Contacts of the helix formed by residues 61 - 75 (chain R) in PDB entry 1OCR
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 PHE 61 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Q GLU* 3.0 18.8 + - - +
48Q TRP* 3.6 41.9 - + + +
51Q LEU* 4.7 0.9 - - + -
56Q LYS* 3.2 62.8 - - + -
59Q LEU* 3.9 19.7 - - + -
60Q TYR* 5.6 0.9 - - + -
60R ASP* 1.3 73.8 - - - +
62R ALA* 1.3 58.5 + - - +
64R ALA* 2.8 32.6 + - - +
65R VAL* 3.3 31.6 + - + -
97R GLY 4.1 0.2 - - - -
98R ILE* 3.9 11.9 - - + -
99R SER 3.8 19.3 - - - -
104R LEU* 4.0 5.8 - - + -
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Residues in contact with ALA 62 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Q GLU* 4.2 2.7 + - - +
59Q LEU* 4.0 4.9 - - + +
60Q TYR* 3.7 26.1 - - - +
63Q LYS* 3.6 31.4 - - + -
64Q PHE* 3.5 10.5 - - + -
60R ASP* 3.4 5.1 + - - +
61R PHE* 1.3 84.9 - - - +
63R SER* 1.3 58.5 + - - +
65R VAL* 3.0 7.2 + - - +
66R ARG 2.9 23.9 + - - -
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Residues in contact with SER 63 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q LEU* 4.1 18.0 - - - +
63Q LYS* 3.9 10.7 - - - -
64Q PHE* 4.2 9.0 - - - -
29R LEU* 4.5 11.4 - - - +
30R ARG* 6.0 0.9 - - - +
55R CYS* 3.8 15.5 - - - -
60R ASP* 2.8 34.2 + - - -
62R ALA* 1.3 75.8 - - - +
64R ALA* 1.3 58.1 + - - +
66R ARG* 3.8 0.3 - - - +
67R ILE* 2.8 34.7 + - - +
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Residues in contact with ALA 64 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Q TRP* 4.6 3.8 - - + -
52R LEU* 3.8 21.7 - - + +
55R CYS* 3.7 19.9 - - + -
60R ASP 4.2 3.8 - - - +
61R PHE* 2.8 16.7 + - + +
63R SER* 1.3 75.9 - - - +
65R VAL* 1.3 64.5 + - - +
67R ILE* 3.4 3.3 + - - +
68R LEU* 3.2 25.2 + - - +
98R ILE* 4.2 24.5 - - + -
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Residues in contact with VAL 65 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Q TYR* 3.6 24.2 - - + -
61R PHE* 3.3 23.9 + - + +
62R ALA 3.0 9.2 + - - +
64R ALA* 1.3 78.8 - - - +
66R ARG* 1.3 64.0 + - - +
68R LEU* 2.9 21.1 + - - +
69R GLU* 3.1 10.3 + - - +
98R ILE* 4.8 1.1 - - + -
99R SER 3.4 21.8 - - - +
101R PRO* 3.7 16.7 - - + +
104R LEU* 3.5 19.7 - - + -
106R LEU* 3.8 15.7 - - + -
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Residues in contact with ARG 66 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16Q TYR* 4.3 0.2 + - - -
18Q ASP* 3.3 22.0 + - - +
19Q ARG 5.3 0.4 - - - +
22Q TYR 5.1 0.6 + - - -
23Q PRO* 2.8 37.9 + - + +
24Q LEU* 4.2 6.7 - - + -
25Q PRO* 4.3 3.4 - - - +
60Q TYR* 3.1 19.6 + - + -
64Q PHE* 3.5 45.8 - - + +
66Q GLU 2.4 32.3 + - - -
67Q SER* 4.0 1.4 - - - +
68Q PHE* 3.6 12.5 - - + -
71Q MET* 3.4 20.1 - - - +
62R ALA 2.9 8.3 + - - +
63R SER 4.0 2.0 - - - +
65R VAL* 1.3 76.2 - - - +
67R ILE* 1.3 62.0 + - - +
69R GLU* 3.0 16.2 + - - +
70R VAL* 3.0 21.5 + - - +
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Residues in contact with ILE 67 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24Q LEU* 4.7 13.0 - - + -
29R LEU* 4.8 3.6 - - + -
33R MET* 3.8 41.7 - - + -
48R ILE* 4.2 26.5 - - + -
51R ALA* 4.0 17.7 - - + +
52R LEU* 4.4 7.2 - - + -
55R CYS* 3.9 22.0 - - - -
63R SER 2.8 25.9 + - - +
64R ALA* 3.6 6.1 - - - +
65R VAL 3.2 0.2 - - - -
66R ARG* 1.3 76.0 - - - +
68R LEU* 1.3 61.6 + - - +
70R VAL* 3.3 10.8 + - - +
71R VAL* 3.2 22.0 + - - +
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Residues in contact with LEU 68 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48R ILE* 4.4 7.4 - - + -
52R LEU* 4.3 12.8 - - + -
64R ALA 3.2 14.2 + - - +
65R VAL* 2.9 9.0 + - - +
67R ILE* 1.3 74.4 - - - +
69R GLU* 1.3 65.5 + - - +
71R VAL* 3.3 13.0 + - + +
72R LYS 3.4 9.0 + - - -
82R TYR* 3.5 17.1 - - + +
85R VAL* 5.9 0.4 - - + -
86R ILE* 4.2 11.9 - - + -
89R LEU* 3.9 27.6 - - + -
93R LEU* 4.2 18.4 - - + -
98R ILE* 4.3 4.9 - - + -
99R SER 4.2 5.8 - - - +
100R THR* 4.1 17.3 - - + -
101R PRO* 3.8 26.2 - - + -
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Residues in contact with GLU 69 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Q TYR* 2.5 32.0 + - - -
67Q SER* 3.2 10.9 - - - -
68Q PHE* 2.9 44.9 + - + +
69Q ALA 4.5 0.5 + - - -
65R VAL* 3.1 6.8 + - - +
66R ARG* 3.0 26.4 + - - +
68R LEU* 1.3 77.8 - - - +
70R VAL* 1.3 62.1 + - - +
72R LYS* 3.2 9.6 + - - +
73R ASP* 3.0 22.3 + - - +
82R TYR* 5.6 0.2 - - - -
101R PRO* 3.7 27.1 - - + +
106R LEU* 4.4 6.2 - - - +
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Residues in contact with VAL 70 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q ARG 5.3 1.3 - - - +
23Q PRO* 3.2 36.8 - - + -
68Q PHE* 3.6 11.7 - - + -
33R MET* 4.0 13.7 - - + -
37R VAL* 3.6 25.6 - - + -
43R PRO* 6.0 3.8 - - + -
66R ARG 3.0 15.0 + - - +
67R ILE* 3.4 12.8 - - - +
68R LEU 3.2 0.2 - - - -
69R GLU* 1.3 77.6 - - - +
71R VAL* 1.3 66.5 + - + +
73R ASP* 3.0 8.7 + - - +
74R LYS* 2.9 30.7 + - + +
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Residues in contact with VAL 71 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42R VAL* 3.6 30.3 - - + +
43R PRO* 5.0 3.8 - - + -
48R ILE* 3.7 38.8 - - + -
67R ILE* 3.2 14.3 + - + +
68R LEU* 3.3 11.6 + - + +
70R VAL* 1.3 81.2 - - + +
72R LYS* 1.3 62.2 + - - +
74R LYS* 3.6 2.7 + - - +
75R ALA* 3.5 15.8 + - - +
82R TYR* 4.2 11.3 - - + +
85R VAL* 3.9 28.5 - - + -
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Residues in contact with LYS 72 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68R LEU 3.4 3.0 + - - +
69R GLU* 3.2 11.3 + - - +
70R VAL 3.2 0.4 - - - -
71R VAL* 1.3 80.0 - - - +
73R ASP* 1.3 64.4 + - - +
75R ALA* 3.3 16.6 + - - +
76R GLY* 3.7 6.2 + - - +
82R TYR* 3.6 41.5 - - + -
102R GLU* 3.9 24.3 + - - +
107R ASP* 4.3 18.6 + - - +
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Residues in contact with ASP 73 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O LYS* 4.8 1.6 - - - +
51O THR* 5.7 0.2 - - - +
20Q ARG* 3.1 47.2 + - - +
68Q PHE* 3.8 21.1 - - + -
72Q ASN* 3.3 25.3 + - - -
69R GLU 3.0 13.9 + - - +
70R VAL* 3.0 8.3 + - - +
72R LYS* 1.3 77.2 - - - +
74R LYS* 1.3 63.0 + - + +
76R GLY* 3.1 20.0 + - - -
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Residues in contact with LYS 74 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49O LYS 6.0 0.7 - - - -
50O LEU* 3.8 16.8 - - - +
51O THR* 2.9 40.8 + - - +
20Q ARG* 6.0 0.2 - - - +
36R LEU 5.1 0.2 - - - -
37R VAL* 2.9 33.6 + - + +
39R TYR 2.6 28.5 + - - -
41R LEU 3.3 23.5 - - - +
42R VAL* 3.7 17.1 - - + +
43R PRO* 5.3 4.7 - - + -
70R VAL* 2.9 29.1 + - + +
71R VAL* 4.1 3.6 - - - +
72R LYS 3.4 0.4 - - - -
73R ASP* 1.3 79.4 - - - +
75R ALA* 1.3 62.5 + - - +
76R GLY 3.1 2.4 + - - -
12V LEU* 4.4 2.8 - - - +
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Residues in contact with ALA 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50O LEU* 4.0 2.6 - - - +
42R VAL* 3.8 8.3 - - - -
71R VAL 3.5 10.6 + - - +
72R LYS* 3.3 14.1 + - + +
73R ASP 3.2 0.6 - - - -
74R LYS* 1.3 77.4 - - - +
76R GLY* 1.3 67.0 + - - +
77R PRO* 3.1 3.5 - - - +
78R HIS* 3.0 43.6 + - - +
79R LYS* 5.8 0.7 - - - -
81R ILE* 3.9 21.8 - - + -
82R TYR* 4.7 5.2 - - + +
12V LEU* 4.9 0.4 - - - -
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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