Contacts of the helix formed by residues 23 - 44 (chain O) in PDB entry 4ADV
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 23 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750A C 3.5 0.8 + - - -
751A U 3.1 21.6 + - - -
14O PHE 4.6 1.7 + - - -
15O GLY* 4.7 1.5 - - - -
16O ARG* 4.8 7.7 + - - +
20O ASP* 3.2 24.1 + - - -
22O GLY* 1.3 75.4 - - - +
24O THR* 1.3 65.7 + - - +
25O GLU* 3.4 21.8 + - - +
26O VAL* 2.8 13.6 + - - +
27O GLN 2.8 21.5 + - - -
76O ARG* 4.5 5.9 + - - -
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Residues in contact with THR 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751A U 3.9 17.5 + - - +
754A C 5.2 2.9 - - + -
22O GLY 3.3 3.5 + - - +
23O SER* 1.3 69.8 + - - +
25O GLU* 1.3 73.3 + - - +
27O GLN* 4.5 3.1 - - - +
28O VAL* 2.7 34.0 + - - +
65O LEU* 3.5 27.8 - - + -
68O TYR* 3.9 22.4 - - + -
69O LEU* 3.2 33.9 - - - +
76O ARG* 3.7 10.3 + - - +
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Residues in contact with GLU 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14O PHE* 3.5 32.3 - - + +
16O ARG* 5.3 5.2 - - + -
23O SER* 3.2 11.6 + - - +
24O THR* 1.3 81.8 + - - +
26O VAL* 1.3 62.5 + - - +
29O ALA* 3.4 18.4 + - - +
69O LEU* 4.2 4.7 - - - +
76O ARG* 2.7 64.4 + - - +
79O ARG* 5.1 3.8 - - - +
80O LEU* 3.4 41.0 + - + +
83O ARG* 5.7 3.0 + - - +
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Residues in contact with VAL 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A U 5.5 0.9 - - - +
10O ILE* 4.8 2.8 - - + +
11O VAL* 3.6 37.5 - - + +
14O PHE* 3.7 6.7 - - + -
15O GLY* 3.2 39.5 - - - +
20O ASP* 3.6 19.1 - - - +
21O THR* 4.4 6.5 - - - +
23O SER* 2.8 14.3 + - - +
24O THR 2.8 0.2 + - - -
25O GLU* 1.3 73.5 - - - +
27O GLN* 1.3 70.2 + - - +
28O VAL 3.2 1.1 - - - -
29O ALA* 2.9 6.4 + - - +
30O LEU* 2.8 27.8 + - + +
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Residues in contact with GLN 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A G 3.0 35.7 + - - +
657A U 3.3 35.7 + - - +
751A U 5.4 2.0 + - - -
21O THR 4.5 0.4 + - - +
22O GLY 3.7 15.2 + - - +
23O SER 2.8 16.4 + - - +
24O THR* 4.1 2.5 - - - +
26O VAL* 1.3 74.0 - - - +
28O VAL* 1.3 63.6 + - - +
30O LEU* 3.0 16.8 + - - +
31O LEU* 2.9 30.6 + - + +
61O GLN* 4.7 4.3 + - - +
65O LEU* 3.3 38.7 - - - +
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Residues in contact with VAL 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24O THR* 2.7 37.3 + - - +
25O GLU 4.4 1.6 - - - +
27O GLN* 1.3 73.4 - - - +
29O ALA* 1.3 64.1 + - - +
31O LEU* 2.9 23.7 + - - +
32O THR* 3.4 6.8 + - - -
62O ARG* 4.2 17.7 - - + +
65O LEU* 3.4 35.9 - - + -
66O LEU* 3.9 26.9 - - + +
69O LEU* 4.6 6.5 - - + -
80O LEU* 4.5 14.4 - - + -
84O LEU* 4.8 4.0 - - + -
86O LEU* 5.5 0.2 - - + -
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Residues in contact with ALA 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O ILE* 3.6 7.4 - - + +
14O PHE* 3.4 34.5 - - + -
25O GLU 3.4 18.0 + - - +
26O VAL 2.9 6.9 + - - +
28O VAL* 1.3 77.2 - - - +
30O LEU* 1.3 63.7 + - - +
31O LEU 3.1 1.2 + - - -
32O THR* 3.1 13.3 + - - -
33O ALA* 3.5 8.0 + - - +
84O LEU* 3.4 25.5 - - + +
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Residues in contact with LEU 30 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A U 3.6 12.6 - - - +
658A C 3.4 45.5 - - - +
2O LEU* 3.9 12.7 - - + +
7O THR* 3.3 27.1 - - + +
10O ILE* 3.4 33.8 - - + +
11O VAL* 6.3 0.9 - - + -
26O VAL* 2.8 16.5 + - + +
27O GLN* 3.2 13.9 - - - +
29O ALA* 1.3 78.0 - - - +
31O LEU* 1.3 63.0 + - + +
33O ALA* 3.8 6.1 + - + +
34O GLN* 3.8 14.2 + - - +
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Residues in contact with LEU 31 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A U 4.9 10.8 - - - +
27O GLN* 2.9 44.9 + - + +
28O VAL* 2.9 11.5 + - - +
30O LEU* 1.3 82.1 - - + +
32O THR* 1.3 66.1 + - - +
33O ALA 3.2 0.2 - - - -
34O GLN* 3.4 9.5 + - - +
35O ILE* 3.1 28.7 + - + +
58O MET* 3.2 45.5 - - + +
61O GLN* 4.7 11.0 - - + +
62O ARG* 4.3 21.1 - - + +
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Residues in contact with THR 32 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28O VAL 3.4 4.6 + - - -
29O ALA 3.1 8.4 + - - -
31O LEU* 1.3 77.5 - - - +
33O ALA* 1.3 53.4 + - - +
35O ILE* 3.0 2.8 + - - +
36O ASN* 2.7 58.2 + - - +
62O ARG* 3.7 22.6 + - - +
84O LEU* 3.4 33.2 - - + +
86O LEU* 3.7 8.7 - - + +
88O ARG* 3.8 18.2 - - - +
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Residues in contact with ALA 33 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2O LEU* 4.8 8.7 - - + -
10O ILE* 5.2 6.7 - - + -
29O ALA 3.5 7.1 + - - +
30O LEU* 3.8 12.8 - - + +
31O LEU 3.2 0.2 - - - -
32O THR* 1.3 76.0 - - - +
34O GLN* 1.3 56.2 + - - +
35O ILE 2.8 6.5 + - - -
36O ASN* 3.7 4.6 - - - +
37O HIS* 2.8 36.9 + - - +
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Residues in contact with GLN 34 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A C 5.5 2.4 + - - -
741A G 3.0 22.8 + - - +
742A G 4.6 10.7 + - - -
1O SER* 3.4 36.1 + - - +
2O LEU* 4.1 21.0 - - + +
30O LEU 3.8 4.7 + - - +
31O LEU* 3.4 11.4 + - + +
33O ALA* 1.3 78.6 - - - +
35O ILE* 1.3 57.7 + - - +
37O HIS* 4.1 9.6 - - + +
38O LEU* 3.0 37.5 + - + +
58O MET* 3.0 33.9 - - + -
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Residues in contact with ILE 35 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31O LEU 3.1 22.2 + - - +
32O THR 3.2 8.5 - - - +
33O ALA 2.8 1.8 + - - -
34O GLN* 1.3 76.0 - - - +
36O ASN* 1.3 76.7 + - - +
38O LEU* 3.1 5.2 + - - +
39O GLN* 3.1 24.6 + - - +
55O LEU* 4.4 13.4 - - + +
58O MET* 3.5 26.7 - - + +
59O VAL* 3.6 39.0 - - + +
62O ARG* 3.6 31.4 - - - +
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Residues in contact with ASN 36 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O THR* 2.7 40.1 + - - +
33O ALA* 3.8 4.1 - - - +
35O ILE* 1.3 82.8 - - - +
37O HIS* 1.3 62.7 + - - +
39O GLN* 3.2 30.7 + - - +
40O GLY 3.8 2.3 + - - -
84O LEU 5.5 0.3 - - - +
88O ARG* 3.9 23.5 + - - +
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Residues in contact with HIS 37 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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739A C 5.2 2.0 - - - -
740A U 3.0 26.5 + - - -
1O SER 5.1 9.9 - - - -
2O LEU* 6.3 2.7 - - + -
33O ALA 2.8 23.9 + - - +
34O GLN* 4.3 7.4 - - + +
36O ASN* 1.3 73.6 - - - +
38O LEU* 1.3 65.4 + - + +
40O GLY* 3.5 10.2 + - - -
41O HIS* 3.8 7.8 + - + +
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Residues in contact with LEU 38 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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740A U 3.1 44.6 - - - +
741A G 3.5 22.7 - - - +
34O GLN* 3.0 24.8 + - + +
35O ILE 3.1 5.8 + - - +
37O HIS* 1.3 79.3 - - + +
39O GLN* 1.3 54.4 + - - +
40O GLY 3.0 2.7 - - - -
41O HIS* 2.7 35.7 + - + +
42O PHE* 2.7 43.7 + - + -
55O LEU* 4.4 6.3 - - + -
58O MET* 3.5 21.3 - - + -
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Residues in contact with GLN 39 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ILE* 3.1 14.2 + - - +
36O ASN* 3.2 26.9 + - - +
38O LEU* 1.3 77.2 - - - +
40O GLY* 1.3 59.7 + - - +
42O PHE* 4.0 8.4 - - - +
43O ALA* 3.1 22.3 + - - +
55O LEU* 5.6 1.8 - - - +
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Residues in contact with GLY 40 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O ASN 3.8 2.8 + - - -
37O HIS 3.5 8.6 + - - -
38O LEU 3.0 0.8 - - - -
39O GLN* 1.3 79.5 - - - +
41O HIS* 1.3 62.3 + - - +
43O ALA* 3.3 17.3 - - - +
44O GLU* 3.8 6.2 + - - +
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Residues in contact with HIS 41 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A G 4.0 0.9 - - - -
739A C 2.8 40.6 + - - +
740A U 3.3 29.9 + - - -
37O HIS* 3.8 6.4 + - + +
38O LEU* 2.7 28.2 + - + +
40O GLY* 1.3 74.8 - - - +
42O PHE* 1.3 66.1 + + - +
43O ALA 3.0 4.0 - - - -
44O GLU* 2.7 33.9 + - - +
45O HIS* 3.3 27.8 + + + -
48O ASP* 3.4 23.7 + - + -
51O SER* 4.5 1.6 - - - -
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Residues in contact with PHE 42 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O LEU* 2.7 59.6 + - + +
39O GLN* 4.3 6.3 - - - +
41O HIS* 1.3 77.8 - + - +
43O ALA* 1.3 65.2 + - - +
44O GLU 3.0 11.1 - - - +
46O LYS* 3.7 16.8 + - - +
48O ASP* 3.8 13.5 - - + -
51O SER* 3.3 33.2 - - - -
52O ARG* 3.3 59.0 + - + +
55O LEU* 3.5 24.5 - - + -
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Residues in contact with ALA 43 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O GLN 3.1 14.6 + - - +
40O GLY* 3.3 16.8 - - - +
41O HIS 3.0 0.2 - - - -
42O PHE* 1.3 79.1 - - - +
44O GLU* 1.3 58.2 + - - +
46O LYS* 3.9 12.1 - - - +
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Residues in contact with GLU 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A G 5.0 8.8 + - - +
40O GLY 3.8 5.1 + - - +
41O HIS* 2.7 18.1 + - - +
42O PHE* 3.0 5.5 - - - +
43O ALA* 1.3 79.9 - - - +
45O HIS* 1.3 94.9 + - + +
46O LYS* 2.6 20.5 + - - -
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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