Contacts of the helix formed by residues 39 - 47 (chain A) in PDB entry 1C9Q
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A MET 3.4 0.2 - - - -
38A TYR* 1.3 116.3 + - - +
40A GLU* 1.3 66.8 + - - +
41A GLU* 4.3 9.2 - - - -
42A ALA* 2.9 22.1 + - - +
43A ARG* 3.0 15.2 + - - +
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Residues in contact with GLU 40 (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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38A TYR 4.1 1.2 + - - -
39A SER* 1.3 70.6 - - - +
41A GLU* 1.3 63.9 + - - +
43A ARG* 3.1 29.5 + - - +
44A LEU* 3.1 10.9 + - - +
59A ARG* 5.4 18.4 + - + +
62A ALA* 3.9 6.6 - - + +
63A SER* 2.8 46.2 + - - +
112A LEU* 4.1 22.7 - - - +
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Residues in contact with GLU 41 (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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39A SER* 3.1 6.2 - - - -
40A GLU* 1.3 77.5 - - - +
42A ALA* 1.3 63.5 + - - +
44A LEU* 2.9 47.4 - - - +
45A LYS* 3.7 2.1 + - - +
59A ARG* 4.4 10.3 + - - +
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Residues in contact with ALA 42 (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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36A ALA 3.5 23.8 - - - +
37A MET* 3.0 18.6 - - + +
38A TYR* 5.6 2.7 - - + -
39A SER* 2.9 19.6 + - - +
41A GLU* 1.3 78.5 - - - +
43A ARG* 1.3 65.2 + - - +
45A LYS* 2.9 24.0 + - - +
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Residues in contact with ARG 43 (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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37A MET* 2.6 38.2 + - + +
38A TYR 2.6 28.0 + - - -
39A SER 3.0 9.4 + - - +
40A GLU* 3.1 16.8 + - - +
42A ALA* 1.3 75.3 - - - +
44A LEU* 1.3 58.6 + - - +
46A SER* 2.7 31.4 + - - +
47A PHE* 3.0 8.6 - - + -
62A ALA* 2.7 63.6 + - + +
63A SER* 4.5 0.6 - - - +
65A GLY* 4.1 3.3 - - - -
66A LEU 4.3 10.5 - - - +
67A TYR* 5.1 0.2 - - + -
78A PHE* 3.0 29.5 - - + -
106A PHE* 4.0 24.0 - - - -
111A ASN* 5.0 4.6 - - - +
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Residues in contact with LEU 44 (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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40A GLU 3.1 7.7 + - - +
41A GLU* 2.9 37.2 + - - +
43A ARG* 1.3 75.8 - - - +
45A LYS* 1.3 62.6 + - - +
47A PHE* 2.9 38.7 + - + +
48A GLN* 4.7 0.3 - - - -
58A PRO* 4.8 6.5 - - + -
59A ARG* 3.7 43.3 - - + +
62A ALA* 5.4 0.2 - - - -
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Residues in contact with LYS 45 (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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36A ALA 5.4 1.8 + - - -
37A MET* 4.5 10.9 - - + +
41A GLU 3.7 1.9 + - - +
42A ALA* 2.9 17.6 + - - +
44A LEU* 1.3 78.9 - - - +
46A SER* 1.3 55.2 + - - +
48A GLN* 2.7 76.9 + - + +
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Residues in contact with SER 46 (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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37A MET* 3.6 21.2 - - - +
42A ALA 3.5 1.4 + - - -
43A ARG* 2.7 20.2 + - - -
45A LYS* 1.3 80.2 - - - +
47A PHE* 1.3 67.5 + - - +
48A GLN* 3.2 4.3 + - - +
67A TYR* 3.9 5.2 - - - -
68A TYR* 3.0 56.7 + - - +
70A GLY 5.2 0.2 + - - -
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Residues in contact with PHE 47 (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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43A ARG 3.0 28.7 - - - -
44A LEU* 2.9 21.0 + - + +
45A LYS 3.6 0.2 - - - -
46A SER* 1.3 91.5 - - - +
48A GLN* 1.3 63.0 + - - -
49A ASN 2.8 5.0 + - - -
50A TRP* 2.8 27.4 + + + +
58A PRO* 2.8 52.0 - - + -
59A ARG* 4.2 0.7 - - - -
61A LEU* 3.5 27.6 - - + -
62A ALA* 3.5 21.8 - - + -
66A LEU 3.6 11.9 - - - -
68A TYR* 3.6 24.0 - - + -
75A VAL* 5.1 1.3 - - + -
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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