Contacts of the helix formed by residues 19 - 38 (chain Q) in PDB entry 4B2Q
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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P GLY 4.8 1.6 - - - +
61P THR* 3.3 27.2 - - + +
64P PHE* 4.4 20.0 - - + -
65P CYS* 3.3 30.1 - - - +
68P VAL* 6.2 0.4 - - + -
15Q SER 4.8 0.2 - - - +
16Q THR* 3.3 22.4 - - + +
17Q ILE 3.0 1.6 - - - -
18Q GLY* 1.3 75.4 - - - +
20Q LEU* 1.3 63.8 + - - +
21Q GLY 3.2 2.9 - - - -
22Q ALA* 3.3 11.0 + - - +
23Q GLY 3.5 0.5 + - - -
61Q THR 4.5 1.3 - - - -
62Q GLY* 3.6 35.0 - - - +
65Q CYS* 3.5 25.6 - - + +
66Q LEU* 3.7 16.2 - - + +
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Residues in contact with LEU 20 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P ILE* 3.5 17.9 - - + +
18P GLY 3.5 11.0 - - - +
20P LEU* 3.5 25.6 - - + -
21P GLY* 3.2 29.8 - - - +
17Q ILE* 3.2 28.2 - - + +
18Q GLY 3.2 1.0 - - - -
19Q LEU* 1.3 76.4 - - - +
21Q GLY* 1.3 64.9 + - - +
23Q GLY* 3.2 1.6 + - - +
24Q ILE* 3.1 37.7 + - + +
20R LEU* 3.6 19.5 - - + -
24R ILE* 4.8 2.6 - - + +
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Residues in contact with GLY 21 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18Q GLY 3.9 1.9 + - - -
19Q LEU 3.2 1.4 - - - -
20Q LEU* 1.3 77.2 - - - +
22Q ALA* 1.3 55.9 + - - +
25Q GLY* 3.1 24.9 + - - -
58Q SER* 3.7 1.2 + - - -
61Q THR* 3.7 5.2 - - - -
20R LEU* 3.2 21.6 - - - +
23R GLY* 3.2 31.3 - - - +
24R ILE* 4.2 9.0 - - - -
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Residues in contact with ALA 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P LEU 5.1 2.3 - - - +
58P SER* 5.2 0.7 - - - -
61P THR* 3.6 19.3 - - + +
19Q LEU 3.3 4.3 + - - +
20Q LEU 3.1 0.8 - - - -
21Q GLY* 1.3 77.2 - - - +
23Q GLY* 1.3 64.0 + - - +
25Q GLY 4.1 0.4 - - - -
26Q ILE* 3.1 37.8 - - + +
58Q SER 3.9 15.7 - - - +
59Q GLU* 5.0 3.4 - - - +
61Q THR* 3.7 1.4 + - - -
62Q GLY* 3.8 27.6 - - - +
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Residues in contact with GLY 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P GLY* 3.2 26.3 - - - +
25P GLY* 3.3 6.4 - - - -
58P SER* 3.4 10.5 + - - -
61P THR* 3.4 21.8 - - - +
19Q LEU 3.5 0.8 + - - -
20Q LEU 3.2 3.4 + - - -
22Q ALA* 1.3 82.1 - - - +
24Q ILE* 1.3 56.4 + - - +
27Q ALA* 3.3 20.3 + - - +
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Residues in contact with ILE 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P LEU* 4.9 4.9 - - + +
21P GLY* 4.2 12.1 - - - -
24P ILE* 4.2 35.4 - - + -
25P GLY* 4.1 2.5 - - - +
28P ILE* 4.4 14.4 - - + -
20Q LEU* 3.1 20.5 + - + +
23Q GLY* 1.3 75.6 - - - +
25Q GLY* 1.3 68.1 + - - +
27Q ALA* 3.2 6.7 - - - +
28Q ILE* 3.2 32.5 + - + +
24R ILE* 4.3 26.0 - - + -
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Residues in contact with GLY 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Q GLY 3.1 22.2 + - - -
24Q ILE* 1.3 77.5 - - - +
26Q ILE* 1.3 63.2 + - - +
27Q ALA 3.1 1.0 + - - -
28Q ILE 3.1 10.9 + - - -
29Q VAL* 3.2 5.1 + - - +
58Q SER* 3.7 4.5 - - - -
23R GLY 3.3 17.9 - - - -
24R ILE* 4.2 4.1 - - - +
27R ALA* 3.2 22.3 - - - +
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Residues in contact with ILE 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P GLY 5.8 0.4 - - - +
57P LEU* 4.3 25.4 - - + +
58P SER* 5.3 2.9 - - - +
61P THR* 6.0 0.4 - - + -
22Q ALA* 3.1 30.5 + - + +
23Q GLY 4.9 0.4 - - - +
25Q GLY* 1.3 74.5 - - - +
27Q ALA* 1.3 55.5 + - - +
29Q VAL* 3.9 7.7 - - + +
30Q PHE* 3.0 33.2 + - + +
55Q PHE* 3.5 35.2 - - + -
58Q SER* 3.3 23.5 + - - +
59Q GLU* 3.3 31.9 - - - +
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Residues in contact with ALA 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P GLY* 3.1 32.3 - - - +
28P ILE* 4.3 9.0 - - + -
29P VAL* 3.4 18.1 - - + +
58P SER* 4.8 1.7 - - - +
23Q GLY 3.3 16.6 + - - +
24Q ILE* 3.2 12.3 + - - +
25Q GLY 3.0 0.2 - - - -
26Q ILE* 1.3 78.4 - - - +
28Q ILE* 1.3 52.7 + - - +
31Q ALA* 2.8 37.7 + - - +
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Residues in contact with ILE 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P ILE* 4.3 19.5 - - + -
24Q ILE* 3.4 24.9 - - + +
25Q GLY 3.1 6.5 + - - +
27Q ALA* 1.3 75.7 - - - +
29Q VAL* 1.3 62.9 + - - +
31Q ALA* 3.6 6.9 - - + +
32Q ALA* 3.1 23.4 + - - +
24R ILE* 4.5 11.9 - - + -
27R ALA* 4.3 10.5 - - + +
28R ILE* 4.3 23.3 - - + -
31R ALA* 3.8 20.2 - - + -
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Residues in contact with VAL 29 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q GLY 3.2 16.3 + - - +
26Q ILE* 3.9 10.5 - - + +
28Q ILE* 1.3 77.9 - - - +
30Q PHE* 1.3 61.6 + - - +
32Q ALA 3.7 2.6 + - - -
33Q LEU* 3.8 1.7 + - - +
51Q ALA* 4.2 21.0 - - + +
54Q GLY* 4.3 17.3 - - - +
55Q PHE* 4.7 1.1 - - - +
58Q SER* 4.8 4.0 - - - -
27R ALA* 3.4 29.6 - - + +
30R PHE* 4.2 18.2 - - + -
31R ALA* 4.5 6.5 - - - -
34R ILE* 3.2 31.4 - - + +
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Residues in contact with PHE 30 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P VAL* 4.3 9.6 - - + -
50P MET* 3.1 42.4 - - + -
51P ALA* 4.6 0.9 - - - -
53P LEU* 4.2 7.4 - - + -
54P GLY* 3.5 17.7 - - - -
57P LEU* 3.5 34.3 - - + -
26Q ILE* 3.0 22.2 + - + +
27Q ALA 3.9 2.5 - - - +
29Q VAL* 1.3 75.4 - - - +
31Q ALA* 1.3 65.2 + - - +
32Q ALA 3.2 0.7 - - - -
33Q LEU* 3.2 29.1 + - + +
34Q ILE* 3.4 25.6 + - + +
48Q PHE* 6.3 2.2 - + - -
51Q ALA* 6.1 3.1 - - + -
55Q PHE* 6.4 0.7 - - + -
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Residues in contact with ALA 31 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P ILE* 3.8 34.3 - - + +
29P VAL* 4.5 1.9 - - - +
32P ALA* 3.8 13.2 - - + +
27Q ALA 2.8 19.7 + - - +
28Q ILE* 3.3 6.0 + - + +
30Q PHE* 1.3 77.0 - - - +
32Q ALA* 1.3 60.4 + - - +
34Q ILE* 3.2 8.4 + - - +
35Q ASN* 3.0 23.4 + - - +
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Residues in contact with ALA 32 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Q ILE 3.1 15.7 + - - +
30Q PHE 3.2 0.2 - - - -
31Q ALA* 1.3 75.2 - - - +
33Q LEU* 1.3 59.7 + - - +
35Q ASN* 3.4 5.6 + - - +
36Q GLY* 2.9 24.4 + - - -
31R ALA* 3.8 18.6 - - + +
34R ILE* 3.3 39.5 - - + +
35R ASN* 4.8 7.1 + - + +
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Residues in contact with LEU 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P MET* 4.3 16.8 - - + -
29Q VAL 3.8 2.8 + - - +
30Q PHE* 3.2 28.7 + - + +
32Q ALA* 1.3 79.1 - - - +
34Q ILE* 1.3 61.0 + - - +
36Q GLY* 4.0 0.6 - - - -
37Q VAL* 3.3 37.5 + - + +
44Q LYS* 5.6 0.7 - - - +
47Q VAL* 3.6 38.6 - - + +
48Q PHE* 4.1 29.6 - - + +
51Q ALA* 3.8 23.8 - - + -
34R ILE* 3.5 7.9 - - + +
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Residues in contact with ILE 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P VAL* 3.2 39.5 - - + +
32P ALA* 3.5 32.1 - - + +
33P LEU* 3.6 4.3 - - - +
36P GLY* 5.3 0.4 - - - -
47P VAL* 3.5 25.1 - - + -
50P MET* 4.9 5.8 - - + -
51P ALA* 4.5 14.6 - - + -
30Q PHE* 3.6 26.5 - - + +
31Q ALA* 3.2 6.5 + - - +
32Q ALA 3.2 0.6 - - - -
33Q LEU* 1.3 78.1 - - - +
35Q ASN* 1.3 58.6 + - - +
36Q GLY 3.1 2.1 + - - -
37Q VAL* 3.5 12.4 - - - +
38Q SER* 3.0 23.5 + - - +
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Residues in contact with ASN 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P ALA* 4.8 8.3 - - + +
35P ASN* 4.1 12.3 - - + +
36P GLY* 5.8 1.2 - - - -
39P ARG* 2.8 29.9 + - - -
31Q ALA 3.0 14.8 + - - +
32Q ALA* 3.4 6.7 + - - +
34Q ILE* 1.3 76.5 - - - +
36Q GLY* 1.3 59.4 + - - +
38Q SER* 4.1 5.1 - - - -
39Q ARG* 3.5 39.1 + - - +
35R ASN* 3.9 13.7 + - - +
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Residues in contact with GLY 36 (chain Q).
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 2.9 16.5 + - - -
33Q LEU* 3.5 2.0 + - - -
34Q ILE 3.1 0.4 - - - -
35Q ASN* 1.3 77.7 - - - +
37Q VAL* 1.3 60.6 + - - +
38Q SER 3.2 1.6 - - - -
39Q ARG* 3.1 4.0 + - - +
40Q ASN* 2.9 25.7 + - - +
47Q VAL* 6.3 0.7 - - - -
34R ILE* 5.0 2.0 - - - -
35R ASN* 5.7 2.2 - - - -
38R SER* 3.2 30.7 + - - -
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Residues in contact with VAL 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40P ASN* 5.0 2.3 + - - -
43P ILE* 5.0 4.8 - - + +
46P THR* 6.2 2.2 - - + -
47P VAL* 3.6 28.5 - - + -
50P MET* 4.7 15.9 - - + -
33Q LEU* 3.3 35.5 + - + +
34Q ILE* 3.5 11.4 - - - +
36Q GLY* 1.3 73.8 - - - +
38Q SER* 1.3 61.5 + - - +
39Q ARG 3.1 2.0 - - - -
40Q ASN 4.0 7.4 - - - -
41Q PRO* 3.2 33.5 - - + +
43Q ILE 4.5 14.6 - - - +
44Q LYS* 5.2 12.3 - - + -
47Q VAL* 5.9 0.7 - - + -
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Residues in contact with SER 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36P GLY* 3.3 37.1 + - - -
39P ARG* 4.5 17.4 + - - +
40P ASN* 3.9 26.5 + - - +
43P ILE* 6.0 0.8 - - - +
47P VAL* 4.7 7.9 - - - +
34Q ILE* 3.0 18.9 + - - +
35Q ASN* 4.2 7.0 - - - -
36Q GLY 3.2 0.2 - - - -
37Q VAL* 1.3 82.3 - - - +
39Q ARG* 1.3 57.8 + - - +
41Q PRO* 5.0 1.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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