Contacts of the helix formed by residues 23 - 34 (chain A) in PDB entry 4M83
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A MET* 3.5 21.8 - - - +
19A HIS 4.8 2.1 + - - -
20A VAL* 3.1 11.5 + - - -
22A PRO* 1.3 77.6 - - - +
24A LEU* 1.3 66.2 + - - +
25A GLU 3.4 2.7 - - - -
26A VAL* 2.9 33.9 - - - +
27A ILE* 3.3 8.7 + - - +
39A TYR* 4.3 3.0 + - - -
130A LEU* 3.8 19.7 - - - +
191A LEU* 3.9 9.4 - - - -
214A CYS* 5.6 0.4 - - - -
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Residues in contact with LEU 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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20A VAL* 3.4 25.6 + - + +
21A ASN* 3.4 37.3 + - + +
22A PRO 3.6 0.2 - - - -
23A SER* 1.3 76.1 - - - +
25A GLU* 1.3 68.6 + - + +
27A ILE* 3.1 10.9 + - + +
28A ARG* 3.1 23.9 + - - +
39A TYR* 5.1 5.2 - - + -
48A LYS* 3.9 23.8 - - + +
49A VAL* 4.4 6.5 - - + -
52A THR* 3.7 27.0 - - + +
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Residues in contact with GLU 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 ASN 5.2 0.2 + - - -
23A SER 3.4 0.8 - - - -
24A LEU* 1.3 79.1 - - + +
26A VAL* 1.3 57.3 + - - +
28A ARG* 3.3 36.3 + - - +
29A GLU* 2.9 22.9 + - - +
214A CYS* 3.9 19.5 + - + +
215A GLN* 3.9 17.0 - - - +
386A THR* 3.2 28.9 - - + +
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Residues in contact with VAL 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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23A SER* 2.9 40.7 + - - +
25A GLU* 1.3 75.6 - - - +
27A ILE* 1.3 73.4 + - + +
29A GLU* 3.2 2.4 + - - +
30A LEU* 3.1 23.6 + - + +
130A LEU* 4.5 9.6 - - + -
191A LEU* 5.5 4.3 - - + -
214A CYS* 5.1 5.0 - - - +
386A THR* 3.7 11.1 + - + +
389A ALA* 3.6 32.3 - - + -
390A ALA* 3.8 11.7 - - - +
393A ILE* 3.6 22.4 - - + -
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Residues in contact with ILE 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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11A MET* 3.8 32.1 - - + -
23A SER* 3.4 16.6 - - - +
24A LEU* 3.1 8.3 + - - +
26A VAL* 1.3 83.0 - - + +
28A ARG* 1.3 63.8 + - - +
29A GLU 3.1 0.7 + - - -
30A LEU* 3.1 6.3 + - + +
31A VAL* 3.0 25.9 + - + +
37A VAL* 3.8 14.3 - - + +
39A TYR* 4.2 20.4 - - + -
52A THR* 3.6 21.1 - - + +
54A ALA* 3.8 17.5 - - + -
108A LEU* 3.9 20.6 - - + -
130A LEU* 5.3 0.4 - - + -
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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 LEU* 3.1 7.7 + - - +
25A GLU* 3.3 41.8 + - - +
27A ILE* 1.3 79.2 - - - +
29A GLU* 1.3 56.6 + - - +
31A VAL* 3.4 3.3 + - - +
32A ALA* 2.8 29.0 + - - +
51A ALA* 2.8 43.2 + - - +
52A THR* 3.5 36.3 - - + +
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Residues in contact with GLU 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 GLU 2.9 17.6 + - - +
26A VAL 3.6 4.9 - - - +
27A ILE 3.1 0.6 - - - -
28A ARG* 1.3 74.5 - - - +
30A LEU* 1.3 54.5 + - - +
32A ALA* 2.9 15.4 + - - +
33A ARG* 2.8 76.5 + - - +
386A THR* 4.0 11.1 - - + +
387A ARG* 4.0 24.1 - - - +
390A ALA* 3.5 17.3 - - + -
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Residues in contact with LEU 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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9A ILE* 4.2 13.9 - - + -
26A VAL 3.1 18.6 + - - +
27A ILE* 3.6 8.1 - - + +
29A GLU* 1.3 75.0 - - - +
31A VAL* 1.3 60.7 + - - +
33A ARG* 3.2 7.8 - - - +
35A HIS* 2.9 38.1 + - + +
37A VAL* 4.2 10.8 - - + -
108A LEU* 3.8 19.5 - - + -
390A ALA* 3.8 33.0 - - + +
393A ILE* 3.7 35.9 - - + -
394A GLU* 4.0 14.1 - - + -
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Residues in contact with VAL 31 (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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27A ILE* 3.0 16.4 + - + +
28A ARG 3.4 8.1 - - - +
30A LEU* 1.3 74.4 - - - +
32A ALA* 1.3 67.1 + - - +
34A GLY* 2.9 17.3 + - - -
35A HIS 4.0 11.4 + - - +
37A VAL* 3.6 28.0 - - + +
52A THR 3.6 22.9 - - - +
53A GLY* 4.3 11.4 - - - -
54A ALA* 4.1 8.1 - - - +
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Residues in contact with ALA 32 (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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28A ARG 2.8 18.6 + - - +
29A GLU* 2.9 21.1 + - - +
31A VAL* 1.3 73.8 - - - +
33A ARG* 1.3 64.2 + - - +
34A GLY* 4.5 0.3 - - - -
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Residues in contact with ARG 33 (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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29A GLU* 2.8 51.7 + - - +
30A LEU* 3.2 17.0 - - + +
32A ALA* 1.3 81.3 - - - +
34A GLY* 1.3 58.6 + - - +
35A HIS* 3.4 12.3 - - + +
387A ARG* 3.4 19.6 + - - +
390A ALA* 3.5 9.9 - - - +
391A ASP* 3.3 22.2 + - - -
394A GLU* 3.0 36.8 + - - +
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Residues in contact with GLY 34 (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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31A VAL 2.9 10.9 + - - -
32A ALA 4.5 0.4 - - - -
33A ARG* 1.3 79.1 - - - +
35A HIS* 1.3 68.7 + - - +
36A ARG 3.9 0.5 + - - -
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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
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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