Contacts of the helix formed by residues 36 - 44 (chain A) in PDB entry 2CSF
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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A MET* 3.4 7.0 - - - -
35A VAL* 1.3 76.1 - - - +
37A GLN* 1.3 76.9 + - - +
38A ALA* 3.0 12.4 + - - +
39A LEU* 3.0 10.0 + - - +
40A PHE* 3.0 22.5 + - - +
49A GLN* 3.6 15.9 + - - -
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Residues in contact with GLN 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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30A MET* 3.1 20.0 - - - +
36A SER* 1.3 76.1 + - - +
38A ALA* 1.3 56.7 + - - +
40A PHE* 4.8 0.7 - - - -
41A ALA* 2.9 32.1 + - - +
49A GLN* 3.7 22.9 - - + +
52A LEU* 3.2 15.1 - - + +
53A CYS* 3.2 35.3 - - - +
56A LEU* 2.8 32.6 - - - +
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Residues in contact with ALA 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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36A SER* 3.0 7.3 + - - +
37A GLN* 1.3 77.5 - - - +
39A LEU* 1.3 54.2 + - - +
41A ALA* 3.6 1.4 - - - +
42A LYS* 2.8 36.8 + - - +
47A LYS 4.2 2.8 - - - +
49A GLN* 3.3 43.8 - - + +
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Residues in contact with LEU 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 VAL* 3.6 22.9 - - + -
36A SER* 3.0 13.3 + - - +
38A ALA* 1.3 75.6 - - - +
40A PHE* 1.3 60.4 + - - +
42A LYS* 2.6 28.0 + - + +
43A VAL* 2.8 17.7 + - + +
91A TYR* 3.3 36.8 - - + -
94A GLU* 3.3 33.2 - - + +
95A SER* 3.5 25.4 - - - -
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Residues in contact with PHE 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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26A ILE* 3.4 43.7 - - + -
29A GLU* 3.6 26.7 - - + -
30A MET* 3.9 15.0 - - + -
35A VAL* 3.9 5.4 - - + +
36A SER 3.0 11.8 + - - +
37A GLN 4.4 1.3 - - - +
39A LEU* 1.3 81.5 - - - +
41A ALA* 1.3 57.6 + - - +
43A VAL* 3.4 9.8 - - - +
44A ALA* 2.7 46.2 + - + +
52A LEU* 4.2 9.0 - - + -
76A ILE* 3.4 29.8 - - + -
79A PHE* 5.3 2.0 - + + -
80A LEU* 3.5 25.6 - - + -
91A TYR* 3.9 12.1 - + - -
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Residues in contact with ALA 41 (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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37A GLN 2.9 22.6 + - - +
38A ALA* 3.6 3.6 - - - +
39A LEU 3.0 0.8 - - - -
40A PHE* 1.3 80.3 - - - +
42A LYS* 1.3 52.2 + - - +
43A VAL 3.4 0.2 - - - -
44A ALA* 3.9 3.8 - - - -
45A ALA* 3.3 5.4 + - - +
46A ASN 2.6 29.3 + - - -
47A LYS 2.8 22.0 + - - +
48A SER 4.8 1.1 - - - +
51A TRP* 4.7 7.0 - - + -
52A LEU* 3.4 28.7 - - + +
76A ILE* 5.8 0.2 - - - -
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Residues in contact with LYS 42 (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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38A ALA 2.8 19.8 + - - +
39A LEU* 2.6 17.1 + - + +
41A ALA* 1.3 73.8 - - - +
43A VAL* 1.3 55.4 + - - -
46A ASN* 3.1 42.0 + - - +
47A LYS 3.8 9.2 - - - +
94A GLU* 3.0 47.6 + - + +
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Residues in contact with VAL 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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39A LEU* 2.8 22.9 + - + +
40A PHE 3.4 5.4 - - - +
42A LYS* 1.3 78.5 - - - +
44A ALA* 1.3 65.1 + - - +
46A ASN* 4.6 0.4 - - - -
79A PHE* 3.1 20.4 - - + -
90A ILE* 3.6 19.3 - - + +
91A TYR* 3.3 35.2 - - + -
94A GLU* 3.3 45.5 - - + +
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Residues in contact with ALA 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 PHE* 2.7 44.2 + - + +
41A ALA* 4.4 0.9 - - - -
43A VAL* 1.3 80.7 - - - +
45A ALA* 1.3 60.2 + - - +
46A ASN* 3.5 0.4 - - - -
75A THR* 3.2 22.8 + - - +
76A ILE* 3.9 16.2 - - + -
79A PHE* 3.6 20.6 - - + -
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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