Contacts of the helix formed by residues 17 - 30 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13B GLY* 4.9 0.8 - - - +
16B ALA* 1.3 68.4 - - - +
18B PHE* 1.3 64.2 + - - +
19B GLU* 3.6 6.6 + - - +
20B ALA* 3.0 35.5 + - + +
21B GLY* 3.0 15.8 + - - -
38B LEU* 5.9 0.2 - - - +
74B LEU* 3.7 11.6 - - - +
75B GLU* 2.8 26.7 + - + +
76B PRO 4.6 5.2 - - - +
77B ILE* 3.7 25.9 - - + +
78B PRO* 5.2 4.5 - - - +
165B CYS* 5.9 1.6 - - - -
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Residues in contact with PHE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ASP* 3.7 35.4 - - + +
13B GLY* 4.4 3.7 - - - +
16B ALA 3.0 7.5 + - - +
17B ASP* 1.3 73.1 - - - +
19B GLU* 1.4 76.5 + - + +
21B GLY* 3.2 1.0 + - - -
22B LEU* 2.8 51.4 + - + +
46B ALA* 5.5 2.0 - - + -
65B TYR* 4.0 28.0 - + + -
70B PHE* 3.6 26.0 - + - -
71B PHE* 3.9 9.6 - + - -
74B LEU* 3.9 9.2 - - + +
102B LEU* 5.2 0.2 - - + -
203B GOL 3.3 39.9 - - - -
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY* 6.1 1.5 - - - -
17B ASP* 3.4 5.9 + - - +
18B PHE* 1.4 92.1 - - + +
20B ALA* 1.3 61.0 + - - +
22B LEU* 3.3 5.8 + - - +
23B LEU* 3.0 24.3 + - - +
38B LEU* 3.7 10.0 - - + +
41B ARG* 2.8 51.4 + - - +
44B PHE 4.0 4.5 - - - +
46B ALA* 4.1 10.7 - - - +
165B CYS* 4.3 16.4 - - - -
166B CYS* 4.0 24.5 - - - -
167B HIS* 3.9 8.4 - - + -
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ASP* 3.0 32.9 + - + +
19B GLU* 1.3 76.9 - - - +
21B GLY* 1.3 58.7 + - - +
23B LEU* 3.4 2.1 + - - +
24B ARG* 2.9 43.5 + - - +
38B LEU* 4.3 22.8 - - + +
75B GLU* 6.0 0.7 - - - +
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Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ASP 3.0 16.0 + - - -
18B PHE 3.6 2.5 - - - -
20B ALA* 1.3 77.6 - - - +
22B LEU* 1.3 58.6 + - - +
24B ARG* 3.6 22.7 + - - +
25B GLY* 2.9 25.5 + - - -
70B PHE* 3.6 13.2 - - - -
74B LEU* 3.9 11.7 - - - -
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PHE* 2.8 38.4 + - + +
19B GLU* 3.6 9.2 - - - +
20B ALA 3.3 0.2 - - - -
21B GLY* 1.3 74.6 - - - +
23B LEU* 1.3 57.5 + - - +
25B GLY 3.8 0.3 - - - -
26B PHE* 2.9 31.6 + - - +
46B ALA* 3.7 29.6 - - + -
50B TYR* 5.5 2.7 - - + -
61B VAL* 3.7 42.0 - - + +
64B VAL* 3.8 13.8 - - + +
65B TYR* 4.0 21.1 - - + -
70B PHE* 3.7 9.0 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLU 3.0 16.3 + - - +
20B ALA* 4.0 3.4 - - - +
22B LEU* 1.3 77.0 - - - +
24B ARG* 1.3 64.6 + - - +
26B PHE* 3.2 4.9 + - + +
27B ARG* 2.9 43.7 + - + +
35B HIS* 3.5 37.2 - - + +
36B VAL 3.9 11.2 - - - +
37B PRO* 4.4 1.1 - - + -
38B LEU* 4.0 32.3 - - + +
50B TYR* 3.6 21.5 - - - +
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ALA* 2.9 39.6 + - - +
21B GLY* 3.6 18.0 + - - +
23B LEU* 1.3 78.0 - - - +
25B GLY* 1.3 62.5 + - - +
27B ARG* 3.4 5.2 + - - +
28B ARG* 3.0 65.0 + - + +
73B ASP 4.5 9.3 + - - -
74B LEU* 5.0 1.2 - - - +
75B GLU* 4.0 39.6 + - - +
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Residues in contact with GLY 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLY 2.9 17.3 + - - -
22B LEU 3.8 0.9 - - - -
24B ARG* 1.3 78.0 - - - +
26B PHE* 1.3 56.3 + - - +
28B ARG* 3.4 8.3 + - - +
29B ARG* 3.0 32.6 + - - +
64B VAL* 3.9 16.3 - - - +
70B PHE* 5.8 0.4 - - - -
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU 2.9 18.8 + - - +
23B LEU* 3.6 6.1 - - + +
25B GLY* 1.3 76.6 - - - +
27B ARG* 1.3 62.5 + - + +
30B PHE* 2.8 54.0 + + + +
33B GLU* 3.8 24.2 - - + -
34B PRO 3.3 26.7 - - - -
35B HIS* 4.0 17.0 - - + -
50B TYR* 3.9 22.9 - + - +
57B LEU* 4.1 9.2 - - + -
60B LYS* 3.9 15.9 - - + -
61B VAL* 3.9 28.3 - - + -
64B VAL* 3.8 11.1 - - + +
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Residues in contact with ARG 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 2.9 47.4 + - + +
24B ARG* 4.0 5.2 - - - +
26B PHE* 1.3 78.8 - - + +
28B ARG* 1.3 62.2 + - + +
30B PHE 4.5 3.4 - - - -
31B PRO* 3.2 26.5 - - + +
35B HIS* 3.7 39.6 + - + -
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ARG* 3.0 56.1 + - + +
25B GLY* 3.7 7.4 - - - +
26B PHE 3.2 0.2 - - - -
27B ARG* 1.3 79.6 - - + +
29B ARG* 1.3 60.7 + - + +
31B PRO* 3.6 9.9 - - - +
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLY 3.0 17.4 + - - +
28B ARG* 1.3 78.0 - - + +
30B PHE* 1.3 92.1 + - + +
31B PRO* 3.3 7.0 - - - +
63B SER* 3.2 46.8 + - - -
64B VAL* 4.4 7.2 - - + +
67B ALA* 4.4 11.1 - - - +
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Residues in contact with PHE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B PHE* 2.8 41.5 + + + +
27B ARG* 4.2 2.3 - - - +
29B ARG* 1.3 109.4 - - + +
31B PRO* 1.3 65.2 - - - +
32B GLU 3.1 4.9 + - - -
33B GLU* 3.1 32.2 + - + +
60B LYS* 3.5 56.5 - - + -
63B SER* 3.7 15.9 - - - -
64B VAL* 4.2 2.7 - - + -
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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