Contacts of the helix formed by residues 72 - 85 (chain A) in PDB entry 1Q20
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LYS 3.4 0.4 - - - -
71A SER* 1.3 81.1 - - - +
73A THR* 1.3 64.2 + - - +
74A THR 3.3 2.7 - - - -
75A TRP* 3.1 23.2 + - - +
76A MET 3.2 5.0 + - - -
145A MET* 3.3 11.3 - - - +
210A TYR* 4.1 11.4 - - - -
314A A3P 3.1 27.4 + - - -
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 4.1 17.9 - - + +
67A THR* 2.7 34.2 + - - +
71A SER 3.7 0.6 - - - -
72A GLY* 1.3 74.4 - - - +
74A THR* 1.3 64.9 + - - +
76A MET* 3.1 7.0 + - - +
77A ILE* 2.8 37.2 + - + +
103A TRP* 3.5 31.9 - - + -
123A SER* 4.7 1.8 - - - -
124A SER 5.7 0.2 - - - +
125A HIS* 3.4 6.1 - - - -
314A A3P 2.5 24.2 + - - -
401A PLO 5.5 0.4 - - - -
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 1.3 75.6 - - - +
75A TRP* 1.3 64.0 + - - +
77A ILE* 3.4 11.4 + - - +
78A GLU* 3.0 18.2 + - - +
97A ILE* 3.7 16.9 - - + +
249A MET* 3.5 24.3 - - + +
255A SER 4.0 12.8 - - - +
257A TYR* 3.8 11.0 + - + -
272A PHE* 3.1 19.5 - - - -
273A LEU* 4.4 9.9 - - + -
314A A3P 2.8 31.1 + - - -
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Residues in contact with TRP 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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72A GLY 3.1 13.8 + - - +
74A THR* 1.3 80.3 - - - +
76A MET* 1.3 63.8 - - - +
78A GLU* 3.1 1.9 + - - +
79A ILE* 2.9 41.9 + - + +
145A MET* 4.7 0.7 - - + -
210A TYR* 3.5 33.7 - + - -
213A LEU* 3.6 51.1 - - + -
214A GLN* 3.7 24.9 - - + -
217A LEU* 4.1 17.5 - - + +
244A SER* 3.0 23.3 + - - -
245A THR* 5.7 0.7 - - - -
246A PHE 5.6 1.3 - - - -
249A MET* 4.1 5.4 - - - -
314A A3P 3.2 51.6 + + + +
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Residues in contact with MET 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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65A ILE* 3.8 30.3 - - + -
72A GLY 3.2 1.6 + - - -
73A THR 3.1 7.9 + - - +
75A TRP* 1.3 78.5 - - - +
77A ILE* 1.3 62.9 + - - +
79A ILE* 3.2 9.1 + - - +
80A ILE* 3.0 37.5 + - + +
143A ILE* 3.9 13.9 - - + -
145A MET* 4.1 20.1 - - + -
208A ILE* 3.5 28.5 - - + -
213A LEU* 4.2 15.5 - - + +
224A ILE* 3.4 35.2 - - + -
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Residues in contact with ILE 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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65A ILE* 3.6 22.6 - - + +
73A THR* 2.8 39.0 + - + +
74A THR* 3.6 9.0 - - - +
76A MET* 1.3 76.9 - - - +
78A GLU* 1.3 62.8 + - - +
80A ILE* 3.4 1.6 + - - +
81A CYS* 3.0 36.6 + - - -
97A ILE* 3.6 27.8 - - + +
101A ALA* 3.6 24.7 - - + +
103A TRP* 4.4 10.8 - - + +
121A LEU* 4.4 0.6 - - + +
123A SER* 3.5 20.6 - - - +
257A TYR* 5.3 2.9 - - - +
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Residues in contact with GLU 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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74A THR 3.0 6.2 + - - +
75A TRP 3.6 3.8 - - - +
77A ILE* 1.3 76.9 - - - +
79A ILE* 1.3 64.8 + - - +
81A CYS* 3.3 2.7 + - - +
82A LEU* 3.1 36.6 + - + +
92A ILE* 3.6 16.9 - - + +
97A ILE* 4.0 2.6 - - + +
100A ARG* 2.8 31.7 + - - -
243A HIS 4.2 8.7 - - - +
244A SER* 4.8 1.6 - - - +
249A MET* 3.5 42.6 - - + +
252A ASN* 3.8 6.8 + - - +
255A SER* 2.5 34.2 + - - -
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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
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75A TRP* 2.9 22.3 + - + +
76A MET* 3.2 10.3 + - - +
78A GLU* 1.3 76.1 - - - +
80A ILE* 1.3 58.6 + - + +
82A LEU* 3.3 4.5 + - - +
83A ILE* 2.9 42.2 + - + +
213A LEU* 3.7 31.4 - - + -
217A LEU* 3.8 20.9 - - + -
221A VAL* 4.3 10.5 - - + -
224A ILE* 4.4 17.7 - - + -
240A VAL* 3.8 9.9 - - + +
244A SER* 3.2 25.4 - - - +
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Residues in contact with ILE 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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63A ILE* 4.5 5.4 - - + -
65A ILE* 4.2 15.7 - - + -
76A MET* 3.0 31.5 + - - +
77A ILE 4.1 2.5 - - - +
78A GLU 3.3 0.2 - - - -
79A ILE* 1.3 72.2 - - + +
81A CYS* 1.3 62.2 + - - +
82A LEU 3.1 1.6 - - - -
83A ILE* 4.1 5.2 - - + -
84A LEU* 2.8 41.5 + - + +
121A LEU* 3.9 24.9 - - + -
143A ILE* 4.1 25.8 - - + -
224A ILE* 4.2 17.7 - - + -
228A LEU* 4.3 21.1 - - + -
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Residues in contact with CYS 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 ILE* 3.0 30.3 + - - +
78A GLU 3.7 2.0 - - - +
80A ILE* 1.3 75.5 - - - +
82A LEU* 1.3 63.0 + - - +
84A LEU* 3.6 3.3 + - - +
85A LYS* 3.4 27.4 + - - +
88A ASP 5.3 0.2 - - - +
91A TRP* 3.8 16.9 - - + -
92A ILE* 3.7 23.2 - - + +
100A ARG* 3.4 40.8 - - - +
121A LEU* 3.9 15.9 - - - -
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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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78A GLU* 3.1 20.9 + - + +
79A ILE 3.5 7.0 - - - +
81A CYS* 1.3 75.0 - - - +
83A ILE* 1.3 63.9 + - - +
85A LYS* 3.2 5.3 + - - +
86A GLU 3.0 4.9 + - - -
87A GLY* 2.8 31.4 + - - +
88A ASP 4.3 5.2 - - - +
89A PRO* 4.2 14.6 - - + -
92A ILE* 3.3 32.5 - - + -
240A VAL* 3.3 40.6 - - + +
243A HIS* 3.5 25.1 - - + -
244A SER* 3.4 13.0 - - - +
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Residues in contact with ILE 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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79A ILE* 2.9 30.3 + - + +
80A ILE* 3.1 11.2 + - + +
82A LEU* 1.3 75.5 - - - +
84A LEU* 1.3 58.3 + - + +
86A GLU* 2.9 25.1 + - - +
221A VAL* 4.2 5.2 - - + +
224A ILE* 3.9 26.9 - - + -
225A CYS* 3.7 32.3 - - - +
228A LEU* 4.6 8.1 - - + -
230A ARG* 4.1 35.1 + - + +
232A LEU* 4.2 8.7 - - + +
240A VAL* 4.2 16.6 - - + -
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Residues in contact with LEU 84 (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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63A ILE* 4.4 15.9 - - + -
80A ILE* 2.8 37.0 + - + +
81A CYS 3.8 4.7 - - - +
82A LEU 3.3 0.2 - - - -
83A ILE* 1.3 74.4 - - + +
85A LYS* 1.3 65.0 + - + +
86A GLU* 3.5 7.3 + - - +
91A TRP* 4.2 22.9 - - + -
119A PRO* 4.7 16.4 - - + +
121A LEU* 4.3 19.3 - - + -
230A ARG* 3.6 51.0 + - - +
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Residues in contact with LYS 85 (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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81A CYS 3.4 15.6 + - - +
82A LEU 3.2 3.3 + - - +
84A LEU* 1.3 81.5 - - - +
86A GLU* 1.3 69.5 + - - +
87A GLY 3.3 1.6 - - - -
88A ASP* 3.2 37.4 + - + +
91A TRP* 3.8 50.3 - - + -
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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