Contacts of the helix formed by residues 56 - 67 (chain D) in PDB entry 2O1S
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 THR 56 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D GLY 3.4 10.7 + - - +
54D LEU 3.0 1.2 + - - -
55D GLY* 1.3 83.2 - - - +
57D VAL* 1.3 56.5 + - - +
58D GLU 3.5 1.6 - - - -
59D LEU* 3.9 14.8 - - + +
60D THR* 2.7 40.0 + - - -
76D TRP* 4.3 11.4 - - + -
81D GLN* 2.9 41.7 + - + +
84D PRO* 3.6 6.0 - - - +
179D ASN* 3.5 31.9 - - - +
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Residues in contact with VAL 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D CYS* 3.3 35.2 - - - +
35D LEU* 4.0 12.7 - - + +
36D ARG* 3.4 33.7 - - + +
39D LEU* 4.2 14.4 - - + -
53D GLY 4.4 1.1 - - - +
54D LEU* 3.2 24.8 + - - +
55D GLY 3.6 0.6 - - - -
56D THR* 1.3 75.1 - - - +
58D GLU* 1.3 77.4 + - - +
60D THR* 3.9 1.0 - - - -
61D VAL* 3.2 24.3 + - - +
84D PRO* 4.6 8.5 - - + -
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Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D CYS* 3.4 31.5 - - + +
36D ARG* 2.4 39.9 + - - -
55D GLY 5.0 0.2 - - - +
56D THR 3.5 0.2 - - - -
57D VAL* 1.3 75.6 + - - +
59D LEU* 1.3 58.1 + - - +
61D VAL* 3.7 1.6 - - - +
62D ALA* 2.8 31.2 + - - +
256D GLY 3.6 13.2 + - - +
257D HIS* 3.0 44.2 - - - +
259D VAL* 3.9 22.1 - - + +
262D LEU* 4.2 3.1 - - + -
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Residues in contact with LEU 59 (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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55D GLY 5.4 0.7 - - - +
56D THR* 3.6 20.5 + - + +
57D VAL 3.2 0.6 - - - -
58D GLU* 1.3 78.0 - - - +
60D THR* 1.3 53.9 + - - +
62D ALA* 3.1 2.6 + - - +
63D LEU* 2.7 55.2 + - + +
76D TRP* 4.1 8.7 - - + -
149D VAL* 4.0 33.0 - - + -
177D ILE* 4.2 24.7 - - + -
179D ASN* 5.0 7.6 - - + +
256D GLY 4.3 4.3 + - - +
262D LEU* 4.1 20.8 - - + +
266D LEU* 4.7 7.4 - - + -
280D ILE* 5.0 11.7 - - + -
282D THR* 6.1 1.1 - - + -
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Residues in contact with THR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D LEU* 5.5 0.2 - - - -
56D THR* 2.7 23.1 + - - -
57D VAL 3.9 2.2 - - - -
59D LEU* 1.3 74.9 - - - +
61D VAL* 1.3 64.4 + - - +
63D LEU* 3.2 2.6 + - - +
64D HIS* 3.0 41.4 + - + +
76D TRP* 3.7 23.7 - - + -
84D PRO* 3.6 17.7 - - - +
85D HIS* 3.5 33.7 + - + +
88D LEU* 3.7 11.9 - - + -
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Residues in contact with VAL 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 4.3 5.4 - - + +
28D LEU* 4.0 26.2 - - + -
31D LEU* 4.3 15.9 - - + -
32D CYS* 3.8 19.1 - - - -
35D LEU* 4.0 22.4 - - + -
57D VAL 3.2 17.1 + - - +
58D GLU 3.7 3.4 - - - +
60D THR* 1.3 76.0 - - - +
62D ALA* 1.3 64.7 + - - +
64D HIS* 3.9 1.6 - - - +
65D TYR* 3.0 22.3 + - - +
88D LEU* 4.1 13.2 - - + -
259D VAL* 3.9 16.8 - - + -
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Residues in contact with ALA 62 (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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58D GLU 2.8 19.1 + - - +
59D LEU* 3.4 5.4 - - - +
61D VAL* 1.3 76.9 - - - +
63D LEU* 1.3 62.5 + - - +
65D TYR* 3.2 10.0 + - - +
66D VAL* 3.2 20.8 + - - +
259D VAL* 4.2 3.6 - - + +
262D LEU* 3.8 21.1 - - + -
263D ILE* 3.8 21.1 - - + -
266D LEU* 3.7 18.6 - - + -
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Residues in contact with LEU 63 (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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59D LEU* 2.7 44.4 + - + +
60D THR* 3.2 4.5 + - - +
62D ALA* 1.3 74.2 - - - +
64D HIS* 1.3 58.7 + - - +
65D TYR 3.2 0.2 + - - -
67D TYR* 2.9 53.4 + - + +
74D LEU* 4.1 19.5 - - + -
76D TRP* 4.0 15.5 - - + -
147D VAL* 3.9 15.9 - - + -
149D VAL* 3.9 21.8 - - + -
177D ILE* 3.9 15.5 - - + -
266D LEU* 3.9 17.5 - - + -
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Residues in contact with HIS 64 (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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17D THR* 3.1 20.3 + - - +
20D LEU* 4.5 15.2 - - + +
21D ARG* 2.7 31.4 + - - +
60D THR* 3.0 36.1 + - + +
61D VAL 4.2 2.0 - - - +
63D LEU* 1.3 76.2 - - - +
65D TYR* 1.3 60.7 + - - +
66D VAL 3.4 0.2 - - - -
67D TYR* 3.4 5.4 - - - +
69D THR* 2.9 33.4 + - + +
74D LEU* 3.7 12.4 - - + +
85D HIS* 2.9 48.3 - + - -
88D LEU* 4.4 7.7 - - + +
89D THR* 4.3 1.3 + - - -
115D TYR* 4.2 9.4 - + - -
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Residues in contact with TYR 65 (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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20D LEU* 3.5 32.5 - - + -
21D ARG* 3.6 31.9 + - - +
23D LEU 2.9 28.6 + - - -
24D PRO* 4.2 0.5 - - - +
25D LYS* 3.5 36.6 + - + +
28D LEU* 3.6 28.0 - - + -
61D VAL 3.0 18.5 + - - +
62D ALA 3.6 4.9 - - - +
63D LEU 3.1 0.4 - - - -
64D HIS* 1.3 79.7 - - - +
66D VAL* 1.3 58.7 + - + +
263D ILE* 3.8 29.6 - - + -
267D LYS* 5.8 0.2 + - - -
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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
----------------------------------------------------------
21D ARG* 5.2 1.1 - - - -
62D ALA 3.2 11.4 + - - +
63D LEU 3.7 2.7 - - - +
65D TYR* 1.3 81.5 - - + +
67D TYR* 1.3 91.4 + - + +
68D ASN 4.0 0.3 + - - -
263D ILE* 3.4 45.1 - - + +
266D LEU* 3.7 19.3 - - + +
267D LYS* 4.6 24.6 + - - +
270D ARG* 3.8 19.5 + - - -
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Residues in contact with TYR 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D ARG* 3.0 21.3 + - - -
63D LEU* 2.9 38.0 + - + +
64D HIS 3.4 3.3 - - - +
66D VAL* 1.3 109.1 - - + +
68D ASN* 1.3 57.9 + - - +
69D THR* 2.9 26.2 + - + -
72D ASP* 3.6 16.6 - - + +
74D LEU* 6.0 0.7 - - + -
145D ARG* 3.8 14.4 - - + -
146D THR 4.8 2.0 + - - -
147D VAL* 3.9 27.2 - - + +
175D LEU* 3.5 25.3 - - + +
266D LEU* 4.7 7.6 - - + -
270D ARG* 3.3 44.5 - - + +
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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
------------------------------------------------------------
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