Contacts of the helix formed by residues 68 - 88 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A HIS* 3.8 22.4 + - + +
48A GLN* 5.4 6.0 - - - +
65A ASN* 3.9 17.0 - - - +
66A PRO* 3.3 22.2 + - + +
67A ASN* 1.3 91.0 + - - +
69A SER* 1.3 64.4 + - - +
70A ASP 3.5 1.8 - - - -
71A LEU* 3.4 35.5 + - + +
72A ILE* 3.5 18.9 + - + +
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Residues in contact with SER 69 (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 MET* 5.4 0.3 - - - +
61A GLU* 6.0 1.6 - - - -
67A ASN* 2.5 28.2 + - - -
68A GLN* 1.3 70.2 - - - +
70A ASP* 1.3 62.6 + - - +
72A ILE* 2.7 32.5 + - - +
73A GLU* 3.1 24.6 + - - +
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Residues in contact with ASP 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN* 4.3 7.6 + - - +
68A GLN* 3.5 0.6 - - - -
69A SER* 1.3 78.8 + - - +
71A LEU* 1.3 59.9 + - + +
73A GLU* 3.1 22.4 + - - +
74A GLN* 3.0 41.6 + - + +
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PRO* 5.1 2.4 - - - +
45A HIS* 3.9 23.0 - - + +
68A GLN* 3.5 29.6 - - + +
69A SER 3.1 0.8 + - - -
70A ASP* 1.3 79.6 - - + +
72A ILE* 1.3 57.6 + - - +
74A GLN* 3.7 23.6 + - - +
75A ALA* 3.2 24.1 + - - +
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A HIS* 3.9 20.9 - - + +
48A GLN* 2.8 51.6 - - + +
49A ALA* 4.1 12.8 - - + +
52A MET* 4.1 18.8 - - + -
59A ASP* 4.8 3.6 - - - +
67A ASN 5.5 0.4 - - - +
68A GLN* 3.7 19.5 - - + +
69A SER* 2.7 11.9 + - - +
71A LEU* 1.3 76.3 - - - +
73A GLU* 1.3 59.2 + - - +
74A GLN 3.2 0.2 - - - -
75A ALA* 3.1 7.1 + - - +
76A ALA* 2.9 27.4 + - - +
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 5.1 2.1 - - - -
12A TRP* 6.1 1.6 - - - -
52A MET* 4.0 29.8 - - + -
69A SER* 3.1 25.8 + - - +
70A ASP* 3.1 26.8 + - - +
72A ILE* 1.3 76.6 - - - +
74A GLN* 1.3 64.3 + - + +
76A ALA* 3.3 4.2 + - - +
77A GLU* 3.1 22.8 + - - +
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Residues in contact with GLN 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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70A ASP* 3.0 24.4 + - + +
71A LEU* 3.8 27.5 + - - +
72A ILE 3.2 0.2 - - - -
73A GLU* 1.3 78.4 - - + +
75A ALA* 1.3 56.3 + - - +
77A GLU* 3.1 15.2 + - - +
78A MET* 2.9 27.9 + - - +
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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
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43A VAL* 4.3 3.6 - - + +
44A PRO* 3.0 41.1 - - + +
45A HIS* 4.5 0.2 - - + -
49A ALA* 3.8 10.1 - - + -
71A LEU 3.2 14.8 + - - +
72A ILE* 3.1 12.5 + - - +
74A GLN* 1.3 76.8 - - - +
76A ALA* 1.3 57.0 + - - +
78A MET* 3.8 6.8 - - - +
79A LEU* 2.8 31.9 + - - +
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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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9A TRP* 3.9 13.2 - - + -
49A ALA* 3.6 27.3 - - + +
52A MET* 4.1 15.3 - - + -
53A ILE* 3.5 14.8 - - + +
72A ILE 2.9 12.7 + - - +
73A GLU 3.5 9.0 - - - +
75A ALA* 1.3 75.7 - - - +
77A GLU* 1.3 54.6 + - - +
80A TYR* 2.8 36.2 + - - +
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Residues in contact with GLU 77 (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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9A TRP* 4.4 10.7 - - + -
13A PHE* 3.6 30.8 - - + -
73A GLU 3.1 13.3 + - - +
74A GLN* 3.1 16.4 + - - +
76A ALA* 1.3 78.7 - - - +
78A MET* 1.3 60.8 + - - +
80A TYR* 3.5 2.5 + - - +
81A GLY* 3.2 17.7 + - - -
158A TYR* 4.5 9.8 - - + -
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Residues in contact with MET 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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42A GLN 4.1 11.7 - - - +
43A VAL* 3.8 24.0 - - + -
44A PRO* 5.0 5.4 - - - -
74A GLN 2.9 12.2 + - - +
75A ALA* 3.3 8.0 + - - +
77A GLU* 1.3 73.4 - - - +
79A LEU* 1.3 65.6 + - - +
81A GLY* 3.1 3.3 + - - -
82A LEU* 3.0 32.9 + - + +
128A PRO* 4.4 19.3 - - + -
158A TYR* 3.5 26.6 - - + +
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Residues in contact with LEU 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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36A LEU* 5.4 0.4 - - + -
39A LEU* 4.0 18.2 - - + -
43A VAL* 3.9 17.4 - - + +
46A TYR* 3.4 42.6 - - + +
49A ALA* 4.3 2.2 - - + -
50A LEU* 3.9 32.5 - - + +
53A ILE* 3.8 10.3 - - + -
75A ALA 2.8 18.3 + - - +
76A ALA 3.9 2.9 - - - +
78A MET* 1.3 75.1 - - - +
80A TYR* 1.3 64.7 + - - +
82A LEU* 3.3 3.3 + - + +
83A ILE* 3.0 45.3 + - + +
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Residues in contact with TYR 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 3.7 24.0 - + + -
10A ILE* 3.6 21.3 - - + +
13A PHE* 3.5 36.6 - + + -
14A CYS* 3.3 14.4 - - - -
22A PHE* 4.2 13.9 - + - -
23A CYS 2.7 25.0 + - - -
24A GLU* 3.5 0.5 - - - -
25A VAL* 3.1 36.9 + - + +
30A ILE* 4.7 3.4 - - + -
53A ILE* 3.8 16.5 - - + +
76A ALA 2.8 21.4 + - - +
77A GLU 3.8 3.1 - - - +
79A LEU* 1.3 72.7 - - - +
81A GLY* 1.3 59.8 + - - +
83A ILE* 3.2 6.6 + - + +
84A HIS* 2.8 30.1 + + - +
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Residues in contact with GLY 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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22A PHE* 4.4 5.6 - - - -
77A GLU 3.2 5.9 + - - -
78A MET 3.1 4.9 + - - -
80A TYR* 1.3 79.8 - - - +
82A LEU* 1.3 61.8 + - - +
84A HIS* 3.0 9.1 + - - +
85A ALA 2.9 19.4 + - - -
158A TYR* 3.4 42.1 - - - -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.6 26.0 - - + +
42A GLN* 3.8 29.2 - - + +
43A VAL* 4.0 26.2 - - + -
78A MET* 3.0 17.4 + - + +
79A LEU* 3.8 6.3 - - - +
81A GLY* 1.3 74.0 - - - +
83A ILE* 1.3 62.6 + - - +
85A ALA* 3.4 8.2 + - + +
86A ARG* 3.3 26.0 + - - +
126A ASP 5.6 1.3 - - - +
128A PRO* 3.8 27.4 - - + -
157A ALA* 5.1 6.3 - - + +
158A TYR* 4.0 11.9 - - + -
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 4.1 19.1 - - + -
29A TYR* 3.8 23.6 - - + -
30A ILE* 4.2 20.0 - - + -
36A LEU* 3.9 23.8 - - + -
39A LEU* 3.6 22.4 - - + -
50A LEU* 4.9 0.4 - - + -
53A ILE* 4.5 6.3 - - + -
79A LEU* 3.0 35.2 + - + +
80A TYR* 3.5 11.9 - - + +
82A LEU* 1.3 73.0 - - - +
84A HIS* 1.3 55.6 + - - +
86A ARG* 3.1 6.6 + - - +
87A TYR* 2.8 32.1 + - - +
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Residues in contact with HIS 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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21A PHE 4.3 1.6 - - - -
22A PHE* 3.5 21.9 - + + -
23A CYS* 3.0 54.5 + - - +
25A VAL* 4.2 10.5 - - + -
80A TYR* 2.8 15.5 + - + +
81A GLY* 3.1 13.9 - - - +
83A ILE* 1.3 76.6 - - - +
85A ALA* 1.3 61.9 + - - +
87A TYR* 3.2 6.5 + + - +
88A ILE* 2.9 41.6 + - + +
97A MET* 4.3 2.2 - - + -
158A TYR 2.9 18.9 + - - +
159A PHE* 3.6 29.2 - + - -
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Residues in contact with ALA 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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81A GLY 2.9 9.0 + - - +
82A LEU* 3.4 13.7 - - + +
83A ILE 3.2 0.2 - - - -
84A HIS* 1.3 78.0 - - - +
86A ARG* 1.3 63.4 + - + +
88A ILE* 3.5 17.2 - - - +
89A LEU* 3.6 14.0 - - - +
157A ALA 3.5 25.1 - - - +
158A TYR 3.5 11.2 + - - +
159A PHE* 4.4 4.1 - - - +
160A GLY* 4.8 5.4 - - - +
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Residues in contact with ARG 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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29A TYR* 3.4 15.4 + - - +
35A ASN 2.8 36.1 + - - -
36A LEU 3.5 2.0 - - - -
37A THR* 3.2 28.4 + - - -
38A GLY* 4.0 3.4 - - - -
39A LEU* 2.9 52.4 - - - +
42A GLN* 4.4 4.0 - - - +
82A LEU 3.3 10.3 - - - +
83A ILE* 3.1 5.3 + - - +
85A ALA* 1.3 76.4 - - + +
87A TYR* 1.3 65.6 + - - +
89A LEU* 3.1 27.6 + - - +
90A THR* 3.7 7.1 - - - +
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Residues in contact with TYR 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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23A CYS* 3.9 16.2 - - - -
24A GLU 3.8 1.1 - - - -
25A VAL* 3.5 39.9 - - + -
26A ASP* 3.1 20.8 - - - -
29A TYR* 3.6 38.5 + + + -
83A ILE 2.8 17.3 + - - +
84A HIS* 3.4 7.6 - - - +
86A ARG* 1.3 77.4 - - - +
88A ILE* 1.3 57.8 + - + +
89A LEU 2.9 4.5 + - - -
90A THR* 2.8 34.6 + - - -
92A ARG* 2.8 20.2 - - + -
93A GLY* 3.5 13.6 - - - -
96A GLN* 2.4 35.1 + - - -
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Residues in contact with ILE 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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23A CYS* 3.9 11.2 - - - -
84A HIS* 2.9 48.3 + - + +
85A ALA 3.5 10.1 - - - +
87A TYR* 1.3 70.9 - - + +
89A LEU* 1.3 57.6 + - + +
90A THR 3.4 0.7 - - - -
93A GLY* 4.0 6.5 - - - -
94A ILE* 3.2 20.1 - - - +
97A MET* 3.6 31.2 - - + -
159A PHE* 3.6 36.6 - - + +
163A PHE* 3.4 34.3 - - + -
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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
------------------------------------------------------------
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