Contacts of the helix formed by residues 25 - 40 (chain A) in PDB entry 1M9H
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 PRO 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LYS 3.3 9.6 - - - +
24A VAL* 1.3 84.4 - - + +
26A PRO* 1.3 70.9 - - + +
27A ALA* 4.4 5.2 - - + +
28A ASP* 2.8 45.1 + - - +
29A THR* 2.9 12.1 + - - -
234A VAL* 6.1 2.5 - - + -
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Residues in contact with PRO 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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24A VAL 3.3 4.9 - - - +
25A PRO* 1.3 88.4 - - + +
27A ALA* 1.3 57.4 + - - +
28A ASP 3.1 4.9 + - - -
29A THR* 3.3 20.0 + - - +
30A GLN 4.6 1.6 + - - -
50A TYR 4.3 7.0 - - - +
51A GLY* 3.4 29.2 - - - +
52A ASN* 3.8 6.0 - - + +
55A GLY* 4.9 6.2 + - - -
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Residues in contact with ALA 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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25A PRO* 3.2 4.4 - - + +
26A PRO* 1.3 77.5 - - - +
28A ASP* 1.3 68.2 + - - +
30A GLN* 5.3 1.7 + - - +
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Residues in contact with ASP 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 VAL* 4.1 9.6 - - + -
25A PRO* 2.8 32.1 + - - +
27A ALA* 1.3 87.3 - - - +
29A THR* 1.3 65.3 + - - +
30A GLN 3.3 3.1 - - - -
31A ARG* 3.3 11.2 + - + +
32A ALA* 3.2 21.1 + - + +
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Residues in contact with THR 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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21A VAL* 4.3 8.1 - - + -
24A VAL* 3.4 11.3 + - - +
25A PRO 2.9 14.7 + - - -
26A PRO 3.3 9.2 + - - -
28A ASP* 1.3 77.5 - - - +
30A GLN* 1.3 57.7 + - - +
32A ALA* 3.4 0.6 + - - +
33A VAL* 2.9 35.7 + - + +
52A ASN* 3.2 50.1 + - + +
55A GLY* 4.3 2.2 - - - -
56A VAL* 3.8 21.5 - - + +
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Residues in contact with GLN 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 PRO 4.6 1.6 + - - -
27A ALA 5.3 2.1 + - - +
28A ASP 3.3 1.2 - - - -
29A THR* 1.3 77.5 - - - +
31A ARG* 1.3 64.2 + - - +
34A GLU* 2.8 50.4 + - - +
55A GLY* 3.5 22.3 - - - +
58A ALA* 3.5 27.9 - - - +
59A ALA* 3.5 13.3 - - - +
62A ALA* 4.0 3.3 - - - +
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Residues in contact with ARG 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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28A ASP* 3.3 11.3 + - + +
30A GLN* 1.3 76.9 - - - +
32A ALA* 1.3 64.6 + - - +
34A GLU* 3.0 14.3 + - - +
35A GLU* 2.9 24.5 + - - +
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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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19A TYR* 3.6 28.3 - - + +
21A VAL* 5.5 0.2 - - + -
24A VAL* 4.1 17.5 - - + -
28A ASP* 3.2 15.3 + - + +
29A THR* 3.6 4.5 - - + +
31A ARG* 1.3 77.4 - - - +
33A VAL* 1.3 56.3 + - + +
35A GLU* 3.2 8.4 + - - +
36A ALA* 3.0 26.0 + - - +
234A VAL* 4.9 8.3 - - + -
239A LEU* 4.8 1.2 - - - +
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Residues in contact with VAL 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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19A TYR* 4.5 2.5 - - + -
21A VAL* 3.7 28.7 - - + -
29A THR* 2.9 25.9 + - + +
32A ALA* 1.3 72.8 - - - +
34A GLU* 1.3 61.9 + - - +
36A ALA* 3.7 5.4 - - - +
37A LEU* 2.8 43.4 + - + +
44A ILE* 4.4 21.5 - - + -
56A VAL* 4.1 17.9 - - + +
59A ALA* 3.4 24.2 - - + -
60A ILE* 4.9 0.9 - - + +
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Residues in contact with GLU 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 GLN* 2.8 52.3 + - - +
31A ARG* 3.0 11.5 + - - +
33A VAL* 1.3 76.1 - - - +
35A GLU* 1.3 57.6 + - - +
37A LEU* 3.5 7.1 - - - +
38A GLU* 2.9 28.3 + - - +
59A ALA* 3.7 19.5 - - + +
62A ALA* 2.9 21.2 - - + +
63A SER* 5.4 2.5 - - - +
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Residues in contact with GLU 35 (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 ARG 2.9 12.6 + - - +
32A ALA* 3.5 10.3 - - - +
34A GLU* 1.3 76.0 - - - +
36A ALA* 1.3 60.2 + - - +
38A GLU* 3.2 9.0 + - - +
39A VAL* 2.7 29.2 + - + +
234A VAL 3.9 9.4 - - - +
236A ARG* 3.0 60.0 + - - +
239A LEU* 4.2 11.3 - - + +
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Residues in contact with ALA 36 (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 TYR* 3.7 31.4 - - + -
32A ALA 3.0 10.1 + - - +
33A VAL* 3.7 5.8 - - - +
35A GLU* 1.3 75.8 - - - +
37A LEU* 1.3 65.5 + - - +
39A VAL 2.8 10.6 + - - -
40A GLY 2.9 0.5 + - - -
41A TYR* 2.9 44.6 + - + -
44A ILE* 5.1 2.5 - - + -
239A LEU* 3.5 15.4 - - + +
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A VAL* 2.8 35.4 + - + +
34A GLU* 3.5 6.7 - - - +
36A ALA* 1.3 77.4 - - - +
38A GLU* 1.3 62.3 + - - +
40A GLY* 3.0 3.5 + - - -
41A TYR 3.2 21.1 - - - +
42A ARG* 2.7 26.4 + - - -
44A ILE* 4.3 14.8 - - + -
59A ALA 3.9 11.9 - - - +
60A ILE* 4.2 10.1 - - + -
63A SER* 3.5 33.2 - - - +
65A ILE* 4.0 18.7 - - + +
70A LEU* 4.0 15.7 - - + -
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Residues in contact with GLU 38 (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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34A GLU 2.9 18.6 + - - +
35A GLU* 3.5 8.1 - - - +
37A LEU* 1.3 76.9 - - - +
39A VAL* 1.3 64.5 + - - +
40A GLY* 3.1 1.7 + - - -
42A ARG* 5.6 0.2 + - - -
236A ARG* 3.8 28.8 + - - +
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Residues in contact with VAL 39 (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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35A GLU* 2.7 19.3 + - + +
36A ALA* 2.8 8.2 + - - +
38A GLU* 1.3 76.7 - - - +
40A GLY* 1.3 56.3 + - - +
41A TYR* 3.8 13.9 - - + -
236A ARG* 3.7 31.0 - - + +
239A LEU* 4.5 9.6 - - + -
240A GLU* 4.1 29.8 - - + +
243A LEU* 3.3 28.6 - - + +
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A VAL* 5.0 9.0 - - - +
36A ALA 2.9 1.0 + - - -
37A LEU 3.0 4.7 + - - -
38A GLU 3.0 1.9 - - - -
39A VAL* 1.3 80.5 - - - +
41A TYR* 1.3 67.9 + - - +
42A ARG* 3.3 27.0 + - - +
243A LEU* 4.2 9.1 - - - +
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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