Contacts of the helix formed by residues 70 - 81 (chain S) in PDB entry 1T9G
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 GLN 70 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S ARG* 3.3 43.4 + - - +
68S PRO* 3.0 24.7 - - + +
69S ALA* 1.3 90.3 - - - +
71S CYS* 1.3 55.3 + - - +
72S GLN 3.0 5.8 - - - -
73S GLU* 3.0 42.6 + - + +
74S THR 3.6 1.6 + - - -
93S PRO* 5.3 3.8 - - - +
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Residues in contact with CYS 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S ARG* 4.1 18.4 - - - -
65S SER* 3.2 24.5 - - - +
66S CYS 3.9 2.9 - - - -
67S GLY* 3.5 35.7 - - - +
68S PRO* 3.7 17.0 - - - +
70S GLN* 1.3 74.4 - - - +
72S GLN* 1.3 60.9 + - - -
73S GLU 3.3 0.2 - - - -
74S THR* 3.7 11.0 - - - -
75S ILE* 2.8 37.1 + - + +
88S HIS* 4.5 7.2 - - + +
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Residues in contact with GLN 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 4.5 4.3 - - - +
69S ALA* 2.7 31.5 + - - +
70S GLN* 4.6 0.7 - - - -
71S CYS* 1.3 69.3 - - - +
73S GLU* 1.3 68.3 + - + +
74S THR 3.0 0.5 + - - -
75S ILE* 3.1 3.2 + - - +
76S ARG* 2.8 37.8 + - - +
88S HIS* 3.3 32.8 + - - +
206S ILE* 3.4 32.3 - - + +
208S VAL* 3.9 17.6 - - - +
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Residues in contact with GLU 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 4.3 27.0 + - + +
21D LYS* 3.5 35.6 + - - +
22D GLU* 3.9 3.1 - - - +
12S ARG* 5.5 2.5 + - - +
36S HIS* 4.5 13.8 - - - +
70S GLN* 3.0 30.1 + - + +
72S GLN* 1.3 80.7 - - + +
74S THR* 1.3 61.8 + - - +
76S ARG* 3.3 4.0 + - - +
77S THR* 3.1 25.6 + - - -
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Residues in contact with THR 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S VAL* 4.1 18.2 - - + -
11S LYS 4.1 2.2 - - - +
12S ARG* 3.0 45.7 - - - +
36S HIS 5.7 0.2 + - - -
37S SER 4.7 2.6 + - - -
38S MET* 3.6 40.4 - - + +
65S SER* 4.4 2.9 - - - +
70S GLN 3.6 1.8 + - - -
71S CYS* 3.8 13.6 - - - -
72S GLN 3.1 0.4 - - - -
73S GLU* 1.3 73.8 - - - +
75S ILE* 1.3 64.8 + - - +
77S THR* 3.1 14.8 + - - -
78S ALA 3.2 8.8 + - - -
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Residues in contact with ILE 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S VAL* 4.5 5.4 - - + -
63S ALA* 4.0 12.6 - - + +
65S SER* 3.5 23.8 - - - +
71S CYS 2.8 20.8 + - - +
72S GLN* 3.1 5.2 + - - +
74S THR* 1.3 73.2 - - - +
76S ARG* 1.3 58.3 + - - +
78S ALA* 3.2 8.5 + - - +
79S LEU* 2.9 31.3 + - + +
86S GLY* 3.5 30.7 - - - -
87S ILE 3.8 4.0 - - - +
88S HIS* 3.5 39.9 - - + +
206S ILE* 3.6 14.8 - - + -
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Residues in contact with ARG 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLU* 3.1 41.0 + - - +
22D GLU* 3.8 10.7 - - - +
72S GLN* 2.8 23.1 + - - +
73S GLU 3.4 9.4 - - - +
75S ILE* 1.3 73.8 - - - +
77S THR* 1.3 62.4 + - - +
79S LEU* 3.3 10.5 + - - +
80S ALA* 3.0 21.5 + - - +
198S ILE 6.1 0.2 - - - -
201S ALA* 3.7 32.7 + - - +
202S LYS* 4.2 15.4 + - - +
204S LYS 3.9 12.3 + - - -
205S LYS* 5.0 1.2 - - - +
206S ILE* 3.5 36.4 - - + +
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Residues in contact with THR 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D GLU* 2.8 24.4 + - + +
38S MET* 4.7 14.4 + - + +
73S GLU 3.1 13.1 + - - -
74S THR* 3.1 9.1 + - - -
76S ARG* 1.3 75.5 - - - +
78S ALA* 1.3 59.0 + - - +
80S ALA* 2.9 20.8 + - - +
81S MET* 3.1 24.6 + - + +
193S ALA* 4.9 14.4 - - + -
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Residues in contact with ALA 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10S VAL* 4.6 1.3 - - + -
38S MET* 3.4 26.1 - - + +
46S VAL* 4.1 18.6 - - + +
63S ALA* 4.1 22.0 - - + -
74S THR 3.2 3.8 + - - +
75S ILE* 3.2 11.0 + - - +
77S THR* 1.3 78.2 - - - +
79S LEU* 1.3 62.1 + - - +
81S MET* 3.0 16.7 + - - +
82S GLY 3.3 8.7 + - - -
83S ALA* 3.4 9.1 + - - +
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Residues in contact with LEU 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63S ALA* 5.6 0.2 - - + -
75S ILE* 2.9 25.7 + - + +
76S ARG* 3.4 21.8 - - - +
78S ALA* 1.3 76.1 - - - +
80S ALA* 1.3 59.3 + - - +
82S GLY 3.3 4.3 + - - -
83S ALA* 3.3 26.0 - - + +
84S ASP 3.7 16.4 - - - +
85S ARG* 3.8 20.9 - - - +
86S GLY* 4.5 2.5 - - - +
201S ALA* 4.0 13.4 - - + +
204S LYS* 3.2 51.4 + - + +
206S ILE* 4.2 19.1 - - + -
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Residues in contact with ALA 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D GLU* 4.1 11.2 - - - +
76S ARG 3.0 12.6 + - - +
77S THR 2.9 12.7 + - - +
79S LEU* 1.3 75.7 - - - +
81S MET* 1.3 59.0 + - - +
82S GLY 3.4 0.4 + - - -
191S ARG* 5.6 0.2 - - - -
192S TYR 5.1 0.7 - - - +
193S ALA* 4.0 25.4 - - + -
194S THR 4.9 0.2 + - - -
197S ASN* 3.3 28.0 - - - +
198S ILE* 4.1 17.3 - - + -
201S ALA* 3.8 8.7 - - + +
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Residues in contact with MET 81 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S MET* 4.6 10.8 - - - +
43S GLU* 3.6 33.7 - - + +
46S VAL* 4.1 23.3 - - + -
47S GLU* 4.1 15.9 - - - +
50S VAL* 3.8 10.6 - - + +
77S THR* 3.1 23.6 + - + +
78S ALA* 3.0 12.1 + - - +
80S ALA* 1.3 80.3 - - - +
82S GLY* 1.3 55.2 + - - +
190S PRO* 4.5 5.2 - - + -
191S ARG* 3.4 54.8 + - + +
192S TYR 5.3 0.7 - - - -
193S ALA* 4.7 11.0 - - + +
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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