Contacts of the helix formed by residues 92 - 103 (chain D) in PDB entry 3ORH
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 ASN 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20D TRP* 2.7 31.4 + - - +
21D GLY 3.8 4.9 + - - -
23D ALA 2.8 21.7 + - - +
25D ALA* 3.4 14.0 - - - +
36D ILE* 3.9 16.0 - - - +
90D GLU* 3.0 15.3 + - - +
91D CYS* 1.3 76.3 - - - +
93D ASP* 1.3 53.4 + - - +
94D GLY* 3.1 6.2 + - - -
95D VAL* 3.1 28.8 + - + +
96D PHE* 2.8 36.3 + - - +
4003D SAH 3.6 11.9 + - - +
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Residues in contact with ASP 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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21D GLY* 3.0 28.6 + - - +
22D ALA* 4.2 8.6 - - - +
91D CYS 4.0 3.3 - - - +
92D ASN* 1.3 71.1 - - - +
94D GLY* 1.3 57.3 + - - +
96D PHE* 3.4 8.5 + - - +
97D GLN* 3.0 28.4 + - - +
114D LYS* 3.3 30.5 - - - +
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Residues in contact with GLY 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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23D ALA 5.1 2.2 + - - -
24D PRO* 6.1 0.2 - - - -
25D ALA* 4.0 17.9 - - - -
27D TYR* 4.7 3.6 - - - -
92D ASN* 3.1 9.5 + - - -
93D ASP* 1.3 75.5 - - - +
95D VAL* 1.3 62.5 + - - +
97D GLN* 3.4 15.5 + - - +
98D ARG* 3.4 10.6 + - - +
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Residues in contact with VAL 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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25D ALA* 4.0 7.0 - - + -
27D TYR* 3.4 26.2 - - - +
34D LEU* 4.2 4.9 - - + -
36D ILE* 3.9 21.3 - - + -
69D PHE* 4.0 6.4 - - + -
70D GLY 3.6 15.5 - - - +
90D GLU* 3.5 29.2 - - + +
92D ASN* 3.1 18.8 + - + +
94D GLY* 1.3 72.2 - - - +
96D PHE* 1.3 61.1 + - - +
98D ARG* 3.1 5.4 + - - +
99D LEU* 3.0 24.6 + - - +
4003D SAH 3.5 12.1 - - - +
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Residues in contact with PHE 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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90D GLU* 3.8 10.9 - - + +
92D ASN 2.8 21.0 + - - +
93D ASP* 3.6 7.0 - - - +
94D GLY 3.3 0.2 - - - -
95D VAL* 1.3 74.6 - - - +
97D GLN* 1.3 55.5 + - - +
99D LEU* 3.2 26.4 + - + +
100D ARG* 2.9 71.4 + - + +
112D PRO* 3.9 20.0 - - + -
113D LEU 3.4 31.0 - - - -
114D LYS* 3.5 42.2 - - + -
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Residues in contact with GLN 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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93D ASP 3.0 14.0 + - - +
94D GLY* 3.6 11.9 - - - +
95D VAL 3.2 0.6 - - - -
96D PHE* 1.3 77.5 - - - +
98D ARG* 1.4 59.5 + - - +
100D ARG* 3.2 28.7 + - - +
101D ASP* 3.1 44.9 + - - +
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Residues in contact with ARG 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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27D TYR* 3.1 48.9 - - + +
31D ASP* 3.2 32.8 + - - -
44D ARG* 4.4 3.2 - - - +
69D PHE* 4.0 8.3 - - + -
70D GLY 4.3 5.6 - - - -
71D MET* 3.3 31.3 + - - +
72D ALA* 4.6 7.7 - - - +
94D GLY 3.4 7.3 + - - +
95D VAL 3.1 10.4 + - - +
97D GLN* 1.4 73.4 - - - +
99D LEU* 1.4 59.4 + - - +
101D ASP* 3.4 9.2 + - + +
102D TRP* 3.0 34.0 + - + +
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Residues in contact with LEU 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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69D PHE* 3.6 36.0 - - + -
88D ILE* 3.8 43.1 - - + +
90D GLU* 4.4 7.4 - - + -
95D VAL 3.0 12.2 + - - +
96D PHE* 3.2 28.2 + - + +
98D ARG* 1.4 77.0 - - - +
100D ARG* 1.4 55.3 + - - +
102D TRP* 3.3 7.3 + - + -
103D ALA* 2.9 34.5 + - - +
110D VAL* 4.2 11.2 - - + -
112D PRO* 3.7 26.0 - - + -
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Residues in contact with ARG 100 (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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96D PHE* 2.9 55.2 + - + +
97D GLN* 3.2 33.1 + - - +
99D LEU* 1.4 75.1 - - - +
101D ASP* 1.3 59.0 + - - +
103D ALA* 4.4 3.8 - - - +
104D PRO* 3.2 24.4 - - - +
112D PRO* 5.6 7.4 - - + -
114D LYS* 5.1 6.1 - - - +
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Residues in contact with ASP 101 (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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97D GLN* 3.1 37.5 + - - +
98D ARG* 3.8 8.8 - - + +
99D LEU 3.3 0.2 - - - -
100D ARG* 1.3 76.7 - - - +
102D TRP* 1.3 62.9 + - - +
104D PRO* 3.4 11.2 - - - +
105D ARG* 3.9 14.8 + - - +
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Residues in contact with TRP 102 (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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69D PHE* 3.6 22.9 - + + -
72D ALA* 4.0 13.1 - - + +
75D ALA* 3.8 34.3 - - + -
76D SER* 3.4 19.3 + - - -
79D GLN* 3.7 13.7 - - + -
86D HIS* 4.0 7.4 - - - -
88D ILE* 3.6 20.2 - - + -
98D ARG* 3.0 21.5 + - + +
99D LEU* 3.7 6.5 - - + +
101D ASP* 1.3 77.5 - - - +
103D ALA* 1.3 75.9 + - - +
105D ARG* 3.3 36.1 - - - +
106D GLN* 2.7 61.4 + - + +
110D VAL* 3.7 17.0 - - + -
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Residues in contact with ALA 103 (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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99D LEU* 2.9 22.0 + - + +
100D ARG* 4.4 4.0 - - - +
102D TRP* 1.3 81.9 - - - +
104D PRO* 1.4 67.1 - - + +
106D GLN* 3.3 19.8 + - - +
110D VAL* 3.8 33.7 + - + +
112D PRO* 5.0 9.0 - - + -
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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