Contacts of the helix formed by residues 65 - 80 (chain B) in PDB entry 3QS7
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 65 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A SER* 3.8 14.4 - - - -
24A ASP 4.1 0.4 - - - -
26A LEU 3.1 7.2 + - - -
28A GLN* 3.0 22.6 + - - -
64B ALA* 1.3 75.3 - - - +
66B SER* 1.3 67.9 + - - +
67B LYS 3.2 2.7 - - - -
68B MET* 2.9 4.7 + - - +
69B GLN* 2.8 21.8 + - - +
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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
----------------------------------------------------------
20A ARG* 4.4 9.9 + - - -
24A ASP* 2.8 33.1 + - - -
64B ALA 4.0 0.2 + - - -
65B GLY* 1.3 70.1 - - - +
67B LYS* 1.3 64.6 + - - +
69B GLN* 3.5 16.1 - - - +
70B GLY* 3.9 3.6 + - - -
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Residues in contact with LYS 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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24A ASP* 2.6 36.2 + - + +
25A TYR* 4.1 23.1 - - + +
66B SER* 1.3 76.7 + - - +
68B MET* 1.3 62.8 + - - +
69B GLN 3.2 2.0 - - - -
70B GLY* 3.4 10.3 + - - +
71B LEU* 3.6 16.3 + - - +
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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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24A ASP 2.7 12.3 + - - +
25A TYR* 3.4 13.7 - - - +
26A LEU 3.9 8.1 - - - +
27A LEU* 3.8 15.7 - - + -
22B LEU* 3.5 26.9 - - + -
25B TYR* 3.3 40.6 - - + +
26B LEU* 3.6 19.5 - - + -
64B ALA* 3.7 15.3 - - + -
65B GLY 2.9 16.2 + - - +
67B LYS* 1.3 72.1 - - - +
69B GLN* 1.3 59.7 + - - +
71B LEU* 3.2 7.6 + - + +
72B LEU* 3.0 31.6 + - + +
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Residues in contact with GLN 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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61B LYS* 4.3 16.3 - - + +
64B ALA* 3.9 13.2 - - + +
65B GLY 2.8 17.1 + - - +
66B SER* 3.5 11.2 - - - +
67B LYS 3.2 0.2 - - - -
68B MET* 1.3 76.5 - - - +
70B GLY* 1.3 56.0 + - - +
72B LEU* 3.8 4.2 - - - +
73B GLU* 2.9 32.1 + - - +
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Residues in contact with GLY 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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66B SER 3.9 3.5 + - - -
67B LYS* 3.4 9.3 + - - -
68B MET 3.2 0.8 - - - -
69B GLN* 1.3 77.6 - - - +
71B LEU* 1.3 58.3 + - - +
73B GLU* 3.9 4.5 - - - +
74B ARG* 2.9 41.6 + - - +
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Residues in contact with LEU 71 (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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25A TYR* 3.8 16.6 - - + -
18B LYS 4.7 1.5 - - - +
21B GLU* 4.1 24.9 - - + +
22B LEU* 3.8 16.2 - - + +
25B TYR* 3.5 44.9 - - + -
67B LYS 3.6 9.4 + - - +
68B MET* 3.2 14.8 + - + +
70B GLY* 1.3 72.9 - - - +
72B LEU* 1.3 64.8 + - - +
74B ARG* 3.6 16.6 + - - +
75B VAL* 3.3 28.4 + - - +
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Residues in contact with LEU 72 (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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27A LEU* 4.6 4.0 - - + -
22B LEU* 3.7 26.5 - - + -
26B LEU* 5.4 0.7 - - + -
57B MET* 4.2 12.6 - - - +
60B LEU* 3.4 60.6 - - + +
61B LYS* 3.5 16.2 - - + +
64B ALA* 3.5 21.1 - - + -
68B MET* 3.0 22.9 + - + +
69B GLN 3.8 1.1 - - - +
71B LEU* 1.3 73.6 - - - +
73B GLU* 1.3 54.0 + - - +
75B VAL* 3.0 7.1 + - - +
76B ASN* 2.7 36.1 + - - +
101B ILE* 5.3 1.6 - - + -
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Residues in contact with GLU 73 (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 LYS* 2.5 42.9 + - - +
69B GLN 2.9 20.2 + - - +
70B GLY* 3.9 5.8 - - - +
72B LEU* 1.3 76.3 - - - +
74B ARG* 1.3 58.1 + - + +
76B ASN* 3.1 13.6 + - - +
77B THR* 2.9 59.1 + - + +
307F ARG* 3.4 19.3 + - - +
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Residues in contact with ARG 74 (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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18B LYS* 4.1 14.5 - - + +
21B GLU* 4.7 12.7 + - - -
70B GLY* 2.9 29.3 + - - +
71B LEU* 3.8 17.4 - - - +
72B LEU 3.2 0.2 - - - -
73B GLU* 1.3 77.5 - - + +
75B VAL* 1.3 57.5 + - - +
77B THR* 2.7 23.6 + - + -
78B GLU* 3.5 13.7 - - - +
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Residues in contact with VAL 75 (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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18B LYS* 3.1 35.0 - - + +
19B ILE* 4.0 19.7 - - + +
22B LEU* 3.8 19.3 - - + -
57B MET* 3.8 27.6 - - + -
71B LEU 3.3 12.7 + - - +
72B LEU 3.0 8.1 + - - +
74B ARG* 1.3 75.7 - - - +
76B ASN* 1.3 65.0 + - - +
77B THR 3.3 0.4 - - - -
78B GLU* 3.3 21.4 + - + +
79B ILE* 3.6 12.3 - - + +
105B LEU* 4.9 2.0 - - + -
108B THR* 5.4 4.5 - - + -
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Residues in contact with ASN 76 (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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54B GLN* 2.9 26.4 + - - +
57B MET* 3.7 23.5 - - + +
58B GLU* 3.1 22.0 + - - -
61B LYS* 3.6 9.1 - - + +
72B LEU 2.7 13.5 + - - +
73B GLU* 3.1 32.8 + - - +
75B VAL* 1.3 77.7 - - - +
77B THR* 1.3 49.3 + - - +
79B ILE* 3.2 8.2 + - - +
80B HIS* 2.8 35.8 + - - +
307F ARG* 3.6 12.9 - - - +
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Residues in contact with THR 77 (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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73B GLU* 2.9 38.0 + - + +
74B ARG* 2.7 27.5 + - + -
76B ASN* 1.3 76.4 - - - +
78B GLU* 1.4 65.6 + - - +
79B ILE 3.3 0.9 + - - -
80B HIS* 3.6 15.9 + - - +
81B PHE 4.8 1.4 + - - -
303F TYR* 3.7 37.2 + - + +
305F THR 5.5 3.6 - - - +
307F ARG* 3.7 29.2 - - + +
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Residues in contact with GLU 78 (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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10B PRO 4.2 4.3 - - - +
11B ILE* 5.0 2.1 - - - -
12B SER* 2.5 34.7 + - - -
14B ASP 4.8 0.9 - - - +
15B PHE* 3.3 28.4 - - + +
18B LYS* 4.3 13.3 - - + +
19B ILE* 5.8 2.2 - - + -
74B ARG 3.5 18.1 - - - +
75B VAL* 3.3 12.3 + - + +
76B ASN 3.2 0.8 - - - -
77B THR* 1.4 79.3 + - - +
79B ILE* 1.3 64.5 + - + +
80B HIS 3.8 0.2 - - - -
81B PHE* 3.4 19.0 - - - -
112B LEU* 4.1 8.0 - - + +
302F THR* 4.5 3.6 + - - -
303F TYR* 3.5 30.9 + - - +
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Residues in contact with ILE 79 (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 LEU* 3.8 25.6 - - + +
53B ALA* 4.1 10.5 - - + -
54B GLN* 3.5 39.5 - - + +
57B MET* 4.1 14.6 - - + -
75B VAL* 3.6 12.1 - - + +
76B ASN* 3.6 10.5 - - - +
78B GLU* 1.3 83.4 - - + +
80B HIS* 1.3 63.5 + - - +
81B PHE* 3.2 11.7 + - + -
82B VAL* 3.2 24.1 + - - +
108B THR* 4.0 11.4 - - + -
112B LEU* 3.7 26.0 - - + -
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Residues in contact with HIS 80 (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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54B GLN* 3.3 22.1 + - - -
58B GLU* 3.9 11.3 + - - -
76B ASN* 2.8 16.2 + - - +
77B THR 3.6 8.5 + - - +
79B ILE* 1.3 72.7 - - - +
81B PHE* 1.3 62.2 + - - +
82B VAL* 3.1 4.5 + - - -
83B THR* 2.6 48.1 + - + -
84B LYS 4.3 0.2 + - - -
307F ARG* 3.1 55.6 + - - +
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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