Contacts of the helix formed by residues 81 - 95 (chain H) in PDB entry 2R9R
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 81 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H ILE* 3.4 9.0 - - - +
80H ARG* 1.3 77.8 - - - +
82H ARG* 1.3 61.4 + - - +
83H PRO* 3.4 14.4 - - - +
84H SER* 2.7 43.4 + - - +
85H PHE* 4.3 5.5 + - - +
104H VAL* 4.5 2.1 - - - +
108H ILE* 3.9 24.8 - - + +
112H GLU* 4.1 24.2 + - - +
116H TYR* 5.1 1.6 + - - -
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Residues in contact with ARG 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H ILE* 3.9 18.1 + - - +
40H SER* 2.8 37.1 + - - -
41H GLY* 3.4 7.1 + - - -
42H LEU* 3.3 62.7 - - + +
44H PHE* 4.5 0.3 - - - -
80H ARG 4.1 0.9 - - - +
81H ASN* 1.3 71.4 - - - +
83H PRO* 1.4 77.1 - - + +
84H SER 3.1 2.8 + - - -
85H PHE* 3.3 15.6 + - - +
86H ASP* 4.3 2.9 + - - +
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Residues in contact with PRO 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H LEU* 5.9 0.2 - - + -
81H ASN* 3.4 16.6 - - - +
82H ARG* 1.4 96.0 - - + +
84H SER* 1.3 61.5 + - - +
86H ASP* 3.9 11.3 + - + +
101H PRO* 3.8 15.1 - - - +
103H ASN* 4.3 14.1 - - - +
104H VAL* 3.5 22.0 - - + -
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Residues in contact with SER 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H ASN* 2.7 27.0 + - - -
82H ARG 3.1 0.6 - - - -
83H PRO* 1.3 78.7 - - - +
85H PHE* 1.3 63.6 + - - +
87H ALA* 3.2 18.4 + - - +
88H ILE* 3.4 11.6 + - - +
101H PRO* 4.7 0.4 - - - -
104H VAL* 3.5 19.3 - - - +
108H ILE* 4.1 2.8 - - - +
109H PHE* 3.6 18.3 - - - -
112H GLU* 3.6 31.6 - - - +
116H TYR* 6.0 0.7 - - - -
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Residues in contact with PHE 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 3.8 21.3 - - + -
39H ILE* 3.5 23.3 - - + -
44H PHE* 3.4 45.3 - + + -
59H LEU* 3.8 31.4 - - + -
81H ASN 4.3 2.3 + - - +
82H ARG 3.3 12.1 + - - +
84H SER* 1.3 75.3 - - - +
86H ASP* 1.3 67.0 + - - +
88H ILE* 3.0 15.3 + - + -
89H LEU* 2.9 39.0 + - + +
116H TYR* 3.6 36.8 - + + +
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Residues in contact with ASP 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H LEU* 6.0 0.7 - - - +
44H PHE* 3.9 26.1 - - + -
82H ARG 4.3 1.0 + - - +
83H PRO* 3.9 12.0 + - + +
84H SER 3.3 0.2 - - - -
85H PHE* 1.3 77.4 - - - +
87H ALA* 1.3 57.4 + - - +
89H LEU* 3.5 2.9 + - - +
90H TYR* 3.1 28.3 + - - +
101H PRO* 5.6 2.7 - - + -
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Residues in contact with ALA 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H PRO 4.7 0.4 + - - -
84H SER 3.2 10.2 + - - +
85H PHE 3.1 0.2 - - - -
86H ASP* 1.3 77.7 - - - +
88H ILE* 1.3 67.0 + - - +
90H TYR* 3.4 7.5 + - - +
91H TYR* 3.1 21.7 + - - +
97H ARG 4.6 2.1 - - - +
98H LEU* 4.5 4.5 - - - +
99H ARG 3.2 27.7 + - - +
101H PRO* 3.8 12.1 - - + -
109H PHE* 3.6 16.6 - - + -
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Residues in contact with ILE 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H LEU* 5.0 0.9 - - + -
84H SER 3.5 14.6 - - - +
85H PHE* 3.0 25.9 + - + +
87H ALA* 1.3 77.0 - - - +
89H LEU* 1.3 62.0 + - - +
91H TYR* 3.1 21.2 - - - +
92H TYR* 3.3 24.1 - - + -
98H LEU* 4.5 1.1 - - + -
109H PHE* 4.1 22.7 - - + -
112H GLU* 4.6 3.4 - - + -
113H ILE* 4.5 12.3 - - + +
116H TYR* 3.9 42.2 - - + -
118H LEU* 4.1 23.6 - - + -
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Residues in contact with LEU 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 5.2 2.0 - - + -
44H PHE* 4.1 27.4 - - + -
45H GLU 4.1 16.6 - - - +
46H THR* 3.8 29.6 - - + +
51H LEU* 4.2 14.6 - - + -
59H LEU* 6.0 0.2 - - + -
85H PHE* 2.9 31.7 + - + +
86H ASP 3.9 3.6 - - - +
88H ILE* 1.3 75.0 - - - +
90H TYR* 1.3 66.1 + - - +
92H TYR* 3.1 9.0 + - + +
93H GLN* 3.0 44.2 + - + +
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Residues in contact with TYR 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H ASP* 3.1 18.9 + - - +
87H ALA* 3.8 7.9 - - - +
88H ILE 3.3 0.4 - - - -
89H LEU* 1.3 73.6 - - - +
91H TYR* 1.3 58.2 + - - +
93H GLN* 3.5 23.4 + - + +
94H SER* 2.7 62.4 + - - -
97H ARG* 3.2 40.6 + - + -
99H ARG* 5.7 7.9 - - + -
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Residues in contact with TYR 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H PHE* 3.5 42.8 - + + -
57H THR* 5.0 0.8 - - + +
87H ALA 3.1 11.6 + - - +
88H ILE* 3.1 11.9 - - - +
90H TYR* 1.3 80.0 - - - +
92H TYR* 1.3 71.9 + + - +
95H GLY 3.1 0.9 + - - -
96H GLY* 2.9 62.4 + - - -
97H ARG 3.2 18.6 + - - +
98H LEU* 3.9 17.9 - - + -
118H LEU* 3.6 43.7 + - + -
122H ALA* 4.0 23.4 - - + +
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Residues in contact with TYR 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H THR* 3.4 32.1 - - + +
51H LEU* 3.6 33.4 - - + -
53H GLN* 2.8 25.5 + - - -
54H PHE* 3.6 28.3 - + + -
57H THR* 2.6 37.8 + - + +
59H LEU* 3.6 25.7 + - + +
60H GLY 4.6 0.4 - - - -
88H ILE* 3.3 27.8 - - + -
89H LEU* 3.1 10.3 + - + +
91H TYR* 1.3 86.7 - + - +
93H GLN* 1.3 63.0 + - - +
95H GLY 3.5 3.5 + - - -
116H TYR* 4.4 2.9 + - - +
118H LEU* 3.9 13.0 - - + +
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Residues in contact with GLN 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45H GLU 4.7 4.6 + - - -
46H THR* 4.4 7.6 + - - +
50H THR* 4.0 19.1 - - + -
53H GLN* 5.3 0.2 + - - -
89H LEU* 3.0 38.8 + - + +
90H TYR* 3.1 33.8 + - + +
92H TYR* 1.3 79.2 - - - +
94H SER* 1.3 61.1 + - - +
95H GLY* 3.4 0.7 + - - -
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Residues in contact with SER 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H TYR* 2.7 55.4 + - - -
91H TYR 3.3 0.7 + - - -
93H GLN* 1.3 73.5 - - - +
95H GLY* 1.3 61.0 + - - +
96H GLY 3.5 0.2 - - - -
97H ARG* 3.0 42.1 + - - +
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Residues in contact with GLY 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H GLN* 4.0 17.5 - - - +
54H PHE* 3.8 12.8 - - - -
91H TYR 3.1 6.0 + - - -
92H TYR 3.9 8.3 - - - -
93H GLN 3.2 4.6 - - - -
94H SER* 1.3 80.2 + - - +
96H GLY* 1.3 57.2 + - - +
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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