Contacts of the helix formed by residues 88 - 99 (chain D) in PDB entry 1IBM
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 VAL 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D GLY* 1.3 68.3 - - - -
89D THR* 1.3 64.8 + - - +
90D GLY* 3.1 17.4 + - - +
91D SER* 3.2 24.9 + - - +
92D VAL* 3.0 20.3 - - - +
204D ILE* 5.5 0.4 - - + -
96E PRO* 4.2 25.8 - - + +
97E GLY* 4.0 13.9 - - - +
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Residues in contact with THR 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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5A U 5.5 1.9 + - - -
79D PHE* 4.3 17.5 - - + -
82D ALA* 3.9 4.3 - - + +
83D SER* 3.3 43.2 + - - +
87D GLY 3.1 3.3 + - - -
88D VAL* 1.3 73.1 - - - +
90D GLY* 1.3 65.7 + - - +
92D VAL* 3.6 2.8 - - - +
93D PHE* 3.3 19.2 + - - +
204D ILE* 4.4 4.3 - - + -
215D MG 3.0 15.0 - - - -
96E PRO 4.7 0.9 + - - -
97E GLY* 3.4 26.3 + - - -
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Residues in contact with GLY 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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79D PHE* 6.3 0.2 - - - -
88D VAL* 3.1 10.2 - - - +
89D THR* 1.3 76.5 - - - +
91D SER* 1.3 69.1 + - - +
93D PHE* 3.0 21.8 + - - +
94D LEU* 3.3 7.6 + - - +
200D GLU* 4.6 18.1 - - - +
204D ILE* 3.8 22.4 - - - +
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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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88D VAL* 3.2 28.3 + - - +
90D GLY* 1.3 70.3 - - - +
92D VAL* 1.3 79.1 + - - +
94D LEU* 2.8 23.0 + - - +
95D GLY* 2.8 10.5 + - - -
189D PRO 5.5 0.7 - - - +
190D ASP* 5.8 1.6 - - - -
191D ARG* 4.7 24.5 - - - +
200D GLU* 5.5 1.4 + - - +
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Residues in contact with VAL 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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82D ALA* 3.4 31.6 - - + +
85D LYS* 4.0 16.8 - - + -
86D LYS 3.6 21.3 - - - +
87D GLY* 4.5 2.7 - - - -
88D VAL 3.0 20.0 - - - +
89D THR 3.6 4.7 - - - +
91D SER* 1.3 83.9 + - - +
93D PHE* 1.3 62.9 + - - +
95D GLY* 3.0 4.5 + - - +
96D LEU* 2.8 36.0 + - + +
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Residues in contact with PHE 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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64D LEU* 4.1 4.7 - - + -
75D PHE* 3.4 46.2 - + - -
78D LEU* 3.6 20.0 - - + -
79D PHE* 3.2 56.8 - + + -
82D ALA* 3.7 6.7 - - + -
89D THR 3.3 9.4 + - - +
90D GLY* 3.0 14.4 + - - +
91D SER 2.8 2.6 + - - -
92D VAL* 1.3 76.1 - - - +
94D LEU* 1.3 68.4 + - + +
96D LEU* 3.0 5.9 + - - +
97D LEU* 2.7 40.9 + - + +
200D GLU* 6.0 3.8 - - + -
203D VAL* 4.2 13.9 - - + -
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Residues in contact with LEU 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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64D LEU* 4.0 20.4 - - + -
68D TYR* 4.6 2.9 - - - +
90D GLY 4.1 8.3 - - - +
91D SER* 2.8 10.9 + - - +
93D PHE* 1.3 78.5 - - + +
95D GLY* 1.3 54.2 + - - +
97D LEU* 3.4 12.1 - - + +
98D GLU* 2.6 40.8 + - - +
189D PRO* 5.5 1.8 - - - +
191D ARG* 3.7 44.6 - - + +
194D LEU* 4.9 13.7 - - + -
196D LEU* 3.8 25.6 - - + -
198D VAL* 5.5 4.0 - - + -
200D GLU* 3.8 18.2 - - + +
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Residues in contact with GLY 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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91D SER 2.8 13.1 + - - -
92D VAL* 3.3 5.6 - - - -
94D LEU* 1.3 79.9 - - - +
96D LEU* 1.3 65.1 + - - +
98D GLU* 3.0 12.4 + - - +
99D SER* 3.0 19.1 + - - -
188D LEU* 4.1 12.6 - - - +
189D PRO* 4.5 16.9 + - - +
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Residues in contact with LEU 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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78D LEU* 3.3 36.1 - - + +
81D GLU* 4.2 13.2 - - + -
82D ALA* 4.2 12.1 - - + +
85D LYS* 4.4 13.2 - - + -
92D VAL* 2.8 41.5 + - + +
93D PHE 3.6 5.4 - - - +
95D GLY* 1.3 72.8 - - - -
97D LEU* 1.3 63.7 + - - +
99D SER* 3.1 19.2 + - - +
100D ARG* 3.8 5.9 + - - +
139D ARG* 3.7 29.4 + - - +
188D LEU* 5.0 14.4 - - + -
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Residues in contact with LEU 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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64D LEU* 3.6 28.0 - - + -
68D TYR* 3.7 44.7 - - + -
70D ILE* 4.7 8.5 - - + -
75D PHE* 4.3 19.5 - - + -
78D LEU* 4.2 16.1 - - + +
93D PHE* 2.7 48.8 + - + +
94D LEU* 3.4 15.7 - - + +
96D LEU* 1.3 73.3 - - - +
98D GLU* 1.3 58.6 + - - +
99D SER 3.0 5.0 + - - -
100D ARG* 3.3 21.1 + - - +
103D ASN* 4.3 1.0 - - - +
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Residues in contact with GLU 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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68D TYR* 2.5 27.4 + - - -
94D LEU 2.6 20.9 + - - +
95D GLY 3.0 5.4 + - - +
97D LEU* 1.3 70.8 - - - +
99D SER* 1.3 58.2 + - - +
103D ASN* 2.7 36.8 + - - +
104D VAL* 4.1 7.1 - - - +
107D ARG* 2.6 35.7 + - - -
114D ARG* 3.7 0.3 + - - -
173D TRP* 4.0 12.1 + - + -
185D PHE* 4.3 7.3 - - - -
189D PRO* 3.5 28.9 - - + -
194D LEU* 3.0 19.8 - - + +
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Residues in contact with SER 99 (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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95D GLY 3.0 5.4 + - - -
96D LEU* 3.5 13.7 - - - -
97D LEU 3.0 1.6 - - - -
98D GLU* 1.3 77.7 - - - +
100D ARG* 1.3 64.9 + - - +
101D LEU 3.1 0.2 + - - -
104D VAL* 4.3 2.5 - - - -
138D TYR 3.6 0.7 - - - +
139D ARG* 3.7 15.4 - - - -
140D VAL* 2.9 44.2 + - - +
185D PHE* 3.7 11.0 - - - -
188D LEU* 3.0 33.4 - - - +
189D PRO* 5.3 0.2 - - - +
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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