Contacts of the helix formed by residues 74 - 90 (chain A) in PDB entry 1QQJ
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 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A MET 3.5 4.8 + - - -
72A GLY 3.3 3.4 - - - -
73A LEU* 1.3 78.6 - - - +
75A GLN* 1.3 64.7 + - - -
76A ALA 3.4 2.5 - - - -
77A ALA* 3.2 5.0 + - - +
78A TRP* 3.1 29.9 + - - +
208A PRO* 3.4 27.8 - - - -
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Residues in contact with GLN 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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74A GLY* 1.3 68.1 - - - -
76A ALA* 1.3 60.8 + - - +
78A TRP* 3.5 30.3 - - + +
79A LYS* 2.9 57.2 + - + +
222A HIS* 3.4 37.6 + - - -
223A GLU* 3.7 32.0 + - + +
225A ILE 5.8 0.2 + - - -
267A ASP* 5.8 0.8 + - - -
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Residues in contact with ALA 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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54A ALA* 4.1 12.0 - - + +
73A LEU 6.1 0.2 - - - +
74A GLY 3.4 0.8 - - - -
75A GLN* 1.3 77.9 - - - +
77A ALA* 1.3 57.7 + - - +
79A LYS* 3.5 7.1 + - - +
80A GLU* 3.0 30.1 + - - +
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Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ALA* 3.9 18.3 - - + +
55A LEU* 3.9 11.8 - - + +
70A PHE* 4.5 2.5 - - + -
73A LEU* 3.5 40.1 + - + +
74A GLY 3.2 10.3 + - - +
76A ALA* 1.3 76.4 - - - +
78A TRP* 1.3 61.5 + - + +
80A GLU* 3.4 1.6 + - - +
81A ALA* 2.9 30.5 + - - +
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Residues in contact with TRP 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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19A TYR* 4.4 4.2 + - + +
70A PHE* 3.0 44.6 + + + -
71A MET 3.1 20.1 + - - -
74A GLY* 3.1 15.8 + - - +
75A GLN* 3.2 33.6 + - + +
77A ALA* 1.3 75.5 - - + +
79A LYS* 1.3 60.7 + - + +
81A ALA* 3.3 2.9 + - - +
82A ARG* 3.0 29.7 + - - +
207A GLY* 3.6 12.1 - - - -
208A PRO* 3.7 9.6 - - + -
223A GLU 3.6 17.7 - - - -
225A ILE 3.6 19.7 - - - -
226A PHE* 3.4 47.1 - + + -
265A PRO* 6.4 2.2 - - + -
267A ASP* 4.9 5.4 - - - +
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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 GLN* 2.9 46.4 + - + +
76A ALA* 3.9 6.3 - - - +
78A TRP* 1.3 75.0 - - + +
80A GLU* 1.3 57.5 - - - +
82A ARG* 3.4 4.4 + - - +
83A ALA* 2.9 29.7 + - - +
267A ASP* 2.9 43.5 + - - +
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Residues in contact with GLU 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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52A GLY* 3.2 24.8 + - - -
53A PRO* 3.2 14.4 - - + +
54A ALA* 2.8 29.4 + - + +
55A LEU* 2.9 34.7 + - + +
76A ALA 3.0 18.3 + - - +
77A ALA 3.8 3.4 - - - +
79A LYS* 1.3 74.9 - - - +
81A ALA* 1.3 59.1 + - - +
83A ALA* 3.3 6.7 + - + +
84A SER* 2.9 39.9 + - - +
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Residues in contact with ALA 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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19A TYR* 3.8 6.1 - - + +
50A PHE* 3.7 10.9 - - + -
55A LEU* 3.6 19.8 - - + +
62A PHE* 4.4 3.6 - - + -
70A PHE* 3.7 23.6 - - + -
77A ALA 2.9 17.8 + - - +
78A TRP 3.6 5.2 - - - +
80A GLU* 1.3 76.5 - - - +
82A ARG* 1.3 58.9 + - - +
84A SER* 3.3 1.6 + - - -
85A LEU* 2.9 37.5 + - + +
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Residues in contact with ARG 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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14A ILE 4.7 0.8 + - - -
15A GLN* 2.9 30.9 + - - +
16A ASN 2.7 23.2 + - - -
17A LEU* 4.1 12.4 + - + +
19A TYR* 4.0 10.5 + - - +
78A TRP 3.0 16.8 + - - +
79A LYS* 3.7 5.4 - - - +
81A ALA* 1.3 77.4 - - - +
83A ALA* 1.3 56.7 + - - +
85A LEU* 3.3 7.0 + - - +
86A GLN* 2.9 61.2 + - + +
265A PRO* 3.7 18.1 - - + +
267A ASP* 3.7 30.9 + - - +
268A ALA* 3.6 17.8 - - - +
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Residues in contact with ALA 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 LYS 2.9 17.4 + - - +
80A GLU* 3.8 6.7 - - + +
82A ARG* 1.3 74.7 - - - +
84A SER* 1.3 62.5 + - - +
86A GLN* 3.3 14.6 + - - +
87A ASN* 2.9 39.5 + - - +
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Residues in contact with SER 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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49A LEU 4.7 8.6 + - - -
50A PHE* 3.6 29.4 - - - -
51A THR 5.0 1.9 + - - -
52A GLY 5.3 2.1 + - - -
80A GLU* 2.9 26.6 + - - +
81A ALA 3.6 4.0 - - - -
83A ALA* 1.3 76.9 - - - +
85A LEU* 1.3 57.9 + - - +
87A ASN* 3.4 6.4 + - - +
88A LEU* 2.8 38.1 + - - +
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Residues in contact with LEU 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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17A LEU* 4.2 15.9 - - + -
19A TYR* 3.8 23.3 - - + +
34A VAL* 4.0 24.0 - - + -
41A LEU* 3.9 28.7 - - + -
43A LEU* 3.9 16.8 - - + -
46A ILE* 4.3 4.5 - - + -
50A PHE* 4.0 17.7 - - + -
81A ALA* 2.9 23.5 + - + +
82A ARG* 3.7 4.9 - - - +
84A SER* 1.3 76.1 - - - +
86A GLN* 1.3 57.9 + - - +
88A LEU* 3.9 4.4 - - + +
89A LEU* 2.8 41.1 + - + +
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Residues in contact with GLN 86 (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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14A ILE* 3.9 22.4 + - + +
15A GLN* 6.1 0.4 - - - +
17A LEU* 4.0 17.0 - - + -
82A ARG* 2.9 56.7 + - + +
83A ALA* 3.4 15.8 - - - +
85A LEU* 1.3 71.8 - - - +
87A ASN* 1.3 65.2 + - - +
89A LEU 3.6 0.2 + - - -
90A SER* 3.1 24.4 + - - -
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Residues in contact with ASN 87 (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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83A ALA* 2.9 30.5 + - - +
84A SER* 3.8 5.6 - - - +
86A GLN* 1.3 79.2 - - - +
88A LEU* 1.3 63.2 + - + +
90A SER* 3.4 8.5 + - - -
93A GLN* 3.0 36.3 + - + +
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Residues in contact with LEU 88 (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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3A PHE* 3.3 18.4 - - - -
41A LEU* 5.9 0.2 - - + -
46A ILE* 4.4 14.4 - - + -
49A LEU* 3.7 47.8 - - + +
50A PHE* 5.5 2.2 - - + -
84A SER* 2.8 28.4 + - - +
85A LEU* 3.9 7.6 - - + +
87A ASN* 1.3 77.4 - - + +
89A LEU* 1.3 62.5 + - + +
90A SER 3.6 2.1 + - - +
93A GLN* 4.7 7.7 - - + +
95A ARG* 4.0 29.2 - - + -
96A LEU* 4.3 20.4 + - + +
97A ARG 4.8 0.2 + - - -
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Residues in contact with LEU 89 (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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2A SER* 2.7 39.6 + - - +
3A PHE* 3.1 11.2 + - + -
4A ILE* 4.3 6.3 - - + -
14A ILE* 3.8 12.6 - - + -
17A LEU* 3.6 33.4 - - + -
34A VAL* 5.2 1.8 - - + -
36A ILE* 4.3 14.4 - - + -
41A LEU* 4.1 20.6 - - + -
85A LEU* 2.8 26.7 + - + +
88A LEU* 1.3 72.1 - - + +
90A SER* 1.3 68.0 + - - +
96A LEU* 4.7 1.6 - - + -
107A PHE* 3.8 33.2 - - + -
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Residues in contact with SER 90 (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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1A MET 3.6 11.4 + - - -
3A PHE* 3.6 9.4 - - - -
14A ILE* 4.2 2.2 - - - -
86A GLN 3.1 17.6 + - - -
87A ASN* 3.6 11.0 - - - -
88A LEU 3.3 1.7 - - - +
89A LEU* 1.3 80.5 - - - +
91A ALA* 1.3 65.7 + - - +
92A SER* 3.1 21.1 + - - -
93A GLN* 3.3 19.9 + - - +
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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