Contacts of the helix formed by residues 60 - 80 (chain A) in PDB entry 1QL6
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 ALA 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A SER* 1.3 71.0 + - - +
61A GLU* 1.3 67.3 + - - +
63A VAL* 2.8 29.5 + - - +
64A GLN* 3.4 5.1 + - - +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 2.9 9.8 + - - +
60A ALA* 1.3 73.0 - - - +
62A GLU* 1.3 65.6 + - + +
64A GLN* 3.0 20.3 + - - +
65A GLU* 3.1 31.2 + - + +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PHE* 2.7 51.1 - - + +
59A SER* 2.7 19.3 + - - +
61A GLU* 1.3 73.1 - - + +
63A VAL* 1.3 50.3 + - - +
65A GLU* 2.8 25.1 + - - +
66A LEU* 2.7 38.0 + - - +
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Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.3 39.6 - - + +
53A THR* 3.9 24.0 - - + +
58A PHE* 4.7 2.4 - - + +
59A SER 3.3 10.6 + - - +
60A ALA* 2.8 25.6 + - - +
62A GLU* 1.3 71.5 - - - +
64A GLN* 1.3 59.4 + - - +
66A LEU 3.3 1.0 + - - -
67A ARG* 2.9 27.5 + - + +
96A ASN 5.5 2.0 - - - +
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Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA 3.4 3.6 + - - +
61A GLU* 3.0 11.7 + - - +
63A VAL* 1.3 79.9 - - + +
65A GLU* 1.3 61.3 + - + +
66A LEU 3.3 0.7 - - - -
67A ARG* 3.8 22.9 - - - +
68A GLU* 3.2 43.7 + - + +
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Residues in contact with GLU 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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61A GLU* 3.2 29.9 - - + +
62A GLU* 2.8 36.7 + - - +
64A GLN* 1.3 78.3 - - + +
66A LEU* 1.3 60.4 + - - +
68A GLU* 4.0 2.8 - - - +
69A ALA* 3.1 25.3 + - - +
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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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30A SER* 3.6 25.6 - - - +
50A ILE* 4.8 7.0 - - + -
51A ASP 4.2 7.0 - - - +
52A VAL* 4.1 17.0 - - - +
58A PHE* 3.5 33.0 - - + -
62A GLU 2.7 14.3 + - - +
63A VAL 4.0 3.8 - - - +
65A GLU* 1.3 78.1 - - - +
67A ARG* 1.3 57.1 + - - +
69A ALA* 3.2 30.7 - - + +
70A THR* 3.2 23.2 + - - +
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Residues in contact with ARG 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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52A VAL* 4.4 10.7 - - + +
63A VAL* 2.9 18.5 + - + +
64A GLN* 3.8 22.5 - - - +
66A LEU* 1.3 78.3 - - - +
68A GLU* 1.3 67.4 + - - +
70A THR 3.9 0.2 + - - -
71A LEU* 3.1 64.9 + - - +
94A GLU* 2.8 35.9 + - - +
99A PHE* 3.6 24.5 - - + -
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Residues in contact with GLU 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 GLN* 3.2 39.6 + - + +
65A GLU* 4.0 3.6 - - - +
66A LEU 3.4 0.2 - - - -
67A ARG* 1.3 83.3 + - - +
69A ALA* 1.3 57.3 + - - +
71A LEU* 3.7 25.6 - - + +
72A LYS* 3.2 27.0 + - - +
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Residues in contact with ALA 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 GLU 3.1 21.1 + - - +
66A LEU* 3.2 23.8 + - + +
68A GLU* 1.3 75.4 - - - +
70A THR* 1.3 59.6 + - - +
72A LYS* 3.3 10.0 + - - +
73A GLU* 2.9 25.8 + - - +
169A GLY 5.0 10.0 - - - +
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Residues in contact with THR 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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50A ILE* 3.3 46.0 - - + +
66A LEU* 3.2 19.8 + - - +
69A ALA* 1.3 72.7 - - - +
71A LEU* 1.4 59.9 + - - +
73A GLU* 3.1 10.6 + - - +
74A VAL* 2.9 29.9 + - - +
99A PHE* 3.8 35.6 - - + -
101A LEU* 4.5 12.1 - - + -
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Residues in contact with LEU 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 ARG* 3.1 63.0 + - - +
68A GLU* 3.7 24.5 - - - +
69A ALA 3.3 0.4 - - - -
70A THR* 1.4 75.1 - - - +
72A LYS* 1.3 62.3 + - - +
74A VAL* 3.6 8.8 + - + +
75A ASP* 3.1 23.6 + - - +
94A GLU* 4.3 9.9 - - - +
99A PHE* 4.1 18.6 - - + -
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Residues in contact with LYS 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 GLU 3.2 19.5 + - - +
69A ALA* 3.4 9.6 - - - +
71A LEU* 1.3 75.2 - - - +
73A GLU* 1.3 63.1 + - - +
75A ASP* 3.1 8.0 + - - +
76A ILE* 2.9 29.1 + - + +
148A ARG* 3.8 2.8 - - - +
170A PHE 5.5 0.4 - - - -
171A SER 3.2 25.6 + - - +
172A CYS* 3.5 24.2 - - - +
304A SO4 2.6 38.0 + - - -
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Residues in contact with GLU 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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48A LYS* 3.1 34.0 + - - +
50A ILE* 4.6 6.3 - - - +
69A ALA 2.9 14.8 + - - +
70A THR* 3.1 14.9 + - + +
72A LYS* 1.3 74.9 - - - +
74A VAL* 1.3 55.7 + - - +
76A ILE* 3.4 3.7 + - - +
77A LEU* 2.9 41.7 + - + +
101A LEU* 4.2 14.0 - - + +
103A PHE* 4.7 3.1 - - - -
167A ASP* 4.8 1.4 - - - -
168A PHE* 3.8 29.5 + - + +
169A GLY* 3.4 25.2 + - - -
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Residues in contact with VAL 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 THR* 2.9 18.6 + - + +
71A LEU* 3.9 10.5 - - + +
73A GLU* 1.3 74.1 - - - +
75A ASP* 1.3 60.3 + - - +
77A LEU* 3.2 10.4 + - - +
78A ARG* 2.8 67.9 + - - +
89A LEU* 3.9 8.3 - - + -
92A THR* 3.8 9.4 - - + +
99A PHE* 5.5 5.2 - - + -
101A LEU* 3.6 35.7 - - + -
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Residues in contact with ASP 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 LEU 3.1 14.9 + - - +
72A LYS* 3.1 6.6 + - - +
74A VAL* 1.3 80.0 - - - +
76A ILE* 1.3 67.5 + - + +
78A ARG* 3.3 14.4 + - - +
79A LYS* 3.0 48.5 + - - +
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Residues in contact with ILE 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 LYS* 2.9 26.2 + - + +
73A GLU* 3.9 4.7 - - - +
75A ASP* 1.3 75.1 - - - +
77A LEU* 1.3 58.7 + - - +
79A LYS* 2.7 36.8 + - + +
80A VAL* 3.0 19.0 + - + +
145A ILE* 4.4 13.9 - - + -
168A PHE* 3.6 33.4 - - + +
171A SER* 3.8 32.5 - - - +
172A CYS* 4.2 2.5 - - - -
173A GLN* 4.0 24.5 - - + +
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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 GLU* 2.9 36.4 + - + +
74A VAL 3.2 6.7 + - - +
76A ILE* 1.3 75.3 - - - +
78A ARG* 1.3 62.1 + - - +
80A VAL* 3.3 8.9 + - + +
81A SER* 2.9 25.7 + - - -
87A ILE* 3.9 27.6 - - + +
89A LEU* 4.0 25.7 + - + +
101A LEU* 4.2 5.8 - - + -
103A PHE* 3.7 29.2 - - + -
168A PHE* 3.7 32.1 - - + +
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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
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74A VAL* 2.8 47.2 + - + +
75A ASP* 3.3 15.1 + - - +
77A LEU* 1.3 72.5 - - - +
79A LYS* 1.3 65.9 + - + +
81A SER* 3.5 19.1 + - - -
89A LEU* 4.7 9.6 - - + +
92A THR* 3.6 24.4 + - - +
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Residues in contact with LYS 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 ASP* 3.0 39.9 + - - +
76A ILE* 2.7 21.2 + - + +
78A ARG* 1.3 80.9 - - + +
80A VAL* 1.3 58.2 + - - +
81A SER 3.6 2.6 + - - +
143A LEU* 4.3 14.0 - - + +
145A ILE* 4.2 13.0 - - + -
173A GLN* 2.5 38.0 + - - +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ILE* 3.0 15.4 + - + +
77A LEU* 3.3 18.6 + - + +
79A LYS* 1.3 77.2 - - - +
81A SER* 1.3 69.7 + - - +
83A HIS* 3.6 17.2 + - - +
86A ILE* 3.5 37.9 - - + +
87A ILE 5.1 0.9 - - - +
140A LEU* 3.5 24.9 - - + -
143A LEU* 4.9 7.9 - - + -
145A ILE* 3.9 17.3 - - + -
168A PHE* 4.1 15.5 - - + -
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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