Contacts of the helix formed by residues 88 - 98 (chain F) in PDB entry 5IRC
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 SER 88 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1285A VAL* 5.6 4.7 - - - +
1286A SER 5.7 0.3 + - - -
13F ASP* 5.1 0.2 + - - -
85F SER* 2.9 14.4 + - - +
86F ILE 3.2 1.2 - - - -
87F ASP* 1.3 88.3 - - - +
89F PRO* 1.3 62.7 - - - +
90F ASP* 3.7 9.1 + - - +
91F SER* 2.6 52.9 + - - -
92F LEU 3.3 3.3 + - - -
131F LEU* 5.5 0.2 - - - -
139F VAL* 4.2 3.4 - - - +
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Residues in contact with PRO 89 (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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1288A ASN* 5.4 0.2 - - - -
87F ASP 3.7 8.3 - - - +
88F SER* 1.3 87.3 - - - +
90F ASP* 1.3 64.2 + - - +
92F LEU* 3.2 4.4 + - + +
93F GLU* 3.0 22.7 + - - +
131F LEU* 4.5 2.9 - - + -
136F GLN* 3.6 36.3 - - + +
137F GLU 4.0 22.4 - - - +
139F VAL* 4.0 16.1 - - + -
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Residues in contact with ASP 90 (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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1286A SER 4.8 9.7 - - - +
1287A GLY 4.9 0.7 - - - -
1288A ASN* 3.1 48.1 + - + +
1313A THR* 4.0 17.1 + - - +
1315A ASN* 5.0 9.0 + - - +
1316A THR* 4.8 0.2 + - - -
88F SER* 3.1 8.0 - - - +
89F PRO* 1.3 79.0 - - - +
91F SER* 1.3 62.2 + - - +
93F GLU* 3.1 3.6 + - - +
94F ASN* 3.0 27.9 + - - -
136F GLN* 4.2 18.7 + - - -
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Residues in contact with SER 91 (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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13F ASP* 3.1 33.6 + - - +
16F CYS* 4.8 3.1 - - - -
83F CYS 4.9 0.5 - - - +
84F PHE* 3.3 13.2 - - - +
85F SER 2.9 30.1 + - - -
88F SER* 2.6 35.8 + - - -
90F ASP* 1.3 76.7 - - - +
92F LEU* 1.3 60.6 + - - +
94F ASN* 3.5 9.4 + - - +
95F ILE* 3.5 11.4 + - - +
99F TRP* 5.0 0.5 - - - -
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Residues in contact with LEU 92 (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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84F PHE* 3.9 40.6 - - + -
88F SER 3.3 0.4 + - - -
89F PRO* 3.2 9.1 + - + +
90F ASP 3.2 0.8 - - - -
91F SER* 1.3 79.0 + - - +
93F GLU* 1.3 67.7 + - - +
95F ILE* 3.0 23.0 + - + +
96F PRO* 3.3 5.4 - - - +
114F LEU* 5.0 0.2 - - + -
139F VAL* 3.8 32.8 - - + -
143F GLU* 4.3 20.4 - - + +
144F GLY* 4.9 1.3 - - - -
147F MET* 3.9 34.9 - - + +
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Residues in contact with GLU 93 (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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1288A ASN* 2.8 39.1 + - - +
1290A SER* 3.8 20.9 + - - -
1291A GLU* 4.7 7.8 - - - +
89F PRO 3.0 13.5 + - - +
90F ASP 3.1 7.6 + - - +
92F LEU* 1.3 77.2 - - - +
94F ASN* 1.3 61.3 + - - +
96F PRO* 3.2 17.8 - - + +
97F GLU* 3.4 13.6 - - + +
147F MET* 5.3 2.5 - - - -
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Residues in contact with ASN 94 (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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1286A SER* 4.4 0.8 - - - -
1287A GLY 2.9 25.4 + - - -
1288A ASN* 3.8 3.0 - - - +
1289A LYS* 2.9 34.0 + - - +
13F ASP* 2.8 39.0 + - - +
90F ASP 3.0 16.4 + - - +
91F SER 3.7 4.7 - - - +
92F LEU 3.1 0.4 - - - -
93F GLU* 1.3 78.0 - - - +
95F ILE* 1.3 58.3 + - - +
96F PRO 3.5 0.2 - - - -
97F GLU* 3.8 6.7 - - - +
98F LYS* 2.9 27.4 + - + +
99F TRP* 3.0 15.7 + - + +
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Residues in contact with ILE 95 (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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82F MET* 3.7 29.2 - - + -
83F CYS 3.7 25.8 - - - +
84F PHE* 4.1 6.5 - - + -
91F SER 3.5 9.8 + - - +
92F LEU* 3.0 22.4 + - + +
94F ASN* 1.3 78.0 - - - +
96F PRO* 1.3 62.5 - - + +
99F TRP* 4.2 7.9 - - + -
100F THR* 2.9 42.0 + - - +
114F LEU* 3.8 21.1 - - + -
147F MET* 3.8 21.1 - - + -
151F ILE* 4.0 7.2 - - + -
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Residues in contact with PRO 96 (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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92F LEU 3.3 10.3 - - - +
93F GLU* 3.2 17.9 - - + +
95F ILE* 1.3 90.4 - - + +
97F GLU* 1.3 62.4 + - + +
100F THR* 4.2 8.3 - - - +
101F PRO* 3.2 18.4 - - - +
147F MET* 3.6 30.5 - - + -
150F ARG* 5.2 7.4 - - - -
151F ILE* 4.8 6.3 - - + -
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Residues in contact with GLU 97 (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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1289A LYS* 3.9 31.2 + - + +
1290A SER* 3.9 27.4 + - - +
1293A GLU* 4.0 17.0 - - - +
93F GLU* 3.4 18.2 + - + +
94F ASN* 4.2 6.1 - - - +
95F ILE 3.3 0.2 - - - -
96F PRO* 1.3 84.2 - - + +
98F LYS* 1.3 58.6 + - - +
101F PRO* 3.8 9.6 - - - +
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Residues in contact with LYS 98 (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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1289A LYS* 3.9 33.9 - - + +
62F GLY 5.0 2.0 + - - -
64F GLU* 4.5 10.5 - - - +
67F ASP* 3.0 31.9 + - - -
70F ARG* 4.7 0.2 - - - +
94F ASN* 2.9 20.2 + - + +
96F PRO 3.5 0.2 - - - -
97F GLU* 1.3 79.8 - - - +
99F TRP* 1.3 104.1 + - + +
100F THR 3.5 1.6 - - - -
101F PRO* 3.5 4.3 - - - +
102F GLU* 3.2 48.1 + - - +
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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