Contacts of the helix formed by residues 81 - 91 (chain D) in PDB entry 1Q90
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 PHE 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B VAL* 3.2 29.6 - - + -
133B VAL* 3.6 27.8 - - + -
77D PRO* 3.9 14.4 - - + -
78D GLU* 2.8 28.2 + - - +
80D TYR* 1.3 94.0 - + - +
82D TYR* 1.3 67.2 + - - +
83D PRO* 3.0 5.5 - - - -
84D VAL* 3.0 10.0 + - + +
85D PHE* 2.8 22.9 + - + +
910D CLA 3.3 39.3 - - + -
920D TDS 4.0 38.8 - - + -
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Residues in contact with TYR 82 (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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76D LEU* 3.6 15.3 - - + +
77D PRO* 3.0 40.1 + - + -
78D GLU 3.3 10.5 - - - -
79D TRP* 2.9 24.2 + - + +
81D PHE* 1.3 76.6 - - - +
83D PRO* 1.3 59.6 - - + +
85D PHE* 3.4 5.5 - - - +
86D GLN* 3.0 24.4 + - - +
144D GLY* 3.7 11.0 - - - -
147D SER* 3.3 27.8 - - - +
148D THR* 4.0 16.2 - - + -
953D LMG 3.7 31.2 - - + -
1G MET 4.4 1.9 + - - -
2G VAL* 3.6 26.9 - - + +
3G GLU* 4.3 4.0 + - - +
7G CYS* 4.3 7.6 - - - -
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Residues in contact with PRO 83 (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 TRP 3.9 3.4 - - - +
80D TYR 3.8 10.1 - - - +
81D PHE 3.2 4.7 - - - -
82D TYR* 1.3 91.8 - - + +
84D VAL* 1.3 65.9 + - - +
86D GLN* 3.2 4.9 + - - +
87D ILE* 3.0 28.2 + - - +
140D ALA 3.5 24.5 - - - +
143D LEU* 4.0 5.9 - - + +
144D GLY* 4.0 12.1 - - - +
910D CLA 3.2 43.3 - - + +
953D LMG 4.5 7.6 - - + -
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Residues in contact with VAL 84 (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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81D PHE* 3.0 13.1 + - + +
83D PRO* 1.3 75.8 - - - +
85D PHE* 1.3 69.2 + - - +
87D ILE* 3.0 14.8 + - + +
88D LEU* 2.9 23.3 + - + +
101D MET* 3.2 55.6 - - + -
104D VAL* 4.7 5.8 - - + -
910D CLA 3.9 37.7 - - + +
920D TDS 3.9 13.0 - - + -
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Residues in contact with PHE 85 (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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153C PRO 5.7 0.2 - - - -
154C CYS 3.2 27.1 - - - -
155C HIS* 3.8 7.2 - + - -
75D ILE 4.5 2.5 - - - -
76D LEU* 3.4 30.7 - - + -
77D PRO* 3.9 17.9 - - + -
81D PHE 2.8 11.9 + - - +
82D TYR* 3.4 7.0 - - - +
84D VAL* 1.3 77.3 - - - +
86D GLN* 1.3 59.1 - - - +
88D LEU* 3.1 8.2 + - - +
89D ARG* 3.1 47.1 + - - +
147D SER* 3.3 29.4 - - - -
920D TDS 3.4 45.0 - + + +
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Residues in contact with GLN 86 (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 TYR 3.0 9.8 + - - +
83D PRO 3.4 8.3 - - - +
85D PHE* 1.3 73.5 - - - +
87D ILE* 1.3 68.0 + - - +
89D ARG* 2.8 35.1 + - - +
90D VAL* 2.9 40.2 + - + +
143D LEU* 3.4 42.2 - - + +
146D GLY* 3.2 2.9 - - - -
147D SER* 3.1 16.9 + - - -
154D SER* 2.7 29.6 + - - -
155D LEU* 3.8 19.2 - - - +
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Residues in contact with ILE 87 (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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83D PRO 3.0 20.9 + - - +
84D VAL* 3.3 17.9 - - + +
86D GLN* 1.3 77.7 - - - +
88D LEU* 1.3 60.8 + - + +
90D VAL* 3.1 9.8 - - - +
91D VAL* 2.8 39.1 + - + +
97D GLY 4.6 6.3 - - - +
100D LEU* 3.7 47.1 - - + +
101D MET 5.5 0.4 - - - +
104D VAL* 5.9 0.9 - - + -
143D LEU* 3.6 18.2 - - + -
910D CLA 4.0 25.1 - - + -
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Residues in contact with LEU 88 (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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154B VAL* 5.5 1.3 - - + -
136C HIS* 4.6 5.8 - - + +
137C LEU* 3.8 26.7 - - + -
155C HIS* 4.0 12.8 - - + +
169C PRO* 3.3 10.2 - - - +
84D VAL* 2.9 27.2 + - + +
85D PHE 3.1 10.1 + - - +
87D ILE* 1.3 79.6 - - + +
89D ARG* 1.3 62.8 + - - +
90D VAL 3.2 0.2 + - - -
91D VAL* 3.1 23.3 - - - +
93D ASN 5.3 0.5 - - - +
94D LYS 6.1 0.2 - - - +
97D GLY* 3.9 32.3 - - - +
98D VAL* 4.4 7.6 - - + +
101D MET* 4.4 7.9 - - + -
920D TDS 3.4 26.9 - - + -
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Residues in contact with ARG 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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154C CYS 5.0 1.2 + - - -
155C HIS* 3.6 35.4 - - + +
167C ARG* 3.2 25.6 + - - -
169C PRO* 4.4 4.8 - - - +
85D PHE* 3.1 40.4 + - - +
86D GLN* 2.8 47.5 + - - +
88D LEU* 1.3 78.3 - - - +
90D VAL* 1.3 59.1 + - + +
91D VAL 3.8 0.5 + - - +
147D SER* 3.7 13.0 + - - +
149D PHE 3.1 27.8 + - - -
150D PRO* 4.4 0.8 - - - +
151D ILE* 3.0 37.2 - - + +
154D SER* 3.7 11.9 + - - -
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Residues in contact with VAL 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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167C ARG* 5.3 1.1 - - - +
86D GLN* 2.9 28.2 + - + +
87D ILE* 3.1 23.3 - - - +
89D ARG* 1.3 80.4 - - + +
91D VAL* 1.3 65.7 + - + +
92D PRO* 3.8 6.6 - - - +
143D LEU* 5.6 2.2 - - + -
151D ILE* 5.0 9.9 - - + +
154D SER* 4.7 2.7 - - - +
155D LEU* 3.3 46.0 - - + -
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Residues in contact with VAL 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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169C PRO* 3.3 12.0 - - - +
87D ILE* 2.8 35.6 + - + +
88D LEU 3.1 15.3 - - - +
89D ARG 4.8 0.2 - - - -
90D VAL* 1.3 86.1 - - + +
92D PRO* 1.3 74.2 - - + +
93D ASN* 3.7 20.5 - - - +
96D LEU* 3.4 27.4 - - + -
97D GLY* 4.0 8.3 - - - +
100D LEU* 4.1 10.3 - - + -
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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