Contacts of the helix formed by residues 58 - 67 (chain A) in PDB entry 2OUX
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 SER 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ARG* 4.2 3.8 - - - +
57A LEU* 1.3 74.8 - - - +
59A PRO* 1.3 74.9 - - - +
60A LYS* 3.5 9.2 + - - +
61A GLU* 3.0 39.6 + - - +
62A LEU* 2.9 21.3 + - - +
87A TYR* 4.0 1.1 - - - -
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Residues in contact with PRO 59 (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 SER* 1.3 86.5 - - - +
60A LYS* 1.3 58.0 + - + +
62A LEU* 3.4 1.3 + - + -
63A ALA* 2.9 30.5 + - - +
87A TYR* 3.6 32.1 - - + +
90A ASP* 3.7 35.9 - - + +
91A MSE 3.5 24.0 - - + +
94A GLU* 4.3 2.5 - - + -
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Residues in contact with LYS 60 (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 SER* 3.2 8.6 + - - +
59A PRO* 1.3 79.3 - - + +
61A GLU* 1.3 66.0 + - + +
63A ALA* 3.1 4.9 + - - +
64A ASP* 3.1 28.4 + - - +
94A GLU* 2.8 56.7 + - + +
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Residues in contact with GLU 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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27A ARG* 2.4 45.2 + - - -
30A PHE* 5.3 2.4 - - - -
31A LEU* 3.8 18.6 - - + +
38A GLN* 4.6 5.2 - - - +
57A LEU* 3.4 21.0 - - + +
58A SER* 3.0 30.3 + - - +
60A LYS* 1.3 78.6 - - + +
62A LEU* 1.3 61.9 + - - +
64A ASP* 3.4 24.4 + - - +
65A MSE 3.7 6.8 + - - +
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Residues in contact with LEU 62 (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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30A PHE* 6.3 0.2 - - - -
53A LEU* 3.6 27.6 - - + -
54A TYR* 3.9 17.7 - - + -
57A LEU* 4.2 11.1 - - + +
58A SER 2.9 16.5 + - - +
59A PRO* 3.8 4.0 - - + +
61A GLU* 1.3 77.6 - - - +
63A ALA* 1.3 59.0 + - - +
65A MSE 3.2 28.9 + - + +
66A PHE* 3.0 40.2 + - + -
83A MSE 4.1 6.1 - - + -
87A TYR* 3.7 30.7 - - + +
91A MSE 3.9 14.6 - - + -
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Residues in contact with ALA 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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59A PRO 2.9 18.2 + - - +
60A LYS 3.1 6.2 + - - +
62A LEU* 1.3 75.1 - - - +
64A ASP* 1.3 66.4 + - - +
66A PHE* 3.9 0.6 - - - +
67A ASP* 2.9 31.1 + - - +
91A MSE 3.4 27.3 - - - +
94A GLU* 3.6 16.4 - - + +
95A MSE 3.6 16.7 - - + +
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Residues in contact with ASP 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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35A ILE* 3.4 37.7 - - + +
38A GLN* 5.3 1.3 - - - +
60A LYS* 3.1 17.2 + - - +
61A GLU* 3.6 17.0 - - - +
62A LEU 3.3 0.6 - - - -
63A ALA* 1.3 77.5 - - - +
65A MSE 1.3 61.8 + - - +
67A ASP* 3.6 17.3 - - - +
94A GLU 5.6 1.7 - - - +
96A TYR* 5.6 4.5 + - - -
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Residues in contact with MSE 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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30A PHE* 4.0 13.7 - - + -
35A ILE* 4.0 9.8 - - - +
38A GLN* 3.4 39.5 - - + +
39A GLY* 3.7 22.0 - - - +
42A TYR* 3.5 31.0 - - + -
61A GLU 3.7 4.6 + - - +
62A LEU* 3.2 32.4 + - + +
63A ALA 3.0 0.4 - - - -
64A ASP* 1.3 79.1 - - - +
66A PHE* 1.3 91.6 + - + +
67A ASP 3.2 0.2 - - - -
68A VAL* 3.0 23.4 + - - +
69A ILE* 3.5 7.0 + - + +
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Residues in contact with PHE 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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42A TYR* 3.6 28.9 - + - -
62A LEU* 3.0 28.1 + - + +
63A ALA 3.2 3.3 + - - +
65A MSE 1.3 95.5 - - + +
67A ASP* 1.3 68.0 + - - +
68A VAL 2.7 2.1 + - - -
69A ILE* 2.9 29.3 + - + +
76A MSE 3.9 24.9 - - + -
79A TYR* 4.2 11.9 - + + -
80A LEU* 4.1 10.5 - - + -
83A MSE 5.2 1.8 - - - -
91A MSE 3.2 37.0 - - + -
95A MSE 4.0 17.3 - - + +
103A LEU* 4.2 17.2 - - + +
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Residues in contact with ASP 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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35A ILE* 5.3 1.6 - - + -
63A ALA 2.9 21.9 + - - +
64A ASP* 3.6 19.9 - - - +
65A MSE 3.2 0.2 - - - -
66A PHE* 1.3 76.0 - - - +
68A VAL* 1.3 65.9 + - + +
69A ILE 4.6 1.6 - - - +
94A GLU 5.1 0.9 - - - +
95A MSE 3.3 11.4 - - - +
96A TYR* 2.9 51.8 + - + -
99A ASN* 2.9 41.7 + - - +
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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