Contacts of the helix formed by residues 56 - 70 (chain B) in PDB entry 2QY7
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 GLN 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLU* 6.1 0.3 - - - +
24B ILE* 3.5 32.7 + - + +
27B LYS* 5.9 1.2 + - - -
50B ALA* 3.7 19.8 - - + +
53B MET* 3.0 49.3 + - + +
55B GLU* 1.3 81.9 - - + +
57B PHE* 1.3 66.2 + - - +
58B PRO* 3.4 2.1 - - - -
59B GLU* 3.4 8.9 + - - +
60B LEU* 3.2 21.9 + - - +
30C GLU* 5.7 3.0 + - - -
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Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ALA 4.7 3.1 - - - -
51B THR* 3.6 32.8 - - + +
53B MET 3.1 6.9 + - - +
55B GLU 3.6 0.2 - - - -
56B GLN* 1.3 76.5 - - - +
58B PRO* 1.4 67.2 - - + +
60B LEU* 3.3 7.3 + - - +
61B MET* 2.9 57.0 + - + +
96B ARG* 3.3 72.2 - - + +
97B VAL* 3.7 25.8 - - + -
100B SER* 4.3 7.0 - - - -
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Residues in contact with PRO 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A TYR* 3.7 18.6 - - + +
127A ASN* 3.6 13.7 - - - +
130A GLN* 4.2 17.7 - - + +
131A LYS* 5.6 11.0 - - + +
134A GLU* 6.1 0.7 - - - +
54B TYR 3.4 16.6 - - - +
55B GLU 4.1 5.6 - - - +
56B GLN 3.6 3.4 - - - -
57B PHE* 1.4 99.2 - - + +
59B GLU* 1.3 56.8 + - - +
61B MET* 3.3 2.8 + - + +
62B ASN* 2.9 36.7 + - - +
96B ARG* 4.4 11.4 - - - +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TRP* 4.4 0.8 - - + -
77A ARG* 2.9 29.5 + - - -
80A TYR* 3.6 26.7 + - + -
84A LEU* 5.7 0.7 - - - +
122A LYS* 5.2 0.2 + - - -
127A ASN* 3.5 30.1 - - - +
22B SER* 3.4 18.6 + - - -
24B ILE* 4.3 7.2 - - + +
25B GLU* 3.9 20.7 - - + +
55B GLU 4.1 10.4 - - - +
56B GLN* 3.4 7.8 + - - +
58B PRO* 1.3 75.1 - - - +
60B LEU* 1.3 61.5 + - - +
62B ASN* 4.2 0.6 - - - +
63B MET* 2.9 32.4 + - - +
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Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ILE* 3.6 24.0 - - + +
28B VAL* 3.9 11.1 - - + +
47B ILE* 3.5 42.6 - - + +
50B ALA* 3.7 17.0 - - + +
51B THR* 3.7 26.9 - - + +
56B GLN 3.2 9.8 + - - +
57B PHE* 3.3 9.6 - - - +
59B GLU* 1.3 79.8 - - - +
61B MET* 1.3 66.7 + - + +
63B MET* 3.4 2.6 + - - +
64B LEU* 3.0 26.5 + - + +
89B LEU* 4.0 17.3 - - + -
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Residues in contact with MET 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B PHE* 2.9 58.4 + - + +
58B PRO* 4.1 2.7 - - + +
60B LEU* 1.3 84.9 - - + +
62B ASN* 1.3 62.8 + - - +
64B LEU* 3.2 17.4 + - + +
65B TRP* 2.8 70.1 + - + +
86B LEU* 4.3 16.2 - - + -
89B LEU* 4.6 1.6 - - - -
97B VAL* 4.4 17.5 - - + +
100B SER* 3.6 17.3 - - - +
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Residues in contact with ASN 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS* 3.8 11.0 + - - +
126A ILE* 3.6 31.0 - - + +
127A ASN* 2.8 29.3 + - - +
130A GLN* 2.8 41.6 + - - +
58B PRO 2.9 16.7 + - - +
59B GLU 4.2 0.9 - - - +
61B MET* 1.3 75.2 - - - +
63B MET* 1.3 65.7 + - - +
65B TRP* 4.0 12.4 - - - +
66B SER* 3.0 26.2 + - - -
104B HIS* 5.6 0.9 - - - -
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Residues in contact with MET 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS* 3.5 34.6 - - + +
21B TYR* 3.6 33.2 - - + -
25B GLU* 3.7 32.3 - - + +
28B VAL* 3.9 14.4 - - + -
29B ARG* 3.7 29.6 - - + +
59B GLU 2.9 19.9 + - - +
60B LEU 3.7 3.4 - - - +
62B ASN* 1.3 76.8 - - - +
64B LEU* 1.3 61.6 + - - +
66B SER* 3.3 2.6 + - - -
67B ARG* 2.9 33.6 + - + +
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 3.7 13.8 - - + +
32B THR* 5.9 0.4 - - - -
60B LEU* 3.0 15.5 + - + +
61B MET* 3.2 25.5 + - + +
63B MET* 1.3 75.2 - - - +
65B TRP* 1.3 74.9 + - + +
67B ARG* 3.4 3.0 + - - +
68B MET* 3.0 47.4 + - + +
82B SER* 4.4 9.2 - - - +
85B LEU* 4.0 19.1 - - + -
86B LEU* 4.2 18.4 - - + +
89B LEU* 3.8 28.9 - - + -
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Residues in contact with TRP 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B MET* 2.8 48.6 + - + +
62B ASN* 4.1 11.7 - - - +
64B LEU* 1.3 74.3 - - + +
66B SER* 1.3 57.5 - - - +
68B MET* 3.3 30.4 + - + -
69B LEU* 2.9 59.2 + - + +
70B LYS* 6.0 0.7 - - - -
86B LEU* 3.8 19.1 - - + -
100B SER* 3.0 31.8 + - - -
101B ALA* 3.9 11.7 - - - -
104B HIS* 3.7 45.5 - + + +
108B LEU* 3.9 18.4 - - + -
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Residues in contact with SER 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS* 3.5 33.5 - - - +
123A ASP 5.1 0.4 + - - -
62B ASN 3.0 18.9 + - - -
63B MET* 3.6 5.7 - - - -
65B TRP* 1.3 74.2 - - - +
67B ARG* 1.3 63.1 + - - +
70B LYS* 3.0 57.4 + - - +
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Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 5.1 0.9 - - + +
29B ARG* 3.1 66.2 + - + +
32B THR* 2.7 51.9 + - + +
33B ASN* 3.9 6.9 - - - +
63B MET* 2.9 36.6 + - + +
64B LEU* 3.8 3.8 - - - +
66B SER* 1.3 77.2 - - - +
68B MET* 1.3 61.3 + - - +
70B LYS 4.7 2.9 - - - +
72B ASN* 4.8 0.9 - - - +
78B ARG* 3.1 62.2 - - + +
79B VAL* 4.6 2.6 + - - +
82B SER* 4.6 0.7 - - - -
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Residues in contact with MET 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B LEU* 3.0 41.9 + - + +
65B TRP* 3.6 22.7 - - + +
67B ARG* 1.3 78.1 - - - +
69B LEU* 1.3 62.7 + - + +
70B LYS 4.0 0.2 - - - -
72B ASN* 2.9 16.9 - - - +
79B VAL* 3.5 18.2 - - + +
82B SER* 3.1 36.0 - - - +
83B LEU* 3.9 11.7 - - + -
86B LEU* 4.1 8.3 - - + -
108B LEU* 3.7 21.5 - - - -
111B LEU* 3.7 23.5 - - + +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B TRP* 2.9 42.5 + - + +
68B MET* 1.3 84.5 - - + +
70B LYS* 1.3 67.6 + - + +
71B ASP 3.6 2.1 + - - -
72B ASN* 3.7 14.7 + - - +
104B HIS* 6.0 0.2 - - - +
107B ASP* 3.5 50.7 - - + +
110B SER* 4.3 4.0 - - - +
111B LEU* 3.8 29.6 - - + -
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A GLY 4.9 13.6 + - - +
123A ASP* 3.5 35.9 + - - +
65B TRP 4.9 1.1 - - - +
66B SER* 3.0 42.5 + - - +
67B ARG 4.7 1.4 - - - +
69B LEU* 1.3 78.7 - - + +
71B ASP* 1.3 77.4 + - - +
72B ASN* 3.1 4.9 + - - +
78B ARG* 4.7 6.4 + - - -
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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