Contacts of the helix formed by residues 58 - 69 (chain A) in PDB entry 2O1X
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 ALA 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A SER 3.3 12.8 + - - +
55A SER 3.2 4.8 + - - -
56A LEU 3.1 0.4 - - - -
57A GLY* 1.3 76.9 - - - +
59A VAL* 1.3 64.3 + - - +
60A ASP 3.3 2.7 - - - -
61A ILE* 3.7 13.4 + - + +
62A ILE* 3.2 31.4 + - + +
83A GLN* 3.9 23.6 - - + +
151A VAL* 5.7 1.8 - - + -
181A ASN* 4.0 19.1 - - - +
287A THR* 5.5 0.4 - - - -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.5 32.3 - - - +
37A LEU* 4.0 13.5 - - + -
38A ARG* 3.9 21.8 - - + +
41A ILE* 3.7 25.1 - - + -
55A SER 3.3 15.7 + - - +
56A LEU* 3.1 18.4 + - - +
57A GLY 3.4 0.6 - - - -
58A ALA* 1.3 78.3 - - - +
60A ASP* 1.3 58.0 + - - +
62A ILE* 3.9 2.1 - - - +
63A THR* 2.7 35.5 + - - +
86A ALA* 4.3 10.2 - - + +
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Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 2.9 28.2 + - - +
38A ARG* 2.7 43.0 + - - -
57A GLY 5.0 0.4 + - - -
58A ALA* 3.3 0.6 - - - +
59A VAL* 1.3 74.1 - - - +
61A ILE* 1.3 62.2 + - - +
63A THR* 3.5 3.4 + - - -
64A ALA* 3.0 27.4 + - - +
261A GLY 3.5 14.6 - - - +
262A HIS* 2.8 42.5 + - - +
264A VAL* 3.7 8.5 - - + +
267A LEU* 4.3 5.3 - - + +
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ALA* 3.7 20.9 + - + +
60A ASP* 1.3 77.0 - - - +
62A ILE* 1.3 59.3 + - + +
64A ALA* 3.3 4.2 + - + -
65A LEU* 2.7 51.0 + - + +
151A VAL* 4.9 10.5 - - + -
179A VAL* 3.0 48.5 - - + -
181A ASN* 5.6 1.1 - - - -
261A GLY 4.2 2.5 + - - +
267A LEU* 4.1 19.4 - - + +
271A LEU* 5.2 4.7 - - + -
283A LEU* 5.1 2.9 - - + -
285A ILE* 3.8 26.5 - - + -
287A THR* 6.1 0.2 - - + -
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Residues in contact with ILE 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A SER 5.3 0.2 - - - +
58A ALA* 3.2 24.9 + - + +
59A VAL 3.9 2.9 - - - +
61A ILE* 1.3 78.0 - - + +
63A THR* 1.3 57.1 + - - +
65A LEU* 3.4 7.6 + - + +
66A HIS* 3.0 38.9 + - + -
78A PHE* 3.6 25.4 - - + -
83A GLN 3.3 26.9 - - - +
84A ALA* 3.8 14.8 - - - -
86A ALA* 3.8 13.9 - - + -
87A HIS* 3.4 35.4 - - + +
90A LEU* 4.2 2.5 - - + -
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 4.1 4.5 - - + +
30A LEU* 4.2 13.5 - - + +
33A LEU* 3.9 30.5 - - + -
34A THR* 4.4 6.0 + - - +
37A LEU* 3.7 17.8 - - - +
59A VAL* 2.7 26.3 + - - +
60A ASP* 3.6 4.9 - - - -
62A ILE* 1.3 74.2 - - - +
64A ALA* 1.3 66.1 + - - +
65A LEU 3.3 0.2 + - - -
66A HIS* 3.3 2.6 + - - +
67A TYR* 3.0 24.9 + - - +
90A LEU* 4.2 10.1 - - + +
264A VAL* 4.0 15.9 - - + -
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Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASP 3.0 17.8 + - - +
61A ILE* 3.7 4.7 - - - +
63A THR* 1.3 76.8 - - - +
65A LEU* 1.3 57.7 + - - +
67A TYR* 3.4 0.9 + - - +
68A VAL* 3.0 28.2 + - - +
264A VAL* 4.0 5.3 - - + +
267A LEU* 3.7 28.0 - - + -
268A VAL* 3.8 21.5 - - + -
271A LEU* 3.4 18.9 - - + +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 2.7 36.1 + - + +
62A ILE* 3.7 9.4 - - - +
63A THR 3.2 0.2 - - - -
64A ALA* 1.3 72.8 - - - +
66A HIS* 1.3 58.4 + - + +
69A LEU* 3.0 56.1 + - + +
76A ILE* 3.9 23.3 - - + -
78A PHE* 5.1 2.2 - - + -
149A ALA* 4.3 13.7 - - + -
151A VAL* 3.5 32.3 - - + -
177A LEU* 4.7 2.9 - - + -
179A VAL* 4.7 5.2 - - + -
271A LEU* 3.9 27.8 - - + -
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Residues in contact with HIS 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.7 19.6 - - + +
22A LEU* 3.7 23.0 - - + +
23A LYS* 3.2 13.7 + - - -
62A ILE* 3.0 39.3 + - + +
65A LEU* 1.3 75.2 - - + +
67A TYR* 1.3 59.5 + - - +
69A LEU 3.1 17.0 - - - +
70A ASP* 5.0 0.4 - - - -
71A SER* 3.3 27.3 + - - -
76A ILE* 3.6 18.4 - - + +
78A PHE* 5.2 2.3 - + - -
87A HIS* 2.8 33.9 + + - -
90A LEU* 4.5 12.8 - - + -
91A THR* 3.8 15.2 - - + +
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Residues in contact with TYR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU* 3.8 26.4 - - + +
23A LYS* 3.4 33.3 + - + +
25A LEU 3.1 28.5 + - - -
26A SER* 3.9 1.0 - - - -
27A ARG* 3.6 44.6 + - + -
30A LEU* 3.7 31.0 - - + -
63A THR 3.0 18.2 + - - +
64A ALA* 3.7 7.0 - - - +
66A HIS* 1.3 78.9 - - - +
68A VAL* 1.3 63.2 + - + +
268A VAL* 3.9 25.8 - - + -
272A GLU* 4.6 1.8 - - - -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LYS* 4.8 2.9 - - - +
64A ALA 3.0 20.3 + - - +
65A LEU 4.3 0.4 - - - +
67A TYR* 1.3 78.0 - - + +
69A LEU* 1.3 76.5 + - + +
268A VAL* 3.7 33.4 - - + +
271A LEU* 3.8 35.7 - - + +
272A GLU* 4.1 22.4 - - + +
275A VAL* 4.5 7.0 - - + -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 3.3 6.5 + - - -
65A LEU* 3.0 26.9 + - + +
66A HIS* 3.1 18.6 - - - +
68A VAL* 1.3 87.9 - - + +
70A ASP* 1.3 66.0 + - - +
74A ASP* 3.6 16.8 - - + +
75A ARG 5.2 0.2 - - - +
76A ILE* 3.8 29.8 - - + -
147A HIS* 3.8 24.0 - - + +
149A ALA* 4.0 24.2 - - + +
177A LEU* 5.8 0.4 - - + -
271A LEU* 6.2 0.7 - - + -
275A VAL* 3.5 32.1 - - + -
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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