Contacts of the helix formed by residues 73 - 90 (chain A) in PDB entry 3O75
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 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A F1X 3.2 36.7 + - - +
70A ASP* 3.1 27.8 + - + +
71A LEU 4.5 1.1 - - - -
72A GLU* 1.3 78.0 - - - +
74A PRO* 1.3 69.0 - - - +
75A SER* 3.2 23.2 + - - -
76A TYR* 3.0 28.9 + - + +
77A ALA* 3.3 8.8 + - - +
220A PHE* 5.2 3.8 + - - +
247A SER* 3.9 4.4 + - - -
249A VAL* 3.8 22.3 - - + +
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Residues in contact with PRO 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU 5.5 0.2 - - - +
72A GLU 3.2 11.4 - - - +
73A ASN* 1.3 86.5 - - - +
75A SER* 1.3 55.7 + - - +
77A ALA* 3.6 9.6 - - + +
78A ARG* 2.8 32.6 + - - +
248A TYR* 5.9 6.7 - - + -
249A VAL* 4.3 10.3 - - + -
252A GLN* 5.3 5.2 - - - +
276A ASN* 5.6 9.4 - - - +
72B GLU* 5.3 0.5 - - - +
74B PRO* 6.2 3.8 - - + -
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Residues in contact with SER 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A F1X 2.5 36.2 + - - -
73A ASN* 3.0 12.1 + - - -
74A PRO* 1.3 79.2 - - - +
76A TYR* 1.3 57.9 + - - +
78A ARG* 3.2 3.6 - - - +
79A ILE* 2.9 33.9 + - - +
274A GLY* 5.4 0.5 - - - -
291A GLN* 3.5 11.9 - - - -
293A HIS* 3.0 25.6 + - - -
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Residues in contact with TYR 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A F1X 3.0 49.3 + - - -
66A PHE* 4.4 9.4 - + - -
68A LEU* 4.1 20.6 - - + +
69A PRO* 3.5 37.2 - - + +
70A ASP* 3.7 15.0 - - + +
73A ASN* 3.0 28.8 + - + +
75A SER* 1.3 73.6 - - - +
77A ALA* 1.3 62.3 + - - +
79A ILE* 3.2 13.0 + - + +
80A ALA* 2.8 32.2 + - - +
124A ALA* 3.7 13.2 - - + -
147A ILE* 5.7 0.9 - - + -
148A ASP* 3.5 18.2 - - + -
149A ARG* 3.4 14.2 + - - -
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 5.1 1.7 - - - +
71A LEU* 4.2 16.7 + - - +
73A ASN 3.3 9.1 + - - +
74A PRO* 3.6 12.1 - - + +
76A TYR* 1.3 77.6 - - - +
78A ARG* 1.3 56.8 + - - +
80A ALA* 3.5 5.8 + - - +
81A LYS* 3.0 30.5 + - - +
71B LEU* 3.4 31.9 - - + +
72B GLU* 4.2 6.2 - - + +
77B ALA* 5.2 2.2 - - + -
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO 2.8 18.0 + - - +
75A SER 3.2 6.1 - - - +
77A ALA* 1.3 74.2 - - - +
79A ILE* 1.3 65.3 + - - +
81A LYS* 3.4 2.3 + - - +
82A GLN* 3.0 43.2 + - - +
293A HIS* 3.5 45.2 + - + +
72B GLU* 2.9 49.5 + - - +
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Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 4.2 12.1 - - + -
75A SER 2.9 23.4 + - - +
76A TYR* 3.2 16.8 + - + +
78A ARG* 1.3 75.0 - - - +
80A ALA* 1.3 52.1 + - - +
82A GLN* 3.2 7.4 + - - +
83A LEU* 2.7 51.1 + - + +
147A ILE* 4.3 27.6 - - + -
148A ASP* 5.5 2.5 - - + +
291A GLN* 3.8 22.9 - - - +
293A HIS* 4.0 22.0 - - + +
296A ILE* 4.4 7.2 - - + -
297A ALA* 4.0 11.4 - - + +
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.9 23.7 - - + -
68A LEU* 4.1 7.4 - - + -
76A TYR 2.8 18.0 + - - +
77A ALA* 3.7 6.3 - - - +
79A ILE* 1.3 78.4 - - - +
81A LYS* 1.3 57.1 + - - +
83A LEU* 3.4 4.2 - - - +
84A GLU* 2.8 29.5 + - - +
94A LEU* 3.4 3.6 - - - +
96A ILE* 3.8 23.6 - - + -
71B LEU* 4.0 5.8 - - + -
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Residues in contact with LYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA 3.0 17.3 + - - +
78A ARG 3.7 4.0 - - - +
80A ALA* 1.3 72.5 - - - +
82A GLN* 1.3 71.0 + - - +
84A GLU* 3.1 10.1 + - - +
85A GLN* 2.9 51.7 + - - +
70B ASP* 2.7 32.7 + - - +
71B LEU* 3.7 17.6 - - + +
72B GLU* 3.2 38.0 + - + +
100B ASP* 3.5 12.0 + - - -
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Residues in contact with GLN 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 3.0 36.0 + - - +
79A ILE* 3.5 6.1 - - - +
81A LYS* 1.3 79.5 - - - +
83A LEU* 1.3 64.2 + - - +
85A GLN* 4.1 10.8 + - - +
86A GLY* 3.1 20.4 + - - -
293A HIS 4.5 0.7 - - - +
294A GLY* 3.5 37.5 + - - +
297A ALA* 3.5 14.9 - - + +
301A LEU* 5.6 0.2 - - - +
72B GLU* 4.4 12.7 + - - -
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Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.9 29.6 - - + -
79A ILE* 2.7 19.3 + - + +
80A ALA 3.4 5.4 - - - +
82A GLN* 1.3 74.1 - - - +
84A GLU* 1.3 57.7 + - - +
86A GLY* 3.9 0.4 - - - -
87A ALA* 2.9 32.1 + - + +
94A LEU* 3.7 8.1 - - + -
122A PHE* 3.9 35.2 - - + -
147A ILE* 4.0 17.0 - - + -
297A ALA* 3.3 39.6 - - + +
300A ALA* 4.6 2.5 - - + -
301A LEU* 4.3 16.8 - - + +
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Residues in contact with GLU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA 2.8 18.1 + - - +
81A LYS* 3.1 9.4 + - - +
83A LEU* 1.3 74.8 - - - +
85A GLN* 1.3 67.2 + - - +
87A ALA* 3.2 1.7 + - - +
88A ARG* 2.9 43.0 + - - +
92A TYR 4.8 0.5 - - - +
94A LEU* 3.7 25.9 + - + +
96A ILE* 5.5 1.0 - - + +
71B LEU* 3.9 7.7 - - + +
98B SER* 2.6 46.2 + - - +
100B ASP* 2.6 32.1 - - - +
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 2.9 37.8 + - - +
82A GLN* 4.2 10.8 + - - +
84A GLU* 1.3 78.5 - - - +
86A GLY* 1.3 62.1 + - - +
88A ARG* 3.6 10.6 + - - +
89A ALA* 3.2 22.3 + - - +
100B ASP* 3.3 38.1 + - - +
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Residues in contact with GLY 86 (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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82A GLN 3.1 14.7 + - - -
85A GLN* 1.3 77.3 - - - +
87A ALA* 1.3 61.5 + - - +
89A ALA* 3.3 14.5 + - - +
90A ARG* 3.3 18.9 + - - +
301A LEU* 3.5 15.9 - - - +
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Residues in contact with ALA 87 (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* 4.2 17.0 - - + -
83A LEU* 2.9 21.2 + - + +
84A GLU* 3.6 5.6 - - - +
86A GLY* 1.3 76.4 - - - +
88A ARG* 1.3 55.7 + - - +
90A ARG* 3.1 10.5 + - - +
92A TYR* 2.7 51.0 + - + +
94A LEU* 4.8 9.6 - - + -
122A PHE* 6.3 0.2 - - + -
301A LEU* 3.6 12.2 - - + +
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 2.9 32.2 + - - +
85A GLN* 3.8 11.2 - - - +
87A ALA* 1.3 76.6 - - - +
89A ALA* 1.3 57.7 + - - +
91A GLY* 2.8 20.3 + - - -
92A TYR 3.1 14.1 + - - +
93A GLN* 4.1 19.8 - - - +
98B SER 2.8 28.9 + - - -
99B SER* 4.1 1.5 - - - +
100B ASP* 3.1 25.9 + - - +
105B SER* 3.4 36.6 + - - -
108B GLN* 4.4 11.6 + - - +
109B LEU* 4.8 0.6 - - - +
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLN 3.2 13.2 + - - +
86A GLY* 3.7 11.2 - - - +
87A ALA 3.3 0.2 - - - -
88A ARG* 1.3 80.1 - - - +
90A ARG* 1.3 62.5 + - + +
91A GLY 3.3 2.1 + - - -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLY 3.3 12.1 + - - +
87A ALA* 3.1 9.7 + - - +
88A ARG 3.1 0.8 - - - -
89A ALA* 1.3 82.1 - - + +
91A GLY* 1.3 58.0 + - - +
92A TYR* 3.2 22.5 - - + -
301A LEU* 5.0 5.8 - - + -
302A GLU* 6.2 2.2 - - - +
305A LEU* 3.8 34.1 - - + +
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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
------------------------------------------------------------
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