Contacts of the helix formed by residues 31 - 38 (chain A) in PDB entry 1ECD
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 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A VAL 3.3 3.8 + - - +
28A PHE 3.2 6.3 - - - +
29A LYS 3.2 0.6 - - - -
30A ALA* 1.3 83.0 - - - +
32A PRO* 1.3 63.8 - - - +
33A SER* 2.7 33.8 + - - -
34A ILE* 3.0 34.6 + - + +
35A MET 3.8 0.7 + - - -
95A ASP* 5.8 0.3 - - - +
96A GLN* 3.7 13.5 - - - +
99A ASN* 2.8 38.3 - - + +
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Residues in contact with PRO 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 PHE 3.6 12.1 - - - +
29A LYS 4.1 6.3 - - - +
30A ALA 4.0 4.0 - - - +
31A ASP* 1.3 88.0 - - - +
33A SER* 1.3 56.8 + - - +
34A ILE 3.2 0.4 - - - -
35A MET* 3.3 19.3 + - + +
36A ALA* 3.0 25.8 + - - +
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Residues in contact with SER 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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31A ASP* 2.7 25.4 + - - -
32A PRO* 1.3 76.4 - - - +
34A ILE* 1.3 64.6 + - - +
36A ALA* 3.7 13.9 + - - +
37A LYS* 3.6 13.2 - - - +
96A GLN* 3.0 26.6 + - - +
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Residues in contact with ILE 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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27A VAL* 3.8 25.8 - - + +
28A PHE* 3.7 21.5 - - + -
31A ASP* 3.0 33.8 + - + +
33A SER* 1.3 76.2 + - - +
35A MET* 1.3 65.6 + - - +
37A LYS* 3.2 14.4 + - - +
38A PHE* 3.4 13.5 - - + -
96A GLN* 3.6 34.5 - - + +
100A PHE* 4.2 5.6 - - + +
137A HEM 3.8 37.2 - - + -
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Residues in contact with MET 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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28A PHE* 3.8 46.1 - - + +
31A ASP 3.8 0.8 + - - -
32A PRO* 3.3 25.1 + - + +
34A ILE* 1.3 81.1 - - - +
36A ALA* 1.3 57.0 + - - +
38A PHE* 3.2 27.9 + - - +
41A PHE* 3.9 20.6 - - + +
42A ALA* 4.1 2.9 + - - -
43A GLY 5.4 3.1 - - - +
44A LYS 3.6 24.7 - - - +
46A LEU* 4.0 27.1 - - + +
49A ILE* 4.1 11.0 - - - -
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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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32A PRO 3.0 16.2 + - - +
33A SER* 3.7 13.0 - - - +
34A ILE 3.2 0.6 - - - -
35A MET* 1.3 76.7 - - - +
37A LYS* 1.3 58.8 + - - +
38A PHE 3.3 1.3 + - - +
42A ALA* 3.8 25.3 - - + +
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Residues in contact with LYS 37 (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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33A SER 3.6 14.1 - - - +
34A ILE 3.2 9.4 + - - +
35A MET 3.2 1.0 - - - -
36A ALA* 1.3 77.2 - - - +
38A PHE* 1.3 62.6 + - + +
39A THR* 3.6 8.5 + - - +
90A ARG* 2.9 34.0 + - + +
91A GLY* 3.5 16.3 + - - -
92A VAL* 4.4 0.9 - - - +
93A THR* 5.8 0.4 - - - +
96A GLN* 3.8 27.5 + - - +
137A HEM 3.6 37.5 - - + +
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Residues in contact with PHE 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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28A PHE* 3.7 26.0 - + - -
34A ILE* 3.4 24.9 - - + -
35A MET 3.2 7.8 + - - +
37A LYS* 1.3 79.1 - - - +
39A THR* 1.3 61.4 - - - +
40A GLN* 3.0 2.5 - - + +
41A PHE* 3.0 29.6 + + + +
42A ALA* 2.8 31.7 + - - +
58A HIS* 4.0 19.3 - + + -
62A ILE* 3.8 22.4 - - + -
137A HEM 3.5 66.0 - + + -
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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