -
121F GLU* 2.5 35.9 + - - +
122F VAL* 3.2 24.6 + - - +
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Residues in contact with ASP 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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107F ARG* 6.4 0.2 - - + -
111F THR* 5.1 1.3 - - - -
118F THR* 1.3 75.4 - - - +
120F GLU* 1.3 100.2 + - - +
121F GLU 3.2 0.4 - - - -
122F VAL* 3.2 9.2 - - + +
123F ASP* 2.9 44.5 + - - +
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Residues in contact with GLU 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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358A SER* 4.3 17.5 - - - +
365A ARG* 5.1 12.6 + - - +
118F THR* 3.9 13.5 + - - +
119F ASP* 1.3 109.3 + - - +
121F GLU* 1.3 58.3 + - + +
123F ASP* 3.5 6.0 + - - +
124F GLU* 2.9 33.7 + - - +
127F ARG* 4.5 6.8 + - - +
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Residues in contact with GLU 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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344A TRP* 3.6 3.3 + - - +
358A SER* 4.3 6.5 - - - +
359A THR* 3.0 41.5 + - - +
362A TYR* 3.3 30.7 - - - +
365A ARG* 5.7 0.7 - - - +
117F LEU* 3.2 35.3 - - + +
118F THR* 2.5 40.7 + - - +
119F ASP 3.2 0.6 - - - -
120F GLU* 1.3 74.0 - - + +
122F VAL* 1.3 61.6 + - - +
124F GLU* 3.1 11.5 + - - +
125F MET* 2.9 30.1 + - - +
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Residues in contact with VAL 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F LEU* 4.1 9.6 - - + +
107F ARG* 3.7 44.0 - - + +
110F MET* 4.1 12.8 - - + -
111F THR* 3.7 15.3 - - + -
117F LEU* 5.2 1.1 - - + +
118F THR 3.2 16.2 + - - +
119F ASP* 3.2 20.9 - - - +
121F GLU* 1.3 78.3 - - - +
123F ASP* 1.3 56.5 + - - +
125F MET* 3.1 21.2 + - + +
126F ILE* 3.0 34.9 + - + +
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Residues in contact with ASP 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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107F ARG* 3.0 37.2 + - - +
119F ASP* 2.9 33.6 + - - +
120F GLU* 3.8 4.2 + - - +
122F VAL* 1.3 74.7 - - - +
124F GLU* 1.3 58.6 + - - +
126F ILE* 3.2 9.4 + - - +
127F ARG* 2.9 63.1 + - - +
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Residues in contact with GLU 124 (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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344A TRP* 3.5 22.4 - - + +
355A ASP* 5.7 1.0 - - - +
356A LEU* 5.5 6.1 - - - +
358A SER* 3.8 23.7 + - - +
120F GLU 2.9 18.8 + - - +
121F GLU* 3.1 10.9 + - - +
123F ASP* 1.3 73.8 - - - +
125F MET* 1.3 63.5 + - - +
127F ARG* 3.0 31.9 + - - +
128F GLU* 3.0 27.9 + - - +
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Residues in contact with MET 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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340A ILE* 4.7 3.6 - - + +
341A GLN* 4.6 4.0 - - - +
344A TRP* 3.5 55.6 - - + -
110F MET* 3.7 44.9 - - + -
117F LEU* 3.7 22.2 - - + -
121F GLU 2.9 14.4 + - - +
122F VAL* 3.1 17.5 + - + +
124F GLU* 1.3 76.0 - - - +
126F ILE* 1.3 58.5 + - + +
128F GLU* 3.3 1.0 + - - +
129F ALA* 2.8 35.1 + - + +
142F PHE* 4.7 5.1 - - + -
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Residues in contact with ILE 126 (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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103F ALA* 4.0 20.0 - - + +
106F LEU* 3.8 26.0 - - + -
107F ARG* 3.3 45.1 - - + +
122F VAL* 3.0 18.5 + - + +
123F ASP* 3.2 15.9 + - - +
125F MET* 1.3 76.5 - - + +
127F ARG* 1.3 60.0 + - + +
129F ALA* 4.4 2.5 - - - +
130F ASP* 2.8 47.7 + - + +
135F GLY* 4.7 4.5 - - - -
137F VAL* 4.7 1.1 - - + -
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Residues in contact with ARG 127 (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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120F GLU* 4.5 6.7 + - - +
123F ASP* 2.9 49.3 + - - +
124F GLU* 3.0 38.6 + - - +
126F ILE* 1.3 77.4 - - + +
128F GLU* 1.3 59.6 + - - +
130F ASP 3.7 11.7 - - - +
131F ILE* 4.9 5.5 - - - +
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Residues in contact with GLU 128 (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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344A TRP* 3.5 25.3 - - + -
347A TYR* 3.3 9.0 + - - -
353A ARG* 2.5 50.7 + - - -
124F GLU* 3.0 19.6 + - - +
125F MET 3.9 0.4 - - - +
127F ARG* 1.3 80.0 - - - +
129F ALA* 1.3 58.5 + - - +
131F ILE* 3.3 8.7 - - - +
142F PHE* 3.3 17.5 - - + -
145F MET* 3.2 37.4 - - - +
146F MET* 3.9 4.7 - - - -
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Residues in contact with ALA 129 (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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90F PHE* 5.9 2.0 - - + -
106F LEU* 6.2 0.9 - - + -
125F MET* 2.8 18.9 + - + +
126F ILE* 4.2 1.8 - - - +
128F GLU* 1.3 76.9 - - - +
130F ASP* 1.3 59.6 + - - +
131F ILE* 3.0 10.4 + - - +
137F VAL* 3.5 20.2 - - + +
141F GLU* 2.9 24.8 - - - +
142F PHE* 3.4 34.1 - - + +
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Residues in contact with ASP 130 (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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126F ILE* 2.8 28.5 + - + +
127F ARG* 3.7 9.0 - - - +
129F ALA* 1.3 71.0 - - - +
131F ILE* 1.3 64.8 + - - +
132F ASP* 2.8 24.4 - - - +
133F GLY* 3.1 8.3 + - - -
134F ASP* 2.4 24.6 + - - +
135F GLY* 2.4 32.5 + - - -
136F GLN 3.8 6.7 - - - +
137F VAL* 3.5 21.1 - - + +
141F GLU* 3.8 5.4 - - - +
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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