Contacts of the helix formed by residues 19 - 39 (chain R) in PDB entry 6CP3
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 LEU 19 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q GLY* 5.1 7.0 - - - +
61Q THR* 3.5 34.3 - - - +
62Q GLY* 5.1 0.4 - - - -
64Q PHE* 5.6 1.3 - - + -
65Q CYS* 3.9 22.9 - - + +
68Q VAL* 6.3 0.7 - - + -
16R THR* 3.3 21.1 - - + +
17R ILE 3.1 1.0 - - - -
18R GLY* 1.3 73.4 - - - +
20R LEU* 1.3 59.1 + - - +
21R GLY 3.2 1.8 - - - -
22R ALA* 2.8 33.0 + - + +
23R GLY* 3.3 3.5 + - - -
62R GLY* 3.6 17.9 - - - +
65R CYS* 3.0 17.0 - - - -
66R LEU* 3.8 33.9 - - + -
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Residues in contact with LEU 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q ILE* 4.2 1.8 - - + +
18Q GLY* 3.6 23.3 + - - +
20Q LEU* 3.8 30.3 - - + -
21Q GLY* 3.3 32.4 - - - +
17R ILE* 2.9 26.4 + - + +
18R GLY 3.1 0.4 - - - -
19R LEU* 1.3 76.2 - - - +
21R GLY* 1.3 58.0 + - - +
23R GLY* 3.0 17.9 + - - +
24R ILE* 3.2 20.2 + - + +
20S LEU* 3.7 31.2 - - + -
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Residues in contact with GLY 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18R GLY 3.9 4.0 + - - -
19R LEU 3.2 0.8 - - - -
20R LEU* 1.3 75.1 - - - +
22R ALA* 1.3 60.8 + - - +
24R ILE* 4.7 1.6 - - - -
25R GLY* 3.1 15.5 + - - -
26R ILE 4.5 0.2 + - - -
58R SER 5.0 2.3 - - - +
20S LEU* 3.3 19.8 - - - +
23S GLY* 2.9 46.8 - - - +
24S ILE* 4.0 4.5 - - - -
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Residues in contact with ALA 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61Q THR* 3.8 24.7 - - + -
18R GLY 4.9 0.2 + - - -
19R LEU* 2.8 30.4 + - + +
21R GLY* 1.3 76.5 - - - +
23R GLY* 1.3 61.2 + - - +
25R GLY 3.0 11.1 + - - -
26R ILE* 3.2 23.0 + - - +
58R SER 5.2 6.5 - - - -
59R GLU* 4.8 7.2 - - - +
62R GLY* 4.1 16.7 - - - +
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Residues in contact with GLY 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q GLY 5.9 0.4 - - - -
21Q GLY 3.1 12.5 - - - +
22Q ALA* 3.8 18.5 - - - +
25Q GLY* 3.5 10.0 - - - -
26Q ILE* 5.6 0.2 - - - +
58Q SER* 4.2 8.9 - - - +
61Q THR* 3.4 18.2 - - - -
19R LEU 3.3 3.8 + - - -
20R LEU* 3.0 7.4 + - - -
22R ALA* 1.3 79.5 - - - +
24R ILE* 1.3 61.3 + - - +
27R ALA* 3.5 8.1 - - - +
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Residues in contact with ILE 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Q LEU* 6.3 0.2 - - + -
21Q GLY* 3.2 26.4 + - - +
24Q ILE* 4.2 24.2 - - + -
25Q GLY* 4.0 3.6 - - - -
28Q ILE* 4.9 6.5 - - + -
20R LEU* 3.2 20.0 + - + +
21R GLY* 4.8 3.4 - - - +
22R ALA 3.6 0.4 - - - -
23R GLY* 1.3 76.1 - - - +
25R GLY* 1.3 62.7 + - - +
26R ILE 3.7 0.2 - - - -
27R ALA* 2.9 28.1 + - - +
28R ILE* 3.0 32.0 + - + +
24S ILE* 4.5 28.5 - - + -
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Residues in contact with GLY 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21R GLY 3.1 16.9 + - - -
22R ALA 3.0 7.5 + - - -
24R ILE* 1.3 80.4 - - - +
26R ILE* 1.3 62.1 + - - -
28R ILE* 3.1 23.0 + - - +
29R VAL* 3.3 4.1 + - - +
58R SER* 5.5 1.1 - - - -
23S GLY 3.3 14.4 - - - -
24S ILE* 4.9 0.2 - - - -
27S ALA* 3.3 16.7 - - - +
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Residues in contact with ILE 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57Q LEU 3.5 24.7 - - - +
58Q SER* 3.8 14.4 - - - +
61Q THR* 4.1 11.9 - - + -
21R GLY 4.5 0.2 + - - -
22R ALA* 3.2 19.0 + - - +
25R GLY* 1.3 69.8 - - - -
27R ALA* 1.3 64.5 + - - +
29R VAL* 3.0 25.8 + - - +
30R PHE* 3.1 15.4 + - + -
54R GLY 4.9 0.2 - - - -
55R PHE* 3.3 50.6 - - + +
58R SER* 3.8 10.4 + - - +
59R GLU* 3.6 28.7 - - + +
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Residues in contact with ALA 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q GLY 3.4 25.8 - - - +
29Q VAL* 3.2 20.3 - - + +
58Q SER* 3.6 19.5 - - - +
23R GLY 3.5 14.4 - - - +
24R ILE 2.9 14.8 + - - +
26R ILE* 1.3 80.4 - - - +
28R ILE* 1.3 57.1 + - - +
30R PHE* 3.0 17.9 + - - +
31R ALA 3.0 8.8 + - - -
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Residues in contact with ILE 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q GLY* 5.1 0.2 - - - -
28Q ILE* 3.7 40.6 - - + -
24R ILE* 3.0 27.4 + - + +
25R GLY 3.1 14.5 + - - +
27R ALA* 1.3 73.8 - - + +
29R VAL* 1.3 63.4 + - - +
31R ALA* 2.9 26.4 - - + +
32R ALA 3.2 5.0 + - - -
24S ILE* 4.7 5.4 - - + +
27S ALA* 3.8 17.7 - - + -
28S ILE* 3.6 30.3 - - + -
31S ALA* 4.1 10.1 - - + +
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Residues in contact with VAL 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R GLY 3.3 14.5 + - - +
26R ILE* 3.0 13.7 + - - +
28R ILE* 1.3 76.0 - - - +
30R PHE* 1.3 64.1 + - + +
32R ALA* 3.1 4.7 + - - +
33R LEU* 3.0 16.7 + - - -
51R ALA* 4.2 16.4 - - + +
54R GLY* 3.9 23.8 - - - +
55R PHE* 4.8 1.3 - - - +
58R SER* 5.1 0.4 - - - +
27S ALA* 3.4 30.1 - - - +
30S PHE* 4.1 17.5 - - + -
31S ALA* 4.5 6.7 - - - -
34S ILE* 3.4 18.9 - - + +
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Residues in contact with PHE 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q VAL* 4.4 10.5 - - + -
50Q MET 5.0 3.4 - - - +
51Q ALA* 6.0 0.7 - - - +
53Q LEU* 4.8 9.0 - - + -
54Q GLY* 3.6 30.7 - - - -
57Q LEU* 5.1 2.5 - - + -
58Q SER* 3.5 24.5 - - - -
26R ILE 3.1 22.4 + - - -
27R ALA* 3.0 8.1 + - - +
29R VAL* 1.3 78.8 - - + +
31R ALA* 1.3 52.2 + - - +
33R LEU* 3.0 30.5 - - + +
34R ILE* 2.8 42.3 + - + +
48R PHE* 4.6 13.9 - + - -
51R ALA* 5.7 5.6 - - + -
52R ILE* 6.0 2.5 - - + -
55R PHE* 3.6 41.7 - + + -
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Residues in contact with ALA 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q ILE* 4.0 20.6 - - + +
29Q VAL* 4.7 2.6 - - - +
32Q ALA* 3.4 25.3 - - + +
27R ALA 3.0 7.3 + - - +
28R ILE* 2.9 25.4 - - + +
30R PHE* 1.3 74.0 - - - +
32R ALA* 1.3 56.0 + - - +
34R ILE* 3.0 7.1 + - - -
35R ASN* 2.9 31.3 + - - +
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Residues in contact with ALA 32 (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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28R ILE 3.2 1.0 + - - -
29R VAL 3.1 5.8 + - - +
31R ALA* 1.3 79.5 - - - +
33R LEU* 1.3 51.5 + - - +
35R ASN* 3.0 13.9 + - - +
36R GLY 2.4 33.3 + - - -
31S ALA* 3.3 44.4 - - + +
34S ILE* 3.3 14.3 - - + +
35S ASN* 4.1 12.2 - - - +
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Residues in contact with LEU 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Q VAL* 6.4 0.2 - - + -
50Q MET* 3.6 38.6 - - + +
29R VAL 3.0 7.6 + - - +
30R PHE* 3.0 44.2 + - + +
32R ALA* 1.3 75.2 - - - +
34R ILE* 1.3 64.3 + - + +
36R GLY 3.0 9.4 + - - -
37R VAL* 3.0 21.8 + - + +
44R LYS* 6.1 0.9 - - + -
47R VAL* 3.9 26.7 - - + -
48R PHE* 4.0 13.0 - - + -
51R ALA* 4.4 16.4 - - + -
34S ILE* 3.5 13.6 - - + +
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Residues in contact with ILE 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Q VAL* 3.8 33.2 - - + +
32Q ALA 3.7 7.0 - - - +
33Q LEU* 3.7 29.6 - - + +
36Q GLY* 4.5 3.7 - - - -
47Q VAL* 3.7 23.7 - - + +
50Q MET* 5.8 0.9 - - + -
51Q ALA* 3.8 29.4 - - + +
30R PHE* 2.8 24.4 + - + +
31R ALA* 3.0 6.5 + - - +
33R LEU* 1.3 77.5 - - + +
35R ASN* 1.3 63.9 + - - +
37R VAL* 3.5 7.6 - - - +
38R SER* 3.2 22.0 + - - -
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Residues in contact with ASN 35 (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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32Q ALA* 3.9 22.7 - - - +
35Q ASN* 4.9 5.2 - - - +
36Q GLY* 4.7 5.7 + - - -
39Q ARG* 5.2 7.9 + - - +
31R ALA* 2.9 24.7 + - - +
32R ALA* 3.1 18.7 - - - +
34R ILE* 1.3 77.3 - - - +
36R GLY* 1.3 56.6 + - - +
38R SER* 2.4 32.2 + - - -
39R ARG* 3.1 15.3 + - - +
35S ASN* 4.2 16.6 - - - +
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Residues in contact with GLY 36 (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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32R ALA 2.4 19.7 + - - -
33R LEU 3.0 2.6 + - - -
35R ASN* 1.3 74.2 - - - +
37R VAL* 1.3 57.6 + - - +
40R ASN* 3.0 25.8 + - - +
43R ILE* 3.3 14.8 - - - +
47R VAL* 5.5 2.0 - - - -
34S ILE* 4.0 9.9 - - - -
35S ASN* 5.2 0.7 - - - -
38S SER* 3.7 21.4 - - - -
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Residues in contact with VAL 37 (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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40Q ASN* 4.2 4.2 + - - -
43Q ILE* 5.2 6.4 - - + +
46Q THR* 6.0 0.7 - - + -
47Q VAL* 3.7 40.8 - - + -
50Q MET* 6.1 2.7 - - - -
33R LEU* 3.0 23.6 + - + +
34R ILE* 3.5 8.5 - - - +
36R GLY* 1.3 74.2 - - - +
38R SER* 1.3 68.0 + - - +
40R ASN 3.0 20.3 - - - +
41R PRO* 3.5 12.3 - - + +
43R ILE* 4.5 3.1 - - + +
44R LYS* 4.1 37.9 - - + -
47R VAL* 5.4 1.3 - - + +
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Residues in contact with SER 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36Q GLY* 3.3 30.1 - - - -
39Q ARG* 3.9 17.7 - - - +
40Q ASN* 3.3 25.2 + - - +
47Q VAL* 6.1 1.1 - - - -
34R ILE 3.2 15.7 + - - -
35R ASN* 2.4 30.9 + - - -
37R VAL* 1.3 82.9 - - - +
39R ARG* 1.3 64.3 + - - +
40R ASN 3.1 0.9 + - - -
41R PRO* 4.2 6.4 - - - +
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Residues in contact with ARG 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189G GLU* 6.1 1.4 - - - +
199G ILE* 4.4 18.2 + - - +
201G THR* 3.9 27.6 + - + +
39Q ARG* 5.0 15.6 - - - +
35R ASN* 3.4 16.2 - - - +
38R SER* 1.3 80.7 + - - +
40R ASN* 1.3 59.0 + - + +
41R PRO* 4.1 4.1 - - - +
35S ASN* 4.9 8.5 + - - -
38S SER* 3.9 24.0 + - - +
39S ARG* 3.7 36.5 - - - +
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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