Contacts of the helix formed by residues 70 - 83 (chain A) in PDB entry 3Q02
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 GLY 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ASP 3.4 0.8 + - - -
69A LYS* 1.3 77.8 - - - +
71A MET* 1.3 65.8 + - - +
72A ALA 3.4 2.0 - - - -
73A PRO* 3.2 18.4 - - - +
74A ALA* 2.8 28.4 + - - +
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Residues in contact with MET 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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7A TYR* 5.1 16.8 - - + -
8A VAL* 4.4 15.3 - - + +
64A PHE* 3.3 36.1 - - + -
65A LYS 3.2 22.9 - - - +
66A ILE* 3.5 9.4 - - - +
68A ASP* 3.2 27.1 + - + +
69A LYS 3.1 18.8 + - - +
70A GLY* 1.3 80.2 - - - +
72A ALA* 1.3 64.1 + - - +
74A ALA* 3.2 5.8 - - - +
75A LEU* 3.2 22.1 + - - +
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Residues in contact with ALA 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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66A ILE* 3.7 26.5 + - + +
68A ASP 4.3 1.6 + - - +
71A MET* 1.3 73.7 - - - +
73A PRO* 1.3 75.6 - - + +
75A LEU* 3.1 7.3 + - - +
76A ARG* 3.0 26.8 + - - +
116A LEU* 3.6 41.5 - - + +
117A PHE* 5.4 1.9 - - + -
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Residues in contact with PRO 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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68A ASP 5.3 0.4 - - - +
70A GLY* 3.2 26.0 - - - +
72A ALA* 1.3 91.0 - - + +
74A ALA* 1.3 65.0 + - - +
76A ARG* 3.2 28.6 + - - +
77A HIS* 3.0 44.3 + - + +
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Residues in contact with ALA 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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8A VAL* 3.6 26.4 - - + +
70A GLY 2.8 24.7 + - - +
71A MET* 3.2 7.6 - - - +
73A PRO* 1.3 72.0 - - - +
75A LEU* 1.3 58.4 + - - +
77A HIS* 3.1 11.3 + - - +
78A LEU* 2.9 27.5 + - - +
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Residues in contact with LEU 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 VAL* 4.2 20.9 - - + -
12A ALA* 5.0 12.1 - - + -
37A TYR* 4.5 11.3 + - + +
40A ALA* 6.0 1.1 - - + +
41A SER* 5.7 7.2 - - - -
44A ALA* 4.1 17.5 - - + -
64A PHE* 4.1 14.1 - - + -
66A ILE* 3.6 31.2 - - + -
71A MET 3.2 8.2 + - - +
72A ALA* 3.1 9.2 + - - +
74A ALA* 1.3 78.8 - - - +
76A ARG* 1.3 58.0 + - + +
78A LEU* 3.4 16.7 - - + +
79A TYR* 2.9 26.5 + - - +
117A PHE* 5.0 9.2 - - + -
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Residues in contact with ARG 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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72A ALA* 3.0 11.0 + - - +
73A PRO* 3.2 38.3 + - - +
75A LEU* 1.3 73.3 - - + +
77A HIS* 1.3 78.0 + - + +
79A TYR* 3.1 8.8 + - + +
80A LYS* 3.0 34.1 + - + +
115A ARG* 3.5 9.3 + - - +
116A LEU* 2.9 36.5 + - - +
117A PHE* 4.8 6.7 - - + +
118A ARG* 3.2 49.3 - - + +
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Residues in contact with HIS 77 (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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73A PRO* 3.0 32.4 + - + +
74A ALA* 3.6 8.6 + - - +
76A ARG* 1.3 89.4 + - + +
78A LEU* 1.3 57.6 + - - +
80A LYS* 3.3 14.9 + - + +
81A GLU* 2.9 44.4 + - - +
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Residues in contact with LEU 78 (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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6A SER 5.7 0.9 - - - +
8A VAL* 4.2 10.8 - - + +
9A ALA* 3.7 32.1 - - + +
12A ALA* 5.2 1.6 - - + -
37A TYR* 4.2 17.7 - - + -
74A ALA 2.9 12.6 + - - +
75A LEU* 3.4 18.6 - - + +
77A HIS* 1.3 76.7 - - - +
79A TYR* 1.3 62.2 + - - +
81A GLU* 3.0 16.5 + - + +
82A LEU* 3.0 33.9 + - + +
367A THR* 3.9 25.6 - - + +
369A THR* 3.6 20.6 - - + +
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Residues in contact with TYR 79 (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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37A TYR* 3.7 24.2 + + - +
41A SER* 5.9 2.2 - - - -
75A LEU 2.9 14.6 + - - +
76A ARG* 3.1 11.8 + - - +
78A LEU* 1.3 74.3 - - - +
80A LYS* 1.3 67.4 + - + +
82A LEU* 3.3 2.7 + - - -
83A MET* 2.9 60.0 + - + +
93A THR* 3.4 29.7 + - + +
95A ASP* 5.3 7.9 - - - -
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Residues in contact with LYS 80 (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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76A ARG* 3.0 26.2 + - - +
77A HIS* 3.8 11.7 - - + +
79A TYR* 1.3 82.8 - - + +
81A GLU* 1.3 65.3 + - - +
83A MET 4.8 4.0 - - - +
84A GLY* 3.8 18.2 + - - -
118A ARG* 5.9 3.4 - - - +
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Residues in contact with GLU 81 (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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77A HIS* 2.9 30.1 + - - +
78A LEU* 3.0 13.4 + - + +
80A LYS* 1.3 79.4 - - - +
82A LEU* 1.3 63.8 + - - +
84A GLY* 4.9 0.2 - - - -
87A ASN* 4.0 11.8 + - - +
364A HIS* 3.9 22.4 + - + -
366A PRO* 6.4 0.2 - - + -
367A THR* 4.3 20.4 - - + +
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Residues in contact with LEU 82 (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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37A TYR* 3.5 41.5 - - + +
78A LEU* 3.0 25.0 + - + +
79A TYR 3.9 2.0 - - - +
81A GLU* 1.3 76.5 - - - +
83A MET* 1.3 68.9 + - + +
84A GLY 2.8 10.9 + - - -
87A ASN* 4.1 4.0 - - - +
89A ASP* 2.9 12.5 - - - +
91A ILE* 4.9 6.4 - - + +
233A LEU* 6.1 0.7 - - - +
364A HIS* 3.3 49.4 - - + +
367A THR* 4.2 6.1 - - - +
369A THR* 4.1 5.2 - - + -
371A LEU* 3.8 24.7 - - + -
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Residues in contact with MET 83 (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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37A TYR* 5.8 5.4 - - + -
79A TYR* 2.9 55.5 + - + +
80A LYS* 4.1 6.9 - - - +
82A LEU* 1.3 75.9 - - + +
84A GLY* 1.3 57.5 + - - +
85A PRO* 3.2 12.9 - - - +
89A ASP* 3.5 7.9 - - - +
91A ILE* 3.1 59.9 - - + +
92A SER* 4.3 0.2 - - - -
93A THR* 3.8 24.7 - - + +
371A LEU* 6.3 0.9 - - - -
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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