Contacts of the helix formed by residues 25 - 35 (chain D) in PDB entry 1MA1
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 25 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D TYR 4.3 0.7 - - - -
21D GLU* 4.0 11.7 - - - -
22D PRO 4.8 4.1 + - - -
23D HIS 4.2 0.4 - - - -
24D ILE* 1.3 76.6 - - - +
26D ARG* 1.3 58.7 + - - +
27D GLU* 3.5 8.4 + - - +
28D GLN 2.9 17.3 + - - -
29D LEU* 2.9 28.6 + - - +
175D ASP* 2.6 38.0 + - - -
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Residues in contact with ARG 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D TYR* 3.1 37.9 + - + +
18D ASP* 4.0 13.2 - - + +
21D GLU* 3.2 19.4 + - - +
24D ILE 3.9 0.2 + - - -
25D SER* 1.3 74.0 - - - +
27D GLU* 1.3 81.4 + - - +
29D LEU* 3.4 0.9 + - - +
30D THR* 2.6 37.7 + - - +
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Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177C ARG* 2.6 35.1 + - - -
25D SER* 3.2 7.5 + - - +
26D ARG* 1.3 99.5 - - - +
28D GLN* 1.3 63.2 + - - +
30D THR* 3.2 10.4 + - - -
31D ILE* 2.9 24.1 + - + +
174D ILE* 3.6 23.3 - - + +
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Residues in contact with GLN 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C TYR* 5.1 0.2 - - - -
24D ILE* 3.8 10.8 - - + -
25D SER* 2.9 13.2 + - - +
27D GLU* 1.3 77.2 - - - +
29D LEU* 1.3 61.3 + - - +
31D ILE* 3.6 4.5 - - - +
32D HIS* 3.3 19.9 + - + +
170D HIS 2.9 27.3 + - - -
171D ALA* 3.4 21.3 - - - +
172D TYR* 3.1 11.4 - - - -
174D ILE* 3.0 44.6 + - + +
175D ASP* 3.2 34.2 + - - +
176D TYR* 6.3 0.4 - - + -
183D TYR* 6.3 0.2 - - + -
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D LEU* 3.5 27.1 - - + -
15D TYR* 4.1 5.2 - - + -
16D PRO 4.4 0.4 - - - +
17D TYR* 3.5 34.3 - - + +
20D LEU* 3.7 35.9 - - + -
24D ILE* 4.0 11.4 - - + +
25D SER 2.9 16.0 + - - +
28D GLN* 1.3 75.3 - - - +
30D THR* 1.3 65.7 + - - +
32D HIS* 3.5 3.6 + - - +
33D HIS* 3.0 18.9 + - + +
84D TRP* 3.8 28.7 - - + -
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Residues in contact with THR 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D TYR* 3.4 31.2 - - + +
26D ARG* 2.6 28.9 + - - +
27D GLU* 3.2 5.8 + - - -
29D LEU* 1.3 78.4 - - - +
31D ILE* 1.3 58.7 + - - +
34D GLN* 2.8 57.8 + - + +
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C TYR* 3.3 24.5 - - + +
177C ARG* 3.9 22.7 - - + -
178C ASN* 3.4 22.9 - - + +
27D GLU* 2.9 21.3 - - + +
28D GLN* 3.6 6.1 - - - +
30D THR* 1.3 76.5 - - + +
32D HIS* 1.3 66.2 + - - +
34D GLN* 4.9 0.2 - - - -
35D LYS* 2.9 45.3 + - + +
36D HIS* 3.4 1.6 + - + -
174D ILE* 3.7 17.5 - - + -
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Residues in contact with HIS 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C TYR* 5.2 0.2 + - - -
28D GLN* 3.3 20.9 + - - +
29D LEU* 3.8 5.8 - - - +
31D ILE* 1.3 77.0 - - - +
33D HIS* 1.3 58.2 + - - +
36D HIS* 3.4 10.9 + - + -
37D HIS* 3.1 25.6 + - - +
80D HIS* 2.8 16.4 + + - -
83D PHE* 3.8 18.4 - + - -
84D TRP* 3.5 15.3 - + + -
166D ASP* 2.6 19.4 + - + -
170D HIS* 3.7 17.5 - + - +
171D ALA* 3.4 26.7 + - + +
206D FE 2.1 28.1 - - - -
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Residues in contact with HIS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 3.6 24.3 - - + +
11D PRO 2.8 29.8 + - - -
12D GLU* 4.6 2.2 - - - -
13D LEU* 3.2 33.0 - - + +
17D TYR* 2.7 34.2 + - + -
29D LEU* 3.0 18.5 + - + +
30D THR 3.8 2.5 - - - +
32D HIS* 1.3 78.4 - - - +
34D GLN* 1.3 65.5 + - - +
37D HIS* 3.2 26.7 - - - +
38D GLN 3.5 4.7 + - - -
84D TRP* 3.7 25.8 - - + -
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Residues in contact with GLN 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D LEU* 4.6 9.2 - - + +
17D TYR* 2.6 38.7 + - + +
30D THR* 2.8 40.5 + - + +
31D ILE* 4.9 0.4 - - - -
33D HIS* 1.3 79.8 + - + +
35D LYS* 1.3 70.9 + - + +
38D GLN* 3.1 22.4 - - - +
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Residues in contact with LYS 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C ASN* 3.7 39.7 - - + +
31D ILE* 2.9 36.7 + - + +
34D GLN* 1.3 88.8 + - + +
36D HIS* 1.3 61.0 + - + +
38D GLN* 3.6 3.4 - - - +
39D ALA* 3.0 26.9 + - - +
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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