Contacts of the helix formed by residues 59 - 77 (chain A) in PDB entry 1QST
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 THR 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ASP* 2.6 38.9 + - - +
58A GLY* 1.3 81.0 - - - +
60A HIS* 1.3 64.6 + - - +
61A ARG* 4.3 5.8 - - - +
62A ASN* 3.3 15.9 + - - +
63A MET* 2.9 27.2 + - - +
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Residues in contact with HIS 60 (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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58A GLY 4.1 1.3 + - - -
59A THR* 1.3 72.6 - - - +
61A ARG* 1.3 63.7 + - - +
63A MET* 4.3 2.6 - - - +
64A LYS* 3.0 26.5 + - - +
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Residues in contact with ARG 61 (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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59A THR* 3.3 5.9 + - - +
60A HIS* 1.3 82.0 - - - +
62A ASN* 1.3 76.6 + - - +
64A LYS* 3.5 6.6 - - - +
65A LEU* 3.3 47.4 + - + +
100A LEU* 4.0 9.5 - - - +
103A LYS 2.6 30.7 + - - -
104A GLN* 4.1 20.0 + - - +
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Residues in contact with ASN 62 (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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54A LEU* 4.1 14.8 - - + +
55A THR* 2.7 45.7 + - - +
57A ASP* 3.2 28.3 + - - +
59A THR* 3.3 7.0 + - - +
61A ARG* 1.3 89.4 + - - +
63A MET* 1.3 67.4 + - - +
65A LEU* 3.2 9.0 + - - +
66A LEU* 3.0 26.9 + - - +
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Residues in contact with MET 63 (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 ASN* 2.9 36.8 - - - +
57A ASP* 4.3 0.7 - - - +
58A GLY* 3.6 15.7 - - - -
59A THR 2.9 34.3 + - - +
60A HIS* 4.3 2.7 - - - +
62A ASN* 1.3 76.3 - - - +
64A LYS* 1.3 56.3 + - - +
66A LEU* 3.4 6.8 + - - +
67A ILE* 3.0 40.9 + - + +
90A PHE* 3.4 34.2 - - + -
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Residues in contact with LYS 64 (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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60A HIS 3.0 20.4 + - - +
61A ARG* 3.5 8.5 - - - +
62A ASN 3.1 0.2 - - - -
63A MET* 1.3 79.6 - - - +
65A LEU* 1.3 62.8 + - + +
67A ILE* 3.4 9.2 + - + +
68A ASP* 2.8 60.9 + - - +
104A GLN 4.8 8.9 + - - -
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Residues in contact with LEU 65 (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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54A LEU* 3.4 38.1 - - + +
61A ARG* 3.3 48.0 + - + +
62A ASN* 3.2 4.6 + - - +
64A LYS* 1.3 78.8 - - + +
66A LEU* 1.3 60.2 + - - +
68A ASP* 3.4 9.6 + - - +
69A LEU* 3.0 26.7 + - - +
100A LEU* 4.0 17.0 - - + -
104A GLN* 3.6 27.4 - - - +
106A VAL* 3.8 19.3 - - + +
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Residues in contact with LEU 66 (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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54A LEU* 4.0 29.8 - - + +
55A THR 4.1 4.5 - - - +
56A ASN* 3.7 39.7 - - + +
62A ASN 3.0 18.7 + - - +
63A MET* 3.8 11.9 - - - +
64A LYS 3.3 0.2 - - - -
65A LEU* 1.3 76.0 - - - +
67A ILE* 1.3 60.1 + - - +
69A LEU* 3.3 6.5 + - + +
70A LYS* 2.8 28.9 + - - +
89A VAL* 4.1 19.4 - - + +
90A PHE* 3.8 21.5 - - + -
96A SER* 4.1 20.9 - - - +
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Residues in contact with ILE 67 (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 MET* 3.0 28.4 + - + +
64A LYS* 3.7 8.3 - - + +
66A LEU* 1.3 73.1 - - - +
68A ASP* 1.3 67.2 + - - +
70A LYS* 3.1 22.6 + - - +
71A ASN* 2.8 43.7 + - - +
90A PHE* 4.0 18.2 - - + -
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Residues in contact with ASP 68 (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 LYS* 2.8 53.9 + - - +
65A LEU* 3.5 5.7 - - - +
66A LEU 3.3 0.2 - - - -
67A ILE* 1.3 79.1 - - - +
69A LEU* 1.3 60.4 + - - +
71A ASN* 3.3 10.2 + - - +
72A ILE* 3.1 26.4 + - + +
104A GLN 4.8 1.2 - - - +
106A VAL* 3.4 31.5 - - + +
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Residues in contact with LEU 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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65A LEU 3.0 17.1 + - - +
66A LEU* 3.6 9.2 - - + +
67A ILE 3.2 0.2 - - - -
68A ASP* 1.3 73.2 - - - +
70A LYS* 1.3 66.7 + - - +
72A ILE* 3.0 8.4 + - + +
73A PHE* 2.9 53.3 + - + -
89A VAL* 5.5 2.0 - - + -
96A SER* 3.6 31.9 - - - +
98A VAL* 3.8 14.1 - - + -
106A VAL* 4.1 11.2 - - + +
108A GLY* 3.6 26.9 - - - +
109A GLY* 3.7 17.0 - - - +
110A ILE 4.9 0.2 - - - +
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Residues in contact with LYS 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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66A LEU 2.8 14.3 + - - +
67A ILE* 3.3 27.9 - - - +
69A LEU* 1.3 76.1 - - - +
71A ASN* 1.3 85.3 + - - +
73A PHE* 3.3 14.9 + - - +
74A SER* 2.9 25.5 + - - -
82A LYS* 3.7 21.3 - - + +
85A ILE* 3.8 16.6 - - + +
86A VAL* 3.7 35.6 - - + +
89A VAL* 4.6 7.4 - - + +
90A PHE* 4.7 8.3 - - + -
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Residues in contact with ASN 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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67A ILE* 2.8 27.6 + - - +
68A ASP* 3.6 9.5 - - - +
69A LEU 3.1 0.2 - - - -
70A LYS* 1.3 102.7 + - - +
72A ILE* 1.3 66.0 + - + +
74A SER* 3.5 4.3 + - - -
75A ARG* 3.1 48.6 + - - +
82A LYS* 3.0 22.8 - - - +
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Residues in contact with ILE 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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68A ASP* 3.1 13.9 + - + +
69A LEU* 3.0 9.9 + - + +
71A ASN* 1.3 74.1 - - + +
73A PHE* 1.3 69.9 + - + +
75A ARG* 3.2 7.5 + - - +
76A GLN* 2.9 24.6 + - + +
106A VAL* 3.4 45.1 - - + +
107A ILE* 3.8 4.0 - - - -
108A GLY* 3.8 14.1 - - - +
127A ALA* 4.3 19.3 - - + -
128A VAL 4.4 0.2 - - - -
129A THR* 4.0 36.8 - - - +
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Residues in contact with PHE 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 LEU* 2.9 53.9 + - + -
70A LYS* 3.4 7.2 - - - +
72A ILE* 1.3 78.4 - - + +
74A SER* 1.3 57.5 + - - +
76A GLN 3.3 0.2 + - - -
77A LEU* 2.9 42.7 + - + +
85A ILE* 3.9 16.4 - - + -
89A VAL* 4.1 14.8 - - + -
109A GLY 3.5 20.0 - - - -
111A CYS* 3.7 25.1 - - + -
125A PHE* 3.7 44.9 - + + -
126A LEU 3.8 1.8 - - - -
127A ALA* 3.8 19.5 - - + -
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Residues in contact with SER 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 LYS 2.9 17.2 + - - -
71A ASN* 3.6 8.7 - - - -
72A ILE 3.2 0.2 - - - -
73A PHE* 1.3 77.1 - - - +
75A ARG* 1.3 61.6 + - - +
77A LEU 3.2 19.3 - - - +
78A PRO* 3.5 6.2 - - - +
80A MET 5.1 1.9 + - - +
82A LYS* 3.0 43.4 + - - +
85A ILE* 3.6 15.5 - - - +
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Residues in contact with ARG 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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71A ASN* 3.1 45.1 + - - +
72A ILE* 3.8 6.5 - - - +
74A SER* 1.3 79.4 - - - +
76A GLN* 1.3 67.3 + - + +
77A LEU 3.5 0.5 + - - -
78A PRO* 3.6 16.2 - - - +
82A LYS* 5.0 6.0 - - - +
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Residues in contact with GLN 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 ILE* 2.9 21.0 + - + +
73A PHE 4.0 1.3 - - - +
75A ARG* 1.3 80.7 - - + +
77A LEU* 1.3 67.8 + - + +
78A PRO* 3.4 7.3 - - - +
127A ALA* 3.7 22.4 - - + -
128A VAL 3.5 22.6 + - - +
129A THR* 4.7 1.3 - - - -
130A ALA* 3.6 23.9 + - - +
133A GLN* 3.1 18.8 + - - +
162A ASP* 4.9 4.9 - - - +
401A EPE 4.4 22.7 + - - -
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Residues in contact with LEU 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 PHE* 2.9 26.5 + - + +
74A SER* 3.2 10.7 - - - +
76A GLN* 1.3 90.6 - - + +
78A PRO* 1.3 63.9 - - - +
79A LYS 3.3 3.1 - - - -
80A MET* 3.2 40.5 + - + +
85A ILE* 5.0 0.4 - - + -
125A PHE* 3.8 38.8 - - + -
126A LEU 4.7 4.0 - - - +
127A ALA* 5.5 0.2 - - + -
162A ASP* 4.3 19.3 - - + +
401A EPE 3.8 26.7 - - - +
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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