Contacts of the helix formed by residues 65 - 74 (chain D) in PDB entry 1OY1
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 65 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D ASP* 3.4 22.0 + - - +
46D LYS* 3.6 18.9 + - - +
47D GLN* 4.2 3.6 - - - +
48D GLN* 4.1 1.6 - - - -
63D THR* 4.8 1.3 - - + +
64D ARG* 1.3 73.4 - - - +
66D VAL* 1.3 67.6 + - - +
67D LEU* 2.9 32.2 + - - +
68D ILE* 2.9 33.8 + - + +
69D GLU* 2.9 26.7 + - - +
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Residues in contact with VAL 66 (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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12D SER* 3.6 23.3 - - - +
13D GLY* 3.9 2.3 - - - +
43D ALA* 4.1 3.4 - - + -
44D PRO* 3.4 35.2 - - + +
46D LYS* 2.9 26.5 + - + +
47D GLN 4.3 1.6 - - - +
48D GLN* 3.3 31.8 - - + +
64D ARG 3.8 1.8 + - - -
65D ASN* 1.3 69.4 - - - +
67D LEU* 1.3 57.3 + - - +
69D GLU* 3.9 1.0 - - - +
70D ALA* 2.8 29.6 + - - +
103D ASN* 3.8 22.9 - - + -
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Residues in contact with LEU 67 (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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55C LEU* 4.0 23.6 - - + -
43D ALA* 3.7 21.8 - - + +
44D PRO 3.5 11.5 + - - +
45D ASP* 3.8 23.6 - - + +
65D ASN* 2.9 12.8 + - - +
66D VAL* 1.3 75.5 - - - +
68D ILE* 1.3 67.3 + - + +
70D ALA* 3.2 1.4 + - - +
71D ALA* 3.0 22.4 + - - +
78D ILE* 4.1 16.6 - - + +
79D ARG* 3.7 25.8 - - - +
80D PRO* 3.7 27.6 - - + -
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Residues in contact with ILE 68 (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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52C ILE 5.8 0.2 - - - +
53C ASN* 3.3 46.4 - - - +
54C HIS* 4.6 3.4 + - - +
55C LEU* 4.0 19.1 - - + -
56C THR* 5.5 0.7 - - - +
60C MSE 4.3 18.2 - - + -
65D ASN* 2.9 40.4 + - + +
67D LEU* 1.3 77.0 - - + +
69D GLU* 1.3 76.0 + - - +
71D ALA* 3.2 20.1 - - - +
72D ARG* 3.9 7.1 - - - +
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Residues in contact with GLU 69 (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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60C MSE 5.0 2.3 - - - +
64C ARG* 2.8 45.5 + - - -
72C ARG* 5.6 1.9 + - - +
14D CYS* 3.5 22.8 - - + +
48D GLN* 3.4 24.2 - - - +
64D ARG* 3.6 20.4 + - + +
65D ASN 2.9 16.9 + - - +
66D VAL 4.0 0.7 - - - +
68D ILE* 1.3 85.5 - - - +
70D ALA* 1.3 66.9 + - - +
71D ALA 2.9 2.2 - - - -
72D ARG* 2.9 40.6 + - - +
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Residues in contact with ALA 70 (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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11D LEU* 3.7 24.3 - - + +
13D GLY 3.8 18.3 - - - +
14D CYS* 4.7 0.7 - - - -
43D ALA* 3.8 6.7 - - + -
66D VAL 2.8 22.0 + - - +
67D LEU 3.8 1.6 - - - +
69D GLU* 1.3 73.5 - - - +
71D ALA* 1.3 61.9 + - - +
73D ILE* 3.0 22.1 + - - +
74D THR* 3.6 5.0 + - - -
78D ILE* 3.6 21.5 - - + -
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Residues in contact with ALA 71 (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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54C HIS* 4.0 5.4 - - - +
55C LEU* 4.0 26.5 - - + +
67D LEU 3.0 10.9 + - - +
68D ILE 3.2 16.2 - - - +
69D GLU 2.9 0.4 - - - -
70D ALA* 1.3 77.5 - - - +
72D ARG* 1.3 60.0 + - - +
74D THR* 3.3 10.3 + - - -
75D ARG* 3.0 4.2 + - - -
76D GLY* 2.8 28.4 + - - -
78D ILE* 3.6 19.0 - - + +
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Residues in contact with ARG 72 (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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14C CYS* 2.9 33.7 + - - +
15C GLY* 4.5 2.2 - - - -
16C VAL* 4.5 10.0 - - - +
18C ASP* 2.4 47.8 + - - +
21C GLU* 5.6 0.3 - - - +
22C ILE* 3.8 13.6 - - + +
48C GLN* 4.9 2.4 + - - +
51C VAL* 4.8 1.6 - - - +
52C ILE 3.7 5.1 + - - -
53C ASN* 5.7 0.2 - - - +
54C HIS* 3.3 38.4 + - + -
60C MSE 5.6 1.4 - - - -
64C ARG* 3.0 29.2 - - - +
69C GLU* 5.6 2.1 + - - +
14D CYS* 4.1 13.7 - - - -
68D ILE* 3.9 4.5 + - - +
69D GLU* 2.9 43.3 + - - +
71D ALA* 1.3 78.3 - - - +
73D ILE* 1.3 60.9 + - - +
74D THR 3.4 0.5 + - - -
75D ARG* 3.5 9.7 + - - +
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Residues in contact with ILE 73 (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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22C ILE* 4.0 11.9 - - + -
23C HIS* 2.8 29.1 + - - -
11D LEU* 4.3 11.4 - - + -
13D GLY 3.7 22.2 - - - +
14D CYS* 3.6 24.2 - - + -
20D SER* 4.2 9.4 - - - -
22D ILE* 4.3 12.8 - - + -
25D ALA* 4.1 31.9 - - + -
26D VAL* 4.3 13.2 - - + -
29D LEU* 4.2 14.5 - - + +
70D ALA 3.0 10.3 + - - +
72D ARG* 1.3 75.8 - - - +
74D THR* 1.3 59.6 + - - +
75D ARG* 3.8 0.5 + - - +
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Residues in contact with THR 74 (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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23C HIS* 4.5 4.2 - - - -
11D LEU* 3.7 21.3 - - + -
29D LEU* 4.6 5.2 - - + -
41D CYS* 3.5 35.4 - - + -
70D ALA 3.6 1.1 + - - +
71D ALA* 3.3 10.9 + - - -
72D ARG 3.2 0.2 - - - -
73D ILE* 1.3 81.7 - - + +
75D ARG* 1.3 71.7 + - - +
77D GLU* 3.0 32.4 + - - +
78D ILE* 3.3 21.1 - - + +
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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