Contacts of the helix formed by residues 24 - 34 (chain A) in PDB entry 4M7P
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 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A MSE 3.6 23.3 - - - +
20A HIS 4.8 2.9 + - - -
21A VAL 3.3 8.9 + - - -
22A ASN 3.2 0.4 - - - -
23A PRO* 1.3 76.7 - - - +
25A LEU* 1.3 65.4 + - - +
26A GLU 3.1 3.6 - - - -
27A VAL* 3.0 23.7 + - - +
28A ILE* 3.0 17.1 + - - +
40A TYR* 4.4 2.3 + - - -
131A LEU* 4.1 19.7 - - - -
192A LEU* 3.9 15.7 - - - -
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Residues in contact with LEU 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 VAL* 3.3 29.5 + - + +
22A ASN* 3.3 32.7 + - + +
24A SER* 1.3 78.1 - - - +
26A GLU* 1.3 58.2 + - + +
28A ILE* 3.4 5.7 + - - +
29A ARG* 2.9 42.5 + - - +
40A TYR* 4.5 14.4 - - + -
49A LYS* 4.3 24.2 - - + +
50A VAL* 4.7 3.6 - - + -
53A THR* 3.7 26.4 - - + +
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Residues in contact with GLU 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 ASN 4.7 3.1 + - - +
23A PRO 5.4 3.6 - - - +
24A SER 3.1 1.2 - - - -
25A LEU* 1.3 74.6 - - + +
27A VAL* 1.3 62.9 + - + +
29A ARG* 3.2 39.0 + - - +
30A GLU 2.9 25.1 + - - -
216A GLN 3.4 18.3 - - - +
217A GLY* 4.0 9.3 - - - -
218A ASP* 3.5 27.8 + - - +
387A THR* 3.2 28.6 + - + +
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Residues in contact with VAL 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 PRO 5.0 2.2 - - - +
24A SER* 3.0 22.8 + - - +
26A GLU* 1.3 78.3 - - + +
28A ILE* 1.3 65.9 + - + +
30A GLU* 3.2 2.6 + - - +
31A LEU* 3.0 28.2 + - + +
109A LEU* 5.5 0.2 - - + -
131A LEU* 5.6 4.3 - - + -
192A LEU* 4.7 11.4 - - + -
386A GLY 5.2 0.9 - - - +
387A THR* 4.0 17.5 - - - +
390A ALA* 3.9 24.9 - - + -
391A ALA* 4.4 6.3 - - - +
394A ILE* 3.5 32.1 - - + -
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Residues in contact with ILE 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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12A MSE 3.8 35.9 - - + -
24A SER* 3.0 18.5 + - - +
25A LEU* 3.7 7.0 - - - +
27A VAL* 1.3 79.0 - - + +
29A ARG* 1.3 63.4 + - - +
31A LEU* 3.3 8.3 + - + +
32A VAL* 3.0 24.1 + - + +
38A VAL* 4.0 11.7 - - + -
40A TYR* 4.1 21.1 - - + -
53A THR* 3.5 22.9 - - + +
55A ALA* 3.9 18.4 - - + -
109A LEU* 4.2 16.8 - - + -
131A LEU* 5.3 1.6 - - + -
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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 LEU* 2.9 33.5 + - - +
26A GLU* 3.2 42.3 + - - +
28A ILE* 1.3 77.2 - - - +
30A GLU* 1.3 57.9 + - - +
32A VAL* 3.3 5.0 + - - +
33A ALA* 2.9 28.9 + - + +
52A ALA* 3.6 25.0 + - - +
53A THR* 3.7 33.5 - - - +
218A ASP 5.6 0.2 + - - -
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Residues in contact with GLU 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 GLU 2.9 6.5 + - - +
27A VAL 3.2 3.8 + - - +
29A ARG* 1.3 75.6 - - - +
31A LEU* 1.3 58.6 + - - +
33A ALA* 3.0 14.0 + - - +
34A ARG* 2.9 76.6 + - - +
387A THR* 3.2 34.5 - - + +
388A ARG* 4.5 11.6 + - - +
391A ALA* 3.8 11.7 - - + -
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Residues in contact with LEU 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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10A ILE* 4.2 18.8 - - + -
27A VAL* 3.0 22.5 + - + +
28A ILE* 3.7 12.6 - - + +
30A GLU* 1.3 75.2 - - - +
32A VAL* 1.3 62.1 - - - +
34A ARG* 3.2 13.8 + - - +
35A GLY 3.4 0.2 + - - -
36A HIS* 3.4 30.5 + - + +
38A VAL* 4.1 13.9 - - + -
109A LEU* 3.8 30.1 - - + -
391A ALA* 4.1 31.0 - - + +
394A ILE* 4.1 23.1 - - + -
395A GLU* 4.5 4.5 - - + +
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Residues in contact with VAL 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 ILE 3.0 16.5 + - - +
29A ARG 3.5 7.2 - - - +
31A LEU* 1.3 71.4 - - - +
33A ALA* 1.3 58.5 + - - +
34A ARG 3.0 4.9 - - - -
35A GLY* 2.9 21.3 + - - -
36A HIS 4.0 10.9 - - - +
38A VAL* 4.0 21.5 - - + +
53A THR 3.8 19.3 - - - +
54A GLY* 3.9 15.7 - - - +
55A ALA* 3.8 16.4 - - + +
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Residues in contact with ALA 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 ARG* 2.9 17.2 + - + +
30A GLU* 3.0 23.1 + - - +
32A VAL* 1.3 77.6 - - - +
34A ARG* 1.3 58.7 + - - +
35A GLY 3.7 0.2 + - - -
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Residues in contact with ARG 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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30A GLU* 2.9 39.1 + - - +
31A LEU* 3.5 8.7 - - - +
32A VAL 3.0 0.6 - - - -
33A ALA* 1.3 78.9 - - - +
35A GLY* 1.3 56.8 + - - +
36A HIS* 3.5 10.6 + - + -
388A ARG* 3.2 49.5 + - - +
391A ALA* 3.6 10.9 - - - +
392A ASP* 2.8 22.4 + - - +
395A GLU* 2.6 49.2 + - - +
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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