Contacts of the helix formed by residues 68 - 88 (chain B) in PDB entry 1RQF
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 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B HIS* 3.4 28.5 + - - +
48B GLN* 5.1 6.8 + - - +
67B ASN* 1.3 86.3 + - - +
69B SER* 1.3 64.3 + - - +
70B ASP 3.6 0.4 - - - -
71B LEU* 3.6 27.5 + - + +
72B ILE* 3.5 28.3 + - + +
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Residues in contact with SER 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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52B MET* 5.3 1.9 - - - +
67B ASN* 2.8 11.2 - - - +
68B GLN* 1.3 75.4 - - - +
70B ASP* 1.3 62.7 + - - -
72B ILE* 2.8 32.4 + - - +
73B GLU* 3.1 24.9 + - - +
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Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASN* 3.9 8.5 + - - +
69B SER* 1.3 81.0 + - - +
71B LEU* 1.3 57.8 + - + +
73B GLU* 3.2 24.0 + - - +
74B GLN* 3.0 42.1 + - - +
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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
----------------------------------------------------------
44B PRO* 5.6 0.9 - - - +
45B HIS* 4.4 16.1 - - - +
67B ASN* 5.0 6.3 - - - +
68B GLN* 3.6 34.1 + - + +
69B SER 3.0 0.6 + - - -
70B ASP* 1.3 79.7 - - + +
72B ILE* 1.3 58.1 + - - +
74B GLN* 3.5 25.1 - - - +
75B ALA* 3.2 23.4 + - - +
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B HIS* 4.5 17.9 - - + -
48B GLN* 3.4 50.0 - - + +
49B ALA* 4.6 3.8 - - + +
52B MET* 3.6 25.1 - - + -
68B GLN* 3.5 24.9 + - + +
69B SER* 2.8 10.8 + - - +
71B LEU* 1.3 76.7 - - - +
73B GLU* 1.3 59.2 + - - +
74B GLN 3.1 1.1 - - - -
75B ALA* 3.1 6.8 + - - +
76B ALA* 2.9 27.4 + - - +
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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
----------------------------------------------------------
9B TRP* 5.0 2.9 + - - +
12B TRP* 5.7 6.4 - - + -
52B MET* 4.0 25.1 - - + -
69B SER* 3.1 28.4 + - - +
70B ASP* 3.2 28.9 + - - +
72B ILE* 1.3 75.6 - - - +
74B GLN* 1.3 58.1 + - + +
76B ALA* 3.3 3.6 + - - +
77B GLU* 3.1 28.0 + - - +
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Residues in contact with GLN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ASP* 3.0 24.0 + - + +
71B LEU* 3.5 34.2 - - + +
72B ILE 3.1 0.2 - - - -
73B GLU* 1.3 78.9 - - + +
75B ALA* 1.3 56.4 + - - +
77B GLU* 3.4 11.4 + - - +
78B MET* 3.1 25.8 + - - +
34J PHE* 5.9 2.8 - - - -
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.7 2.6 - - + +
44B PRO* 3.5 37.9 - - + +
45B HIS* 4.7 3.1 - - + -
49B ALA* 4.0 10.7 - - + +
71B LEU 3.2 11.7 + - - +
72B ILE* 3.1 11.4 + - - +
74B GLN* 1.3 78.8 - - - +
76B ALA* 1.3 60.5 + - - +
77B GLU 3.2 0.2 - - - -
78B MET* 3.3 5.8 + - - +
79B LEU* 2.8 31.9 + - - +
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Residues in contact with ALA 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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9B TRP* 3.5 20.9 - - + -
49B ALA* 3.9 23.3 - - - +
52B MET* 3.9 18.8 - - + -
53B ILE* 3.7 6.8 - - + +
72B ILE 2.9 11.7 + - - +
73B GLU 3.6 8.7 - - - +
75B ALA* 1.3 77.5 - - - +
77B GLU* 1.3 58.0 + - - +
79B LEU* 4.4 0.9 - - - -
80B TYR* 2.8 32.9 + - - +
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Residues in contact with GLU 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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9B TRP* 4.1 9.6 - - + -
12B TRP* 6.1 0.7 - - - -
13B PHE* 3.3 32.1 - - + -
16B LEU* 5.8 3.3 - - - +
19B ASN* 5.9 0.4 - - - -
73B GLU 3.1 13.8 + - - +
74B GLN* 3.5 14.3 - - - +
75B ALA 3.2 0.2 - - - -
76B ALA* 1.3 78.6 - - - +
78B MET* 1.3 61.4 + - - +
80B TYR* 3.9 2.1 - - - +
81B GLY* 3.2 17.8 + - - -
158B TYR* 4.5 8.6 - - + -
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Residues in contact with MET 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLN 4.4 9.2 - - - +
43B VAL* 4.0 23.1 - - + -
44B PRO* 5.0 6.7 - - - -
74B GLN 3.1 16.9 + - - +
75B ALA* 3.8 6.1 - - - +
77B GLU* 1.3 73.8 - - - +
79B LEU* 1.3 67.9 + - - +
81B GLY* 3.1 2.6 + - - -
82B LEU* 3.0 30.8 + - + +
128B PRO* 4.4 19.3 - - + -
158B TYR* 3.5 27.0 - - + +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 5.6 0.2 - - + -
39B LEU* 4.4 15.7 - - + -
43B VAL* 4.1 18.8 - - + +
46B TYR* 3.8 35.2 - - + -
49B ALA* 4.0 6.5 - - + -
50B LEU* 3.7 33.9 - - + +
53B ILE* 3.6 15.3 - - + -
75B ALA 2.8 18.6 + - - +
76B ALA 3.9 2.2 - - - +
78B MET* 1.3 75.9 - - - +
80B TYR* 1.3 64.8 + - - +
82B LEU* 3.4 3.4 + - + +
83B ILE* 3.1 44.0 + - + +
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Residues in contact with TYR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B TRP* 3.5 25.4 - + + -
10B ILE* 3.6 24.1 - - + +
13B PHE* 3.4 35.7 - + - -
14B CYS* 3.3 15.3 - - - -
22B PHE* 4.2 14.4 - + - -
23B CYS 2.6 24.5 + - - -
24B GLU* 3.4 0.5 - - - -
25B VAL* 3.0 34.6 + - + +
30B ILE* 4.8 3.4 - - + -
53B ILE* 3.7 14.1 - - + +
76B ALA 2.8 22.7 + - - +
77B GLU 3.9 3.4 - - - +
79B LEU* 1.3 71.8 - - - +
81B GLY* 1.3 59.6 + - - +
83B ILE* 3.3 6.1 + - + +
84B HIS* 2.8 30.1 + + - +
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Residues in contact with GLY 81 (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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22B PHE* 4.3 5.8 - - - -
77B GLU 3.2 6.3 + - - -
78B MET 3.1 5.1 + - - -
80B TYR* 1.3 80.3 - - - +
82B LEU* 1.3 61.6 + - - +
84B HIS* 3.0 9.1 + - - +
85B ALA 2.9 19.6 + - - -
158B TYR* 3.4 41.9 - - - -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.9 23.7 - - + +
42B GLN* 4.1 26.2 - - + +
43B VAL* 3.7 30.3 - - + -
78B MET* 3.0 16.4 + - + +
79B LEU* 3.4 6.3 + - + +
81B GLY* 1.3 75.0 - - - +
83B ILE* 1.3 62.2 + - - +
85B ALA* 3.4 19.1 + - + +
86B ARG* 3.4 14.2 + - - +
126B ASP 5.6 1.3 - - - +
128B PRO* 3.8 28.5 - - + -
157B ALA* 5.0 6.1 - - + +
158B TYR* 3.7 12.1 - - + -
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Residues in contact with ILE 83 (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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25B VAL* 4.1 10.1 - - + -
29B TYR* 4.0 21.2 - - + -
30B ILE* 4.1 31.0 - - + -
36B LEU* 4.1 21.8 - - + -
39B LEU* 3.7 23.3 - - + -
50B LEU* 4.8 0.4 - - + -
53B ILE* 4.2 12.3 - - + -
79B LEU* 3.1 34.6 + - + +
80B TYR* 3.5 8.7 - - + +
82B LEU* 1.3 74.0 - - - +
84B HIS* 1.3 56.7 + - - +
86B ARG* 3.2 5.6 + - - +
87B TYR* 2.8 35.3 + - - +
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Residues in contact with HIS 84 (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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21B PHE 4.3 2.0 - - - -
22B PHE* 3.5 21.0 - + + -
23B CYS* 3.0 55.1 + - - -
25B VAL* 4.2 9.4 - - + -
80B TYR* 2.8 17.3 + - + +
81B GLY* 3.0 14.3 + - - +
83B ILE* 1.3 77.7 - - - +
85B ALA* 1.3 63.1 + - - +
87B TYR* 3.2 6.1 + - - +
88B ILE* 3.0 41.9 + - + +
97B MET* 4.4 1.8 - - + -
158B TYR 2.9 19.3 + - - +
159B PHE* 3.7 29.2 - + - -
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Residues in contact with ALA 85 (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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81B GLY 2.9 9.8 + - - +
82B LEU* 3.4 13.0 - - + +
83B ILE 3.2 0.2 - - - -
84B HIS* 1.3 78.0 - - - +
86B ARG* 1.3 65.1 + - + +
88B ILE* 3.5 16.5 - - - +
89B LEU* 3.6 13.7 - - - +
157B ALA 3.5 25.1 - - - +
158B TYR 3.5 10.7 + - - +
159B PHE* 4.4 3.5 - - - +
160B GLY* 4.8 5.6 - - - +
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Residues in contact with ARG 86 (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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29B TYR* 3.5 13.5 - - - +
35B ASN 3.0 27.8 + - - -
36B LEU* 3.8 1.8 - - - -
37B THR* 3.0 30.1 + - - +
38B GLY* 3.8 3.4 - - - -
39B LEU* 2.9 53.0 - - - +
42B GLN* 4.5 3.6 - - - +
82B LEU 3.4 10.1 + - - +
83B ILE* 3.2 5.9 + - - +
85B ALA* 1.3 74.0 - - + +
87B TYR* 1.3 67.7 + - - +
89B LEU* 2.9 29.4 + - - +
90B THR* 3.7 5.9 - - - +
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Residues in contact with TYR 87 (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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23B CYS* 4.0 15.7 - - - -
24B GLU 3.8 1.1 - - - -
25B VAL* 3.5 39.7 - - + -
26B ASP* 3.0 20.6 + - - -
29B TYR* 3.6 40.1 + + + -
83B ILE 2.8 21.6 + - - +
84B HIS* 3.4 7.2 - - - +
86B ARG* 1.3 73.5 - - - +
88B ILE* 1.3 59.5 + - + +
89B LEU 2.9 5.0 + - - -
90B THR* 2.7 33.7 + - - -
92B ARG* 2.8 20.2 - - + -
93B GLY* 3.4 13.5 - - - -
96B GLN* 2.4 34.5 + - - -
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Residues in contact with ILE 88 (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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23B CYS* 3.8 10.3 - - - -
84B HIS* 3.0 48.8 + - + +
85B ALA 3.5 10.3 - - - +
86B ARG 3.2 0.2 + - - -
87B TYR* 1.3 71.1 - - + +
89B LEU* 1.3 57.8 + - + +
90B THR 3.5 0.4 - - - -
93B GLY* 4.0 7.4 - - - +
94B ILE* 3.2 19.5 - - - +
97B MET* 3.6 27.4 - - + -
159B PHE* 3.7 28.3 - - + +
163B PHE* 3.3 45.8 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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