Contacts of the helix formed by residues 72 - 88 (chain A) in PDB entry 1QQA
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 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 3.1 6.0 + - - -
71A ALA* 1.3 70.3 - - - +
73A TYR* 1.3 65.5 + - - +
75A ALA* 3.6 4.4 - - - +
76A GLU* 2.8 32.4 + - - +
249A ILE* 3.9 24.6 - - + +
277A VAL* 3.8 32.1 - - + -
279A ASN* 5.5 1.3 - - - +
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Residues in contact with TYR 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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71A ALA 2.9 0.6 + - - -
72A ALA* 1.3 81.3 - - - +
74A PHE* 1.3 87.2 + + - +
76A GLU* 3.3 5.0 + - - +
77A ILE* 3.0 40.8 + - + +
122A MET* 5.6 1.6 - - - -
160A ASP* 4.8 0.7 + - - -
192A THR* 3.9 10.0 - - + +
196A ARG* 4.1 2.5 - - - -
249A ILE* 5.8 1.2 - - + +
275A ASP* 3.5 28.5 - - + +
277A VAL* 4.4 6.9 - - + +
292A GLN* 3.0 26.4 + - + +
294A LYS* 4.1 24.2 - - + +
297A LEU* 4.7 5.7 - - - +
599A HPA 3.2 57.0 - + + +
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Residues in contact with PHE 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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67A THR* 4.0 19.7 - - + -
68A SER* 3.0 40.2 - - - +
69A SER* 4.2 3.4 - - - +
71A ALA* 2.7 25.9 + - + +
73A TYR* 1.3 97.1 - + + +
75A ALA* 1.3 68.2 + - - +
77A ILE* 2.8 16.8 + - - +
78A ILE* 2.9 21.7 + - + +
122A MET* 4.3 24.0 - - + -
124A SER* 4.0 14.4 - - - -
190A ARG* 4.6 2.2 - - - -
599A HPA 3.4 31.2 - + - -
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Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A SER 3.2 18.3 + - - +
70A GLU* 3.8 8.1 - - - +
71A ALA 2.6 18.9 + - - +
72A ALA* 3.6 7.0 - - - +
74A PHE* 1.3 75.5 - - - +
76A GLU* 1.3 64.1 - - + +
78A ILE* 3.3 8.9 + - - +
79A GLU* 2.9 26.8 + - - +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 2.8 20.9 + - - +
73A TYR* 3.6 5.2 - - - +
75A ALA* 1.3 81.1 - - + +
77A ILE* 1.3 64.9 + - - +
79A GLU* 3.6 5.8 + - - +
80A ALA* 3.4 15.2 + - - +
277A VAL* 3.4 14.3 - - - +
278A ARG* 2.9 68.7 + - + +
294A LYS* 3.2 36.6 + - + +
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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
----------------------------------------------------------
73A TYR* 3.0 57.8 + - + +
74A PHE* 2.8 8.8 + - - +
76A GLU* 1.3 76.7 - - - +
78A ILE* 1.3 62.3 + - - +
80A ALA* 2.7 33.4 + - - +
81A VAL* 3.0 17.3 + - + +
122A MET* 3.9 33.9 - - + -
145A MET* 4.4 11.4 - - + -
294A LYS* 4.0 26.0 - - + +
297A LEU* 5.0 10.5 - - + -
298A GLY* 4.9 4.5 - - - -
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Residues in contact with ILE 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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64A LEU* 3.7 23.1 - - + -
66A ALA* 4.7 7.4 - - + -
68A SER 4.2 6.5 - - - +
69A SER* 4.0 27.6 - - - -
74A PHE* 2.9 23.7 + - + +
75A ALA* 3.8 7.0 - - - +
77A ILE* 1.3 82.4 - - - +
79A GLU* 1.3 69.8 + - + +
81A VAL* 2.9 18.9 + - - +
82A GLU* 2.9 15.1 + - + +
92A LEU* 5.8 6.8 - - + +
94A LEU* 4.4 21.3 - - + -
122A MET* 4.5 9.2 - - + -
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ALA 2.9 14.7 + - - +
76A GLU* 3.8 6.3 - - - +
78A ILE* 1.3 85.1 - - + +
80A ALA* 1.3 65.7 + - - +
82A GLU* 3.3 16.7 - - + +
83A LYS* 3.3 35.6 + - + +
278A ARG* 3.2 25.0 + - - +
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Residues in contact with ALA 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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76A GLU 3.4 8.9 + - - +
77A ILE* 2.7 16.7 + - - +
79A GLU* 1.3 75.9 - - - +
81A VAL* 1.3 68.0 + - - +
83A LYS* 3.0 21.8 + - - +
84A ASN* 3.1 19.0 + - - +
295A ASP* 4.1 30.5 - - + +
298A GLY* 4.4 9.9 - - - -
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Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 4.4 20.2 - - + -
77A ILE* 3.7 20.2 - - + +
78A ILE* 2.9 12.0 + - - +
80A ALA* 1.3 76.1 - - - +
82A GLU* 1.3 65.7 + - - +
84A ASN* 2.8 22.3 + - - +
85A CYS* 2.9 25.2 + - - -
92A LEU* 4.4 10.3 - - + -
120A LEU* 4.5 17.3 - - + -
145A MET* 4.4 10.8 - - + -
298A GLY* 4.2 21.5 - - - +
302A PHE* 5.1 4.7 - - + -
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Residues in contact with GLU 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 ILE* 2.9 12.4 + - + +
79A GLU* 3.3 20.9 - - + +
80A ALA 3.2 0.2 + - - -
81A VAL* 1.3 76.9 - - - +
83A LYS* 1.3 74.6 + - + +
85A CYS* 2.9 19.7 + - - +
86A PHE* 2.9 23.3 + - - +
92A LEU* 4.7 19.1 - - + +
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Residues in contact with LYS 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 GLU* 3.6 29.2 + - + +
80A ALA* 3.0 13.2 + - - +
82A GLU* 1.3 90.5 - - + +
84A ASN* 1.3 68.3 + - - +
86A PHE* 3.4 6.4 + - - +
87A GLN* 2.9 29.8 + - - +
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Residues in contact with ASN 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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80A ALA* 3.1 25.9 + - - +
81A VAL* 2.8 12.1 + - - +
83A LYS* 1.3 75.9 - - - +
85A CYS* 1.3 68.1 + - - +
87A GLN* 3.3 17.5 + - - +
88A LYS* 3.3 29.7 + - - +
295A ASP 5.3 0.2 + - - -
299A GLU* 3.6 44.8 - - - +
302A PHE* 3.5 28.0 - - + -
303A ASN* 4.9 3.3 + - - +
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Residues in contact with CYS 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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62A ILE* 4.0 21.3 - - - -
81A VAL* 2.9 21.9 + - - -
82A GLU* 2.9 11.7 + - - +
84A ASN* 1.3 79.4 - - - +
86A PHE* 1.3 61.7 + - - +
88A LYS* 3.0 6.1 + - - +
90A TYR* 2.7 45.6 + - + +
91A THR 4.7 0.4 - - - -
92A LEU* 4.3 16.4 - - + -
302A PHE* 3.3 30.5 - - - -
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Residues in contact with PHE 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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82A GLU* 2.9 21.6 + - - +
83A LYS* 3.5 11.9 - - - +
85A CYS* 1.3 75.8 - - - +
87A GLN* 1.3 63.8 + - + +
89A GLY* 2.8 21.7 + - - -
90A TYR 3.9 6.9 + - - -
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Residues in contact with GLN 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 LYS* 2.9 17.3 + - - +
84A ASN* 3.4 21.8 + - - +
86A PHE* 1.3 87.5 - - + +
88A LYS* 1.3 82.8 + - + +
89A GLY 3.3 1.6 + - - -
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Residues in contact with LYS 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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60A LYS* 3.9 8.8 + - - -
84A ASN* 3.4 18.6 - - - +
85A CYS 3.0 3.7 + - - +
87A GLN* 1.3 99.7 - - + +
89A GLY* 1.3 64.8 + - - +
90A TYR* 3.1 27.8 - - + -
302A PHE* 3.6 15.3 - - + -
303A ASN* 5.0 8.2 + - - -
306A LEU* 4.2 18.2 - - + +
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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