Contacts of the helix formed by residues 78 - 90 (chain D) in PDB entry 1ORZ
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 CYS 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C LEU* 5.8 2.5 - - + -
45D ALA* 5.4 6.3 - - - +
48D VAL* 3.2 39.5 - - - -
49D VAL* 5.3 3.1 - - - -
52D ALA* 6.0 1.3 - - - -
74D LEU 3.2 5.1 + - - -
75D LEU* 3.0 28.3 + - + +
77D TYR* 1.3 73.3 - - - +
79D TYR* 1.3 50.3 + - - +
80D MET* 2.8 12.2 - - - +
81D GLU* 2.6 50.6 + - - +
82D PHE* 4.0 7.3 + - + -
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Residues in contact with TYR 79 (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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22D ASP 5.4 0.2 - - - -
24D TYR* 3.0 38.4 - + + +
75D LEU 3.6 2.3 + - - -
76D GLY 2.9 18.6 + - - +
77D TYR 2.8 1.4 + - - -
78D CYS* 1.3 76.5 - - - +
80D MET* 1.3 62.6 + - - +
81D GLU 3.0 0.2 - - - -
82D PHE* 2.9 22.8 + + + +
83D ASN* 3.0 9.8 + - + -
86D ILE* 3.8 4.4 - - + +
105D MET* 2.8 62.4 + - + +
108D LEU* 2.9 49.6 - - + +
109D GLY* 3.5 7.6 - - - -
112D VAL* 3.8 17.7 - - + -
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Residues in contact with MET 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ALA* 6.0 0.9 - - + +
24D TYR* 3.9 18.7 - - + +
25D VAL* 4.4 6.1 - - + -
29D GLU* 4.5 7.4 - - - +
41D GLU* 2.8 62.7 - - + +
44D PHE* 3.4 26.2 - - + -
45D ALA* 3.1 23.8 - - + +
77D TYR 3.2 14.1 + - - +
78D CYS* 2.7 8.9 + - - +
79D TYR* 1.3 77.4 - - - +
81D GLU* 1.3 64.7 + - + +
83D ASN* 2.9 12.4 + - - +
84D SER* 2.8 27.2 + - - -
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Residues in contact with GLU 81 (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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46C HIS* 4.8 5.4 + - - -
50C LEU* 3.0 43.6 - - + +
106C HIS* 4.0 17.6 + - - -
29D GLU* 5.1 6.5 - - - +
45D ALA* 5.0 10.1 - - + +
78D CYS* 2.6 34.6 + - - +
80D MET* 1.3 86.1 - - + +
82D PHE* 1.3 60.6 + - + +
84D SER* 3.1 16.8 + - - +
85D CYS* 3.1 18.0 + - - -
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Residues in contact with PHE 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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50C LEU* 3.8 37.5 - - + -
51C VAL* 4.0 22.7 - - + -
54C GLY* 3.5 29.2 - - - -
75D LEU* 5.6 9.0 - - + -
78D CYS* 4.2 10.5 - - + -
79D TYR* 2.9 26.4 + + + +
81D GLU* 1.3 75.0 - - - +
83D ASN* 1.3 61.8 + - - +
85D CYS* 3.2 8.1 + - + +
86D ILE* 2.8 35.1 + - + +
108D LEU* 3.1 39.3 - - + -
112D VAL* 5.9 3.8 - - + -
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Residues in contact with ASN 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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215B ARG* 6.1 0.6 - - - +
20D PRO* 5.5 1.6 - - - +
22D ASP* 3.7 2.8 - - - +
23D ALA* 3.7 32.5 - - - +
24D TYR* 5.6 0.4 - - + -
41D GLU* 4.6 5.3 + - - -
79D TYR* 3.0 12.3 + - + +
80D MET* 2.9 20.1 + - - +
82D PHE* 1.3 78.0 - - - +
84D SER* 1.3 61.0 + - - +
86D ILE* 3.2 9.4 + - - +
87D THR* 3.0 30.1 + - - +
101D TYR* 3.3 13.3 + - - -
105D MET* 2.9 33.9 - - + +
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Residues in contact with SER 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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215B ARG* 3.1 27.8 + - - +
217B HIS* 4.8 5.4 - - - -
47C ARG* 4.6 9.2 + - - -
29D GLU* 4.2 22.5 + - - -
41D GLU* 4.6 6.1 - - - -
80D MET 2.8 12.1 + - - -
81D GLU* 3.1 9.6 + - - -
83D ASN* 1.3 77.9 - - - +
85D CYS* 1.3 64.0 + - - +
87D THR* 2.6 27.1 + - - -
88D ASP* 3.3 4.0 + - - -
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Residues in contact with CYS 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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47C ARG* 3.8 40.8 - - - +
50C LEU* 4.4 16.4 - - - -
51C VAL* 4.8 18.4 - - + -
81D GLU 3.1 18.1 + - - -
82D PHE* 3.2 9.6 + - + +
84D SER* 1.3 76.9 - - - +
86D ILE* 1.3 64.3 + - + +
88D ASP 3.0 10.9 + - - -
89D TYR* 3.1 26.9 + - + -
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Residues in contact with ILE 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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79D TYR* 3.8 12.6 - - - +
82D PHE* 2.8 30.5 + - + +
83D ASN* 3.2 8.0 + - - +
85D CYS* 1.3 77.0 - - + +
87D THR* 1.3 58.1 + - - +
89D TYR* 5.2 0.7 - - - -
90D ILE* 2.8 49.4 + - + +
101D TYR* 3.0 41.0 - - + +
104D TYR* 5.0 7.6 - - + -
105D MET* 3.5 28.7 - - + +
108D LEU* 5.4 2.0 - - + -
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Residues in contact with THR 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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175B ASN* 4.9 7.1 - - - +
211B MET* 4.2 21.5 - - + +
215B ARG* 2.8 21.8 + - - +
83D ASN* 3.0 24.6 + - - +
84D SER* 2.6 20.8 + - - -
86D ILE* 1.3 77.7 - - - +
88D ASP* 1.3 63.0 + - - +
90D ILE 4.4 6.1 + - - +
91D SER* 5.6 0.7 - - - -
101D TYR* 3.0 29.1 - - - +
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Residues in contact with ASP 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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171B SER* 5.4 3.5 + - - +
174B TRP* 3.3 56.3 - - + +
175B ASN* 3.6 14.1 + - - +
215B ARG* 2.9 29.9 + - - -
217B HIS* 4.1 8.5 + - - -
47C ARG* 3.5 23.2 + - - -
84D SER 3.8 2.4 - - - +
85D CYS 3.0 7.8 + - - +
87D THR* 1.3 86.3 + - - +
89D TYR* 1.4 69.8 + - + +
91D SER* 4.9 3.6 + - - -
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Residues in contact with TYR 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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174B TRP* 4.0 34.2 + + - -
47C ARG* 3.1 34.4 + - - -
85D CYS* 3.1 21.0 + - + +
86D ILE* 5.2 0.2 - - - -
88D ASP* 1.4 81.1 - - + +
90D ILE* 1.3 72.6 + - + +
91D SER* 2.9 12.1 + - - -
92D GLU* 4.8 0.7 - - - +
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Residues in contact with ILE 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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86D ILE* 2.8 40.7 + - + +
87D THR 4.4 4.7 - - - +
89D TYR* 1.3 79.3 - - + +
91D SER* 1.3 60.1 + - - +
92D GLU* 2.7 27.4 - - - +
100D LYS* 4.1 15.9 - - + +
101D TYR* 3.2 53.4 - - + +
104D TYR* 5.9 7.0 - - + -
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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