Contacts of the helix formed by residues 23 - 38 (chain B) in PDB entry 4OL0
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 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B ASP* 3.0 22.6 + - - +
22B PRO* 1.3 77.3 - - - +
24B PRO* 1.3 75.7 - - - +
25B SER* 3.6 13.9 + - - -
26B GLY* 3.2 5.5 + - - -
27B LYS* 3.1 16.8 + - - +
29B ARG* 3.5 24.6 + - - -
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Residues in contact with PRO 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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47A VAL* 3.4 43.7 - - + +
49A PRO* 4.5 18.8 - - + -
22B PRO 3.3 10.3 - - - +
23B ASP* 1.3 92.3 - - - +
25B SER* 1.3 62.1 + - - +
27B LYS* 3.1 8.0 + - + +
28B GLU* 2.9 32.4 + - - +
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Residues in contact with SER 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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23B ASP* 3.6 17.3 + - - -
24B PRO* 1.3 77.7 - - - +
26B GLY* 1.3 57.7 + - - +
28B GLU* 3.0 18.0 + - - +
29B ARG* 2.8 47.7 + - - +
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Residues in contact with GLY 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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17B ALA* 4.9 2.6 - - - +
21B ASP* 3.8 17.7 - - - -
23B ASP* 3.2 13.2 + - - -
25B SER* 1.3 79.4 - - - +
27B LYS* 1.3 57.9 + - - +
29B ARG* 3.2 27.0 + - - +
30B ALA* 2.9 30.9 + - - +
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Residues in contact with LYS 27 (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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45A VAL* 5.7 1.8 - - + -
47A VAL* 3.8 27.8 - - + -
62A ASN* 6.4 1.3 - - - -
64A TRP* 3.8 25.8 - - + +
17B ALA 3.9 9.2 - - - +
18B LEU* 2.9 37.4 + - + +
19B TYR* 3.5 21.0 + - - +
20B HIS 3.5 4.0 - - - +
21B ASP* 3.0 31.3 + - - +
22B PRO* 4.9 5.8 - - - -
23B ASP 3.1 8.5 + - - +
24B PRO* 3.1 10.9 + - + +
26B GLY* 1.3 73.8 - - - +
28B GLU* 1.3 57.4 + - - +
30B ALA* 3.4 2.1 + - - +
31B SER* 2.8 30.2 + - - -
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Residues in contact with GLU 28 (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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45A VAL* 3.7 20.9 - - + +
46A GLU* 3.9 17.1 - - - +
47A VAL* 3.6 26.9 + - + +
48A HIS* 5.4 1.4 - - - -
24B PRO* 2.9 24.2 + - - +
25B SER* 3.0 14.2 + - - +
27B LYS* 1.3 75.0 - - + +
29B ARG* 1.3 60.5 + - - +
31B SER* 3.2 8.3 + - - -
32B PHE* 2.9 29.9 + - - +
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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
----------------------------------------------------------
21B ASP* 5.0 2.8 + - - -
23B ASP* 3.5 20.8 + - - -
25B SER* 2.8 30.5 + - - +
26B GLY* 3.4 24.3 - - - +
28B GLU* 1.3 70.7 - - - +
30B ALA* 1.3 58.8 + - - +
32B PHE* 3.1 8.2 + - - +
33B TRP* 2.9 29.4 + - - +
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Residues in contact with ALA 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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14B ALA* 3.3 29.4 - - - +
17B ALA* 4.0 7.9 - - + -
18B LEU* 3.6 16.6 - - - +
26B GLY 2.9 17.4 + - - +
27B LYS 3.6 3.4 - - - +
29B ARG* 1.3 75.3 - - - +
31B SER* 1.3 59.2 + - - +
33B TRP* 3.3 5.9 + - - +
34B LEU* 2.8 37.9 + - - +
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Residues in contact with SER 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU 5.5 0.3 + - - -
44A GLY* 4.8 1.2 - - - -
45A VAL* 3.8 13.5 + - - +
75A LEU* 4.3 8.1 - - - +
79A TYR* 2.6 32.6 + - - -
18B LEU* 3.9 18.3 - - - +
27B LYS 2.8 18.1 + - - -
28B GLU* 3.4 10.1 - - - -
30B ALA* 1.3 75.9 - - - +
32B PHE* 1.3 51.2 + - - +
34B LEU* 3.7 1.0 - - - +
35B GLY* 2.7 32.9 + - - -
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Residues in contact with PHE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 5.6 14.1 - - + -
28B GLU 2.9 12.6 + - - +
29B ARG* 3.4 10.8 - - - +
31B SER* 1.3 76.8 - - - +
33B TRP* 1.3 59.5 + - - +
35B GLY* 2.9 3.4 + - - -
36B GLU* 2.8 61.2 + - + +
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Residues in contact with TRP 33 (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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6B PRO* 3.7 25.4 - - + -
10B LEU* 3.8 22.4 - - + +
11B VAL* 3.7 25.6 - - + -
14B ALA* 3.4 31.0 - - + -
29B ARG 2.9 18.6 + - - +
30B ALA* 3.7 7.2 - - - +
32B PHE* 1.3 76.5 - - - +
34B LEU* 1.3 57.1 + - + +
36B GLU* 3.1 5.5 + - - +
37B LEU* 2.7 64.8 + - + +
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Residues in contact with LEU 34 (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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75A LEU* 3.8 11.4 - - + -
11B VAL* 4.2 10.3 - - + +
14B ALA* 3.5 41.3 - - + +
15B VAL* 4.0 6.5 - - + +
18B LEU* 3.6 30.3 - - + -
30B ALA 2.8 21.6 + - - +
33B TRP* 1.3 85.9 - - + +
35B GLY* 1.3 61.4 + - - +
37B LEU* 3.5 6.3 - - + +
38B GLN* 3.0 28.8 + - - +
62B PHE* 3.7 35.1 - - + -
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Residues in contact with GLY 35 (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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74A GLY* 5.5 6.3 - - - -
75A LEU* 3.8 13.9 - - - -
31B SER 2.7 21.7 + - - -
32B PHE* 2.9 6.9 + - - -
34B LEU* 1.3 76.4 - - - +
36B GLU* 1.3 60.1 + - - +
38B GLN* 3.5 19.4 - - - +
39B ARG* 3.6 15.6 + - - +
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Residues in contact with GLU 36 (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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32B PHE* 2.8 51.2 + - + +
33B TRP* 3.4 3.4 - - - +
35B GLY* 1.3 71.8 - - - -
37B LEU* 1.3 56.3 + - - +
38B GLN 2.8 15.7 - - - +
39B ARG* 4.2 23.0 - - - +
40B SER* 3.9 10.2 - - - -
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Residues in contact with LEU 37 (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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6B PRO* 3.7 13.7 - - + -
11B VAL* 3.5 19.1 - - + -
33B TRP* 2.7 57.3 + - + +
34B LEU* 3.2 10.3 + - + +
36B GLU* 1.3 70.9 - - - +
38B GLN* 1.3 68.2 + - + +
40B SER* 3.1 17.9 + - - -
43B ALA* 3.4 26.1 + - + +
46B ILE* 3.9 21.9 - - + +
62B PHE* 4.6 20.2 - - + -
66B THR* 5.4 1.1 - - + -
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Residues in contact with GLN 38 (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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74A GLY 4.4 8.1 - - - +
75A LEU* 3.4 28.1 - - - +
34B LEU 3.0 13.6 + - - +
35B GLY 3.5 9.7 - - - +
36B GLU 2.8 12.0 - - - +
37B LEU* 1.3 79.4 - - + +
39B ARG* 1.3 60.0 + - + +
40B SER 2.6 19.1 + - - -
43B ALA* 4.2 8.1 - - - -
62B PHE* 3.8 7.7 - - + -
65B GLN* 3.2 21.4 + - - +
66B THR* 3.1 40.1 + - + +
69B MET* 3.8 21.6 - - + +
70B LYS* 4.4 2.9 - - + +
73B THR* 6.4 1.1 - - + -
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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