Contacts of the helix formed by residues 92 - 103 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20C TRP* 2.8 25.9 + - - +
21C GLY 3.9 4.3 + - - -
23C ALA 2.8 24.9 + - - +
25C ALA* 3.4 9.8 - - - +
36C ILE* 3.8 17.3 - - - +
90C GLU* 2.9 16.5 + - - +
91C CYS* 1.3 77.2 - - - +
93C ASP* 1.4 52.2 + - - +
94C GLY* 3.0 10.0 + - - -
95C VAL* 3.0 29.9 + - + -
96C PHE* 2.8 36.8 + - - +
4002C SAH 3.6 11.2 - - - +
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLY* 3.0 29.9 + - - +
22C ALA* 4.2 9.0 - - - +
23C ALA 6.1 0.2 - - - +
91C CYS 3.4 4.2 + - - +
92C ASN* 1.4 69.2 - - - +
94C GLY* 1.3 56.4 + - - +
96C PHE* 3.4 1.9 + - - +
97C GLN* 3.0 28.6 + - - +
114C LYS* 3.2 41.3 + - - +
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Residues in contact with GLY 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C GLY 4.9 0.2 + - - -
23C ALA 5.1 2.2 + - - -
24C PRO* 6.1 0.2 - - - -
25C ALA* 4.1 17.5 - - - -
27C TYR* 4.7 0.4 - - - -
92C ASN* 3.0 9.7 + - - -
93C ASP* 1.3 76.0 - - - +
95C VAL* 1.4 62.8 + - - +
97C GLN* 3.4 14.5 + - - +
98C ARG* 3.4 17.6 + - - +
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Residues in contact with VAL 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA* 4.1 7.0 - - + -
27C TYR* 3.4 26.2 - - - +
34C LEU* 4.2 4.7 - - + -
36C ILE* 3.9 16.4 - - + -
69C PHE* 3.9 7.1 - - + -
70C GLY 3.6 14.8 - - - +
90C GLU* 3.5 28.0 - - + +
92C ASN* 3.0 23.1 + - + +
94C GLY* 1.4 71.0 - - - +
96C PHE* 1.4 60.2 + - - +
98C ARG* 3.1 6.2 + - - +
99C LEU* 2.9 24.3 + - - +
4002C SAH 3.5 13.0 - - - +
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Residues in contact with PHE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU* 3.8 11.3 - - + +
92C ASN 2.8 21.8 + - - +
93C ASP 3.6 5.4 - - - +
95C VAL* 1.4 73.4 - - - +
97C GLN* 1.3 55.9 + - - +
99C LEU* 3.2 25.6 + - + +
100C ARG* 2.9 51.1 + - + +
112C PRO* 3.9 20.6 - - + -
113C LEU 3.5 31.0 - - - -
114C LYS* 3.4 52.0 - - + -
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Residues in contact with GLN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ASP 3.0 13.5 + - - +
94C GLY* 3.6 11.7 - - - +
95C VAL 3.2 0.4 - - - -
96C PHE* 1.3 77.1 - - - +
98C ARG* 1.3 62.7 + - + +
100C ARG* 3.3 38.4 + - - +
101C ASP* 3.1 40.8 + - - +
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Residues in contact with ARG 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C TYR* 3.4 66.5 + - + +
31C ASP* 5.6 4.2 + - - -
69C PHE* 4.0 10.1 - - + -
94C GLY 3.4 14.1 + - - +
95C VAL 3.1 8.6 + - - +
97C GLN* 1.3 75.0 - - + +
99C LEU* 1.3 57.7 + - - +
101C ASP* 3.3 9.6 + - - +
102C TRP* 3.0 28.6 + - - +
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Residues in contact with LEU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C PHE* 3.6 38.3 - - + -
88C ILE* 3.8 40.4 - - + +
90C GLU* 4.3 8.1 - - + -
95C VAL 2.9 11.8 + - - +
96C PHE* 3.2 28.2 + - + +
98C ARG* 1.3 75.9 - - - +
100C ARG* 1.4 55.7 + - - +
102C TRP* 3.2 6.9 + - + -
103C ALA* 2.9 34.4 + - - +
110C VAL* 4.2 10.8 - - + -
112C PRO* 3.7 25.1 - - + -
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C PHE* 2.9 46.2 + - + +
97C GLN* 3.3 40.3 + - - +
99C LEU* 1.4 75.2 - - - +
101C ASP* 1.4 58.7 + - - +
103C ALA* 4.4 4.4 - - - +
104C PRO* 3.2 24.1 - - - +
112C PRO* 5.6 7.0 - - + -
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Residues in contact with ASP 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C GLN* 3.1 35.1 + - - +
98C ARG* 3.8 9.7 - - - +
99C LEU 3.3 0.2 - - - -
100C ARG* 1.4 75.5 - - - +
102C TRP* 1.3 61.4 + - - +
104C PRO* 3.4 10.9 - - - +
105C ARG* 3.7 17.4 + - - +
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Residues in contact with TRP 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C PHE* 3.6 23.3 - + + -
72C ALA* 4.1 11.7 - - + +
75C ALA* 3.8 35.7 - - + -
76C SER* 3.4 19.5 + - - -
79C GLN* 3.8 13.5 - - + -
86C HIS* 3.9 6.7 - - - -
88C ILE* 3.6 21.8 - - + -
98C ARG 3.0 18.1 + - - +
99C LEU* 3.7 6.3 - - + +
101C ASP* 1.3 76.6 - - - +
103C ALA* 1.3 77.2 + - - +
105C ARG* 3.3 14.7 - - - +
106C GLN* 2.7 60.9 + - + +
110C VAL* 3.7 17.0 - - + -
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LEU* 2.9 22.0 + - + +
100C ARG* 4.4 3.6 - - - +
102C TRP* 1.3 81.7 - - + +
104C PRO* 1.4 66.5 - - + +
106C GLN* 3.3 19.6 + - - +
108C HIS 5.3 0.2 - - - +
110C VAL* 3.8 32.9 + - + +
112C PRO* 4.9 9.6 - - + -
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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