Contacts of the helix formed by residues 68 - 76 (chain A) in PDB entry 4OQZ
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 ASP 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LEU* 3.4 3.5 - - - +
67A ILE* 1.3 94.1 - - - +
69A TYR* 1.4 62.5 + - - +
70A ASP* 3.1 14.5 + - - +
71A ALA* 2.8 39.4 + - - +
72A MET* 3.6 8.5 + - - +
92A SER* 3.9 20.8 + - - -
93A SER 5.2 0.9 - - - +
94A ASP* 3.4 22.7 - - + +
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Residues in contact with TYR 69 (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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68A ASP* 1.4 72.3 - - - +
70A ASP* 1.3 62.9 + - - +
72A MET* 3.0 15.5 + - + +
73A TYR* 3.0 25.0 - - + -
90A ASN* 3.2 48.4 + - + +
92A SER 3.5 15.1 + - - -
94A ASP* 3.3 38.8 + - + +
95A THR 4.2 2.0 - - - -
98A LYS* 3.6 34.3 - - + +
99A ALA* 3.6 19.7 - - + -
102A ALA* 3.7 17.5 - - + -
113A HIS* 4.1 8.3 - + - -
115A THR* 3.3 28.6 - - - +
116A GLY 4.9 1.0 + - - -
166A ALA* 5.1 1.8 - - + +
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Residues in contact with ASP 70 (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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68A ASP* 3.1 15.5 + - + +
69A TYR* 1.3 78.3 - - - +
71A ALA* 1.4 56.9 + - - +
72A MET 3.6 0.2 + - - -
73A TYR* 3.8 21.6 + - - +
74A GLY* 4.4 2.6 + - - -
94A ASP* 4.5 1.8 + - - +
98A LYS* 3.5 27.2 - - - +
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Residues in contact with ALA 71 (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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66A LEU* 3.3 22.4 - - + +
67A ILE* 4.0 26.5 - - + +
68A ASP* 2.8 23.6 + - - +
69A TYR 3.2 0.2 - - - -
70A ASP* 1.4 73.5 - - - +
72A MET* 1.3 62.9 + - - +
73A TYR 3.4 0.2 - - - -
74A GLY* 3.4 12.7 + - - -
75A VAL* 3.7 5.9 + - - +
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Residues in contact with MET 72 (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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64A LEU* 4.1 14.1 - - + -
66A LEU* 3.7 12.5 - - + +
68A ASP 3.6 5.0 + - - +
69A TYR* 3.0 19.2 + - + +
71A ALA* 1.3 72.9 - - - +
73A TYR* 1.3 71.4 + - - +
74A GLY 3.2 3.5 + - - -
75A VAL* 3.3 11.2 + - + +
76A LEU* 3.3 43.6 + - + +
88A LEU* 3.8 13.5 - - + -
90A ASN* 3.4 31.2 - - - +
102A ALA* 5.0 10.8 - - + +
105A ARG* 6.5 0.4 - - - -
106A VAL* 3.7 30.1 - - + -
113A HIS* 4.9 4.5 - - - +
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Residues in contact with TYR 73 (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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69A TYR* 3.0 38.6 - - + -
70A ASP* 4.0 14.4 - - - +
71A ALA 3.4 0.4 - - - -
72A MET* 1.3 82.6 - - + +
74A GLY* 1.3 55.9 + - - +
76A LEU* 3.9 9.3 + - + +
77A GLU* 3.2 28.1 + - - +
98A LYS* 4.3 1.7 + - + -
101A ALA* 3.2 28.8 + - - +
102A ALA* 3.2 19.3 + - + +
105A ARG* 4.1 32.5 - - + -
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Residues in contact with GLY 74 (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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70A ASP 4.4 2.0 + - - -
71A ALA 3.4 8.9 + - - -
72A MET 3.2 1.0 - - - -
73A TYR* 1.3 75.9 - - - +
75A VAL* 1.4 63.8 + - - +
77A GLU* 3.3 24.5 + - - +
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Residues in contact with VAL 75 (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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8A ILE* 4.2 25.8 - - + -
31A TRP* 3.8 26.2 - - + -
52A PRO* 3.7 38.5 - - + +
53A GLU* 4.8 0.9 - - - +
56A LEU* 5.5 3.6 - - + -
64A LEU* 4.9 4.5 - - + -
66A LEU* 3.7 28.0 - - + -
71A ALA 3.7 2.3 + - - +
72A MET* 3.3 9.5 + - - +
74A GLY* 1.4 74.7 - - - +
76A LEU* 1.3 73.9 + - + +
77A GLU* 3.3 2.9 + - - -
79A ALA* 3.9 5.8 + - - +
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Residues in contact with LEU 76 (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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56A LEU* 5.5 5.4 - - + -
64A LEU* 5.2 3.1 - - + -
72A MET* 3.3 52.3 + - + +
73A TYR* 3.9 8.5 - - + +
75A VAL* 1.3 89.6 - - + +
77A GLU* 1.4 51.0 + - - +
78A GLY 2.8 16.5 + - - -
79A ALA* 3.1 16.0 + - + -
80A GLU* 3.0 16.4 + - - +
83A VAL* 4.0 27.8 - - + -
88A LEU* 4.5 9.4 - - + -
105A ARG* 5.3 7.2 - - + -
106A VAL* 4.6 9.2 - - + -
109A LEU* 4.1 15.7 - - + -
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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