Contacts of the helix formed by residues 88 - 98 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1285B VAL* 5.7 5.0 - - - +
1286B SER 5.7 0.3 + - - -
13D ASP* 5.2 0.2 + - - -
16D CYS* 6.2 0.2 - - - -
85D SER* 2.9 17.7 + - - +
86D ILE 3.2 1.2 - - - -
87D ASP* 1.3 83.4 - - - +
89D PRO* 1.3 66.0 - - - +
90D ASP* 3.7 8.8 + - - +
91D SER* 2.6 51.8 + - - -
92D LEU 3.3 3.1 + - - -
139D VAL* 4.2 3.0 - - - +
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Residues in contact with PRO 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288B ASN* 5.4 0.2 - - - -
87D ASP 3.8 7.6 - - - +
88D SER* 1.3 85.2 - - - +
90D ASP* 1.3 63.0 + - - +
92D LEU* 3.1 6.0 + - + +
93D GLU* 3.0 21.9 + - - +
131D LEU* 4.6 2.7 - - + -
136D GLN* 4.2 32.1 - - + +
137D GLU 3.2 26.2 - - - +
139D VAL* 4.1 16.6 - - + -
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Residues in contact with ASP 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1286B SER 4.8 9.8 - - - +
1287B GLY* 5.0 1.0 - - - -
1288B ASN* 3.0 49.8 + - + +
1313B THR* 3.9 17.4 + - - +
1315B ASN* 5.2 7.3 + - - +
88D SER* 3.1 7.8 - - - +
89D PRO* 1.3 79.0 - - - +
91D SER* 1.3 56.9 + - - +
93D GLU* 3.1 4.0 + - - +
94D ASN* 2.9 33.3 + - - -
136D GLN* 4.1 18.5 + - - -
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Residues in contact with SER 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ASP* 3.1 31.1 + - - +
16D CYS* 4.8 3.4 - - - -
83D CYS 5.0 0.5 - - - +
84D PHE* 3.2 8.8 - - - +
85D SER 2.9 30.6 + - - -
88D SER* 2.6 34.6 + - - -
90D ASP* 1.3 76.5 - - - +
92D LEU* 1.3 61.8 + - - +
94D ASN* 3.4 9.5 + - - +
95D ILE* 3.5 16.1 + - - +
99D TRP* 5.0 0.5 - - - -
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D PHE* 3.9 40.8 - - + -
88D SER 3.3 0.8 + - - -
89D PRO* 3.1 9.9 + - + +
91D SER* 1.3 79.3 + - - +
93D GLU* 1.3 64.5 + - - +
95D ILE* 3.0 23.6 + - + +
96D PRO* 3.2 5.5 - - - +
114D LEU* 5.0 0.2 - - + -
139D VAL* 3.7 32.8 - - + -
143D GLU* 4.2 21.5 - - + +
144D GLY* 4.8 1.1 - - - -
147D MET* 3.9 36.5 - - + +
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Residues in contact with GLU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288B ASN* 2.9 35.5 + - - +
1290B SER* 3.6 20.0 + - - -
1291B GLU* 4.9 6.6 - - - +
89D PRO 3.0 12.2 + - - +
90D ASP 3.1 8.0 + - - +
92D LEU* 1.3 78.4 - - - +
94D ASN* 1.3 61.1 + - - +
95D ILE 3.1 0.2 - - - -
96D PRO* 3.1 17.5 - - + +
97D GLU* 3.3 24.6 - - + +
147D MET* 5.3 2.7 - - - -
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Residues in contact with ASN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1286B SER* 4.3 1.4 + - - -
1287B GLY 2.9 24.8 + - - -
1288B ASN* 3.8 3.4 - - - +
1289B LYS* 2.9 33.9 + - - +
13D ASP* 2.8 39.4 + - - +
90D ASP 2.9 16.6 + - - +
91D SER 3.7 4.9 - - - +
92D LEU 3.1 0.6 - - - -
93D GLU* 1.3 75.3 - - - +
95D ILE* 1.3 60.2 + - - +
96D PRO 3.5 0.4 - - - -
97D GLU* 4.3 5.0 - - - +
98D LYS* 2.8 29.0 + - + +
99D TRP* 3.0 14.7 + - - +
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Residues in contact with ILE 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D MET* 3.6 33.2 - - + -
83D CYS 3.7 20.9 - - - +
84D PHE* 4.2 6.5 - - + -
91D SER 3.6 9.2 - - - +
92D LEU* 3.0 23.1 + - + +
94D ASN* 1.3 78.3 - - - +
96D PRO* 1.3 63.6 - - + +
99D TRP* 4.2 9.4 - - + -
100D THR* 2.8 42.8 + - - +
114D LEU* 3.8 19.7 - - + -
147D MET* 3.7 20.4 - - + -
151D ILE* 4.1 6.3 - - + -
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Residues in contact with PRO 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1242A TRP* 3.8 18.5 + - + -
92D LEU 3.2 10.5 - - - +
93D GLU* 3.1 19.3 - - + +
95D ILE* 1.3 89.5 - - + +
97D GLU* 1.3 66.2 + - + +
98D LYS 3.4 0.2 - - - -
100D THR* 4.0 9.2 - - - +
101D PRO* 3.2 19.2 - - - +
147D MET* 3.7 19.5 - - + -
150D ARG* 3.5 40.6 - - - +
151D ILE* 5.0 0.7 - - + -
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Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1289B LYS* 3.9 30.1 + - + +
1290B SER* 4.2 27.4 + - - +
1293B GLU* 5.2 4.2 - - - +
93D GLU* 3.3 27.9 + - + +
94D ASN* 4.3 9.9 - - - +
95D ILE 3.4 0.6 - - - -
96D PRO* 1.3 85.1 - - + +
98D LYS* 1.3 60.1 + - - +
101D PRO* 3.7 9.5 - - - +
150D ARG* 5.3 5.7 + - - -
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Residues in contact with LYS 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1289B LYS* 3.9 25.1 - - + +
13D ASP* 5.3 0.7 - - - +
62D GLY 4.8 1.2 + - - -
64D GLU* 4.2 14.3 - - - +
67D ASP* 2.8 38.0 + - - +
70D ARG* 4.2 1.0 - - - +
94D ASN* 2.8 19.8 + - + +
96D PRO 3.4 0.2 - - - -
97D GLU* 1.3 82.0 - - + +
99D TRP* 1.3 104.1 + - + +
100D THR 3.4 1.6 - - - -
101D PRO* 3.3 5.7 - - - +
102D GLU* 3.3 37.7 + - + +
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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