Contacts of the helix formed by residues 17 - 30 (chain A) in PDB entry 4L57
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 ASP 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A GLY* 5.0 0.4 - - - +
16A ALA* 1.3 69.1 - - - +
18A PHE* 1.3 61.3 + - - +
19A GLU* 3.5 7.1 + - - +
20A ALA* 3.0 35.8 + - + +
21A GLY* 3.1 15.9 + - - -
24A ARG* 5.3 0.3 + - - -
38A LEU* 5.9 0.5 - - - +
74A LEU* 3.6 12.0 - - - +
75A GLU* 2.8 27.1 + - + +
76A PRO 4.7 4.6 - - - +
77A ILE* 3.7 26.2 - - + +
78A PRO* 5.4 3.6 - - - +
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Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ASP* 3.8 33.9 - - + +
13A GLY* 4.5 4.5 - - - +
16A ALA 3.0 7.4 + - - +
17A ASP* 1.3 73.2 - - - +
19A GLU* 1.3 63.1 + - - +
21A GLY* 3.2 1.6 + - - -
22A LEU* 2.8 46.4 + - + +
65A TYR* 4.0 27.6 - + + -
70A PHE* 3.6 27.3 - + - -
71A PHE* 3.9 18.4 - + - -
74A LEU* 3.9 8.9 - - + +
102A LEU* 5.0 6.3 - - + -
204A GOL 3.5 39.7 - - - +
207A GOL 3.6 21.1 - - - -
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLY* 6.2 1.1 - - - -
17A ASP* 3.4 5.9 + - - +
18A PHE* 1.3 81.0 - - + +
20A ALA* 1.3 62.7 + - - +
22A LEU* 3.4 7.6 + - - +
23A LEU* 3.1 18.9 + - - +
38A LEU* 3.7 15.8 - - + +
41A ARG* 2.8 50.4 + - - +
46A ALA* 4.5 3.6 - - - +
165A CYS* 4.2 13.9 - - - -
166A CYS* 3.8 25.8 - - - -
167A HIS* 3.7 2.0 - - - -
204A GOL 2.5 32.4 + - - +
207A GOL 3.8 1.7 + - - -
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASP* 3.0 33.7 + - + +
19A GLU* 1.3 77.4 - - - +
21A GLY* 1.3 57.0 + - - +
23A LEU* 3.4 2.3 + - - +
24A ARG* 3.0 44.6 + - - +
38A LEU* 4.3 21.2 - - + +
75A GLU* 5.7 2.2 - - + +
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASP 3.1 14.6 + - - -
18A PHE 3.6 2.7 - - - -
20A ALA* 1.3 78.2 - - - +
22A LEU* 1.3 61.7 + - - +
24A ARG* 3.5 22.9 + - - +
25A GLY* 2.9 20.1 + - - -
70A PHE* 3.6 12.8 - - - -
74A LEU* 3.9 11.0 - - - -
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 2.8 32.3 + - + +
19A GLU* 3.7 10.3 - - - +
21A GLY* 1.3 78.5 - - - +
23A LEU* 1.3 56.9 + - - +
25A GLY* 3.3 0.7 + - - -
26A PHE* 2.9 30.7 + - - +
46A ALA* 3.7 30.5 - - + -
50A TYR* 5.2 4.7 - - + +
61A VAL* 3.6 32.8 - - + +
64A VAL* 3.7 13.4 - - + +
65A TYR* 3.6 26.9 - - + -
70A PHE* 3.6 8.7 - - + -
207A GOL 4.2 4.0 - - - +
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A GLU 3.1 16.5 + - - +
20A ALA* 4.0 3.4 - - - +
22A LEU* 1.3 76.4 - - - +
24A ARG* 1.3 63.8 + - - +
26A PHE* 3.3 4.1 + - + +
27A ARG* 2.9 43.7 + - + +
35A HIS* 3.6 32.3 - - + +
36A VAL 3.8 11.7 - - - +
37A PRO* 4.5 1.1 - - + -
38A LEU* 3.8 34.1 - - + +
50A TYR* 3.6 20.2 - - - +
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASP 5.3 0.4 + - - -
20A ALA* 3.0 41.3 + - - +
21A GLY* 3.5 22.7 + - - +
23A LEU* 1.3 78.7 - - - +
25A GLY* 1.3 57.3 + - - +
27A ARG* 3.4 3.7 + - - +
28A ARG* 3.0 31.0 + - + +
73A ASP 4.6 6.3 + - - -
74A LEU* 4.9 1.4 - - - +
75A GLU* 3.9 42.0 + - - +
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Residues in contact with GLY 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLY 2.9 16.9 + - - -
22A LEU 3.8 0.7 - - - -
24A ARG* 1.3 78.8 - - - +
26A PHE* 1.3 57.9 + - - +
28A ARG* 3.3 17.6 + - - +
29A ARG* 3.0 33.3 + - - +
64A VAL* 3.9 16.8 - - - +
70A PHE* 6.0 0.4 - - - -
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU 2.9 18.2 + - - +
23A LEU* 3.7 6.1 - - - +
25A GLY* 1.3 77.7 - - - +
27A ARG* 1.3 62.7 + - + +
30A PHE* 2.8 61.1 + + + +
33A GLU* 3.9 22.9 - - + -
34A PRO 3.3 27.1 - - - -
35A HIS* 4.0 17.7 - - + -
50A TYR* 3.8 24.7 - + - +
57A LEU* 4.2 9.2 - - + -
60A LYS* 4.1 6.1 - - + -
61A VAL* 3.9 37.2 - - + -
64A VAL* 3.9 10.6 - - + +
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Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 2.9 47.4 + - + +
24A ARG* 4.2 4.5 - - - +
26A PHE* 1.3 78.6 - - + +
28A ARG* 1.3 62.0 + - - +
30A PHE 4.5 4.3 - - - -
31A PRO* 3.3 24.6 - - + +
35A HIS* 3.5 41.6 + - + +
78B PRO* 5.9 6.9 - - - +
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 3.0 20.8 + - + +
25A GLY* 3.6 15.8 + - - +
27A ARG* 1.3 77.2 - - - +
29A ARG* 1.3 82.5 + - - +
31A PRO* 3.5 12.3 - - - +
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLY 3.0 15.5 + - - +
28A ARG* 1.3 94.1 - - - +
30A PHE* 1.3 90.5 + - + +
31A PRO* 3.3 9.2 - - - +
63A SER* 3.2 47.9 + - - -
64A VAL* 4.2 7.3 - - - +
67A ALA* 4.4 10.3 - - - +
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Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PHE* 2.8 49.0 + + + +
27A ARG* 4.5 1.4 - - - -
29A ARG* 1.3 111.7 - - + +
31A PRO* 1.3 64.4 - - - +
32A GLU 3.2 4.4 + - - -
33A GLU* 3.2 36.2 + - - +
60A LYS* 3.3 53.6 - - + -
63A SER* 3.6 17.5 - - - -
64A VAL* 4.0 4.9 - - + -
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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