Contacts of the helix formed by residues 69 - 88 (chain H) 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 SER 69 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 4.7 3.2 + - - -
52H MET* 5.4 1.7 - - - +
68H GLN* 1.3 77.1 - - - +
70H ASP* 1.3 64.9 + - - +
71H LEU 3.1 1.3 - - - -
72H ILE* 2.8 31.1 + - - +
73H GLU* 3.1 25.2 + - - +
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Residues in contact with ASP 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 4.2 14.2 + - - +
166A MET* 6.0 1.9 - - - +
170A VAL* 5.5 5.4 - - - +
69H SER* 1.3 78.7 + - - +
71H LEU* 1.3 59.6 + - + +
73H GLU* 3.2 23.1 + - - +
74H GLN* 3.0 40.5 + - - +
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Residues in contact with LEU 71 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H PRO* 5.8 0.7 - - - +
45H HIS* 4.5 9.6 - - - +
68H GLN* 3.1 46.0 - - - +
69H SER 3.0 0.8 + - - -
70H ASP* 1.3 79.7 - - + +
72H ILE* 1.3 56.7 + - - +
74H GLN* 3.6 29.9 + - - +
75H ALA* 3.2 23.4 + - - +
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Residues in contact with ILE 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H HIS* 4.6 13.7 - - + +
48H GLN* 3.5 47.8 - - + +
49H ALA* 4.8 2.6 - - - +
52H MET* 3.5 25.4 - - + -
68H GLN* 3.6 27.6 - - + +
69H SER* 2.8 11.0 + - - +
71H LEU* 1.3 78.0 - - - +
73H GLU* 1.3 59.8 + - - +
74H GLN 3.1 1.3 - - - -
75H ALA* 3.1 7.4 + - + +
76H ALA* 2.9 27.0 + - - +
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Residues in contact with GLU 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 2.9 36.5 + - - +
9H TRP* 5.0 2.4 + - - +
12H TRP* 5.7 7.1 - - + -
52H MET* 4.0 24.7 - - + -
69H SER* 3.1 23.3 + - - +
70H ASP* 3.2 21.8 + - - +
72H ILE* 1.3 75.8 - - - +
74H GLN* 1.3 63.9 + - + +
76H ALA* 3.3 3.8 + - - +
77H GLU* 3.1 23.1 + - - +
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Residues in contact with GLN 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H ASP* 3.0 27.0 + - + +
71H LEU* 3.6 33.4 + - - +
73H GLU* 1.3 77.0 - - + +
75H ALA* 1.3 56.7 - - - +
77H GLU* 2.9 13.4 + - - +
78H MET* 2.9 28.6 + - - +
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Residues in contact with ALA 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43H VAL* 4.8 2.3 - - + +
44H PRO* 3.5 37.0 - - + +
45H HIS* 4.6 3.8 - - + -
49H ALA* 4.1 9.9 - - + -
71H LEU 3.2 12.3 + - - +
72H ILE* 3.1 12.0 + - - +
74H GLN* 1.3 81.1 - - - +
76H ALA* 1.3 57.1 + - - +
78H MET* 3.3 6.7 + - - +
79H LEU* 2.8 32.2 + - - +
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Residues in contact with ALA 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H TRP* 3.6 18.4 - - + -
49H ALA* 4.0 24.8 - - - +
52H MET* 3.7 21.8 - - + -
53H ILE* 3.7 4.6 - - + +
72H ILE 2.9 13.1 + - - +
73H GLU 3.6 8.1 - - - +
74H GLN 3.2 0.2 - - - -
75H ALA* 1.3 75.6 - - - +
77H GLU* 1.3 54.3 + - - +
79H LEU* 3.7 2.0 - - - -
80H TYR* 2.8 37.4 + - - +
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Residues in contact with GLU 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H TRP* 4.1 4.0 - - + -
12H TRP* 6.0 1.6 - - - -
13H PHE* 3.3 38.2 - - + -
16H LEU* 5.7 4.2 - - - +
19H ASN* 5.9 0.2 - - - -
73H GLU 3.1 12.7 + - - +
74H GLN* 2.9 17.9 + - - +
76H ALA* 1.3 78.4 - - - +
78H MET* 1.3 60.4 + - - +
80H TYR* 3.5 2.1 + - - +
81H GLY* 3.2 18.4 + - - -
158H TYR* 4.5 8.8 - - + -
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Residues in contact with MET 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42H GLN 4.6 8.5 - - - +
43H VAL* 4.1 23.3 - - + -
44H PRO* 5.0 7.2 - - - -
74H GLN 2.9 13.1 + - - +
75H ALA* 3.8 8.5 - - - +
77H GLU* 1.3 76.5 - - - +
79H LEU* 1.3 64.4 + - - +
81H GLY* 3.1 3.1 + - - -
82H LEU* 3.0 31.0 + - + +
128H PRO* 4.4 19.7 - - + -
129H GLY 6.1 0.2 - - - +
158H TYR* 3.4 26.8 - - + +
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Residues in contact with LEU 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H LEU* 5.7 0.2 - - + -
39H LEU* 4.5 12.6 - - + -
43H VAL* 4.0 19.7 - - + +
46H TYR* 3.9 35.7 - - + -
49H ALA* 3.8 9.6 - - + -
50H LEU* 3.6 36.8 - - + +
53H ILE* 3.6 10.5 - - + -
75H ALA 2.8 21.2 + - - +
76H ALA* 3.8 3.4 - - - +
78H MET* 1.3 71.7 - - - +
80H TYR* 1.3 65.3 + - - +
82H LEU* 3.4 3.2 + - + +
83H ILE* 3.1 44.3 + - + +
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Residues in contact with TYR 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H TRP* 3.5 25.4 - + + -
10H ILE* 3.6 22.2 - - + +
13H PHE* 3.4 36.6 - + - -
14H CYS* 3.3 14.6 - - - -
22H PHE* 4.2 13.9 - + - -
23H CYS 2.7 24.4 + - - -
24H GLU* 3.5 0.7 - - - -
25H VAL* 3.1 34.3 + - + +
30H ILE* 4.8 3.4 - - + -
53H ILE* 3.7 17.4 - - + +
76H ALA 2.8 22.5 + - - +
77H GLU 3.9 3.1 - - - +
78H MET 3.3 0.2 - - - -
79H LEU* 1.3 72.9 - - - +
81H GLY* 1.3 59.0 + - - +
83H ILE* 3.3 6.2 + - + +
84H HIS* 2.8 29.3 + + - +
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Residues in contact with GLY 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H PHE* 6.1 0.2 - - - -
22H PHE* 4.3 5.6 - - - -
77H GLU 3.2 6.5 + - - -
78H MET 3.1 5.5 + - - -
80H TYR* 1.3 80.1 - - - +
82H LEU* 1.3 62.7 + - - +
84H HIS* 3.0 8.7 + - - +
85H ALA 2.9 18.9 + - - -
158H TYR* 3.4 41.5 - - - -
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Residues in contact with LEU 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39H LEU* 3.9 21.2 - - + +
42H GLN* 4.1 28.5 - - + +
43H VAL* 3.5 31.0 - - + -
78H MET* 3.0 16.4 + - + +
79H LEU* 3.4 7.6 + - + +
81H GLY* 1.3 74.1 - - - +
83H ILE* 1.3 63.0 + - - +
85H ALA* 3.3 19.7 + - + +
86H ARG* 3.4 13.2 + - - +
126H ASP 5.6 1.1 - - - +
128H PRO* 3.8 28.0 - - + -
157H ALA* 5.1 6.3 - - + +
158H TYR* 3.7 12.3 - - + -
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Residues in contact with ILE 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H VAL* 4.3 9.6 - - + -
29H TYR* 4.1 19.9 - - + -
30H ILE* 4.1 30.3 - - + -
36H LEU* 4.1 23.1 - - + -
39H LEU* 3.7 23.3 - - + -
50H LEU* 4.7 1.3 - - + -
53H ILE* 4.1 13.2 - - + -
79H LEU* 3.1 36.8 + - + +
80H TYR* 3.5 5.8 - - + +
82H LEU* 1.3 73.2 - - - +
84H HIS* 1.3 56.7 + - - +
86H ARG* 3.2 5.1 + - - +
87H TYR* 2.8 31.9 + - - +
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Residues in contact with HIS 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H PHE* 3.5 27.3 - + + -
23H CYS* 3.1 53.3 + - - +
25H VAL* 4.2 9.9 - - + -
80H TYR* 2.8 17.7 + - + +
81H GLY* 3.0 13.9 + - - +
83H ILE* 1.3 75.7 - - - +
85H ALA* 1.3 64.0 + - - +
87H TYR* 3.3 5.8 + - - +
88H ILE* 3.0 42.1 + - + +
97H MET* 4.4 3.1 - - + -
158H TYR 2.9 18.7 + - - +
159H PHE* 3.7 23.8 - + - -
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Residues in contact with ALA 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H GLY 2.9 9.8 + - - +
82H LEU* 3.4 13.9 - - + +
84H HIS* 1.3 77.6 - - - +
86H ARG* 1.3 65.3 + - + +
88H ILE* 3.5 15.9 - - - +
89H LEU* 3.6 13.2 - - - +
157H ALA 3.5 24.7 - - - +
158H TYR 3.5 11.4 + - - +
159H PHE* 4.4 3.8 - - - +
160H GLY* 4.8 5.3 - - - +
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Residues in contact with ARG 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H TYR* 3.5 13.2 - - + +
35H ASN 3.1 27.7 + - - -
36H LEU* 3.5 5.0 - - - -
37H THR* 2.7 31.9 + - - +
38H GLY* 3.6 4.6 - - - -
39H LEU* 2.9 49.3 - - - +
42H GLN* 4.3 4.8 - - - +
82H LEU 3.7 9.9 - - - +
83H ILE 3.2 4.8 + - - +
85H ALA* 1.3 76.0 - - + +
87H TYR* 1.3 67.4 + - - +
89H LEU* 2.8 31.6 + - - +
90H THR* 3.8 4.6 + - - +
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Residues in contact with TYR 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H CYS* 4.0 13.9 - - - -
24H GLU 4.0 1.1 - - - -
25H VAL* 3.4 32.8 - - + -
26H ASP* 3.1 17.8 + - + -
29H TYR* 3.4 54.6 + + + -
83H ILE 2.8 21.6 + - - +
84H HIS* 3.5 4.9 - - - +
86H ARG* 1.3 73.4 - - - +
88H ILE* 1.3 60.4 + - + +
89H LEU 2.9 4.3 + - - -
90H THR* 2.8 33.0 + - - -
92H ARG* 2.8 19.7 - - + -
93H GLY* 3.4 15.9 - - - -
96H GLN* 2.4 36.7 + - - -
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Residues in contact with ILE 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H CYS* 3.9 10.1 - - - -
84H HIS* 3.0 48.1 + - + +
85H ALA 3.5 10.1 - - - +
86H ARG 3.0 0.2 + - - -
87H TYR* 1.3 71.8 - - + +
89H LEU* 1.3 58.1 + - + +
90H THR 3.5 0.4 - - - -
93H GLY* 4.0 7.6 - - - +
94H ILE* 3.2 20.0 - - - +
97H MET* 3.6 28.3 - - + -
159H PHE* 3.6 28.3 - - + +
163H PHE* 3.4 45.4 - - + -
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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
------------------------------------------------------------
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