Contacts of the helix formed by residues 42 - 49 (chain A) in PDB entry 3NYN
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 CYS 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PRO* 4.0 9.9 - - - -
38A HIS 3.7 15.0 - - - -
39A ILE* 2.8 16.7 + - + +
41A GLN* 1.3 81.8 - - - +
43A GLU* 1.3 65.9 + - - +
44A GLU 3.5 1.6 - - - -
45A LEU* 3.0 12.3 + - + +
46A ARG* 2.9 19.9 + - - +
171A LEU* 4.0 21.2 - - + +
172A GLN* 3.8 38.1 - - - -
175A TRP* 4.4 4.7 - - - -
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Residues in contact with GLU 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 ILE* 3.8 10.0 + - - +
40A SER* 3.4 13.6 + - - +
42A CYS* 1.3 73.3 - - - +
44A GLU* 1.3 71.0 + - - +
46A ARG* 2.6 53.4 + - - +
47A LEU* 3.1 26.1 + - + +
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Residues in contact with GLU 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 SER 5.0 1.4 + - - -
41A GLN 5.6 3.6 - - - +
42A CYS 3.5 1.1 - - - -
43A GLU* 1.3 78.1 - - - +
45A LEU* 1.3 60.8 + - - +
47A LEU* 3.6 14.2 - - - +
48A SER* 3.1 22.7 + - - +
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Residues in contact with LEU 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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41A GLN 5.3 1.8 - - - +
42A CYS* 3.0 13.8 + - - +
43A GLU 2.8 3.2 + - - -
44A GLU* 1.3 76.5 - - - +
46A ARG* 1.3 67.8 + - - +
48A SER* 2.9 17.5 + - - +
49A LEU* 3.1 28.2 + - + +
171A LEU* 4.0 12.8 - - + +
174A LYS* 4.1 8.3 - - + +
175A TRP* 3.6 43.3 - - + +
178A ARG* 3.2 39.5 - - + +
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Residues in contact with ARG 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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39A ILE* 5.4 6.1 - - - +
42A CYS* 2.9 8.4 + - - +
43A GLU* 2.6 50.1 + - - +
45A LEU* 1.3 72.2 - - - +
47A LEU* 1.3 68.6 + - - +
49A LEU* 3.0 19.6 + - - +
51A ARG* 4.9 15.2 - - - +
162A LEU 4.5 5.9 + - - -
167A PHE* 4.0 21.3 - - + -
168A ASN* 3.7 25.9 + - - +
171A LEU* 3.6 41.1 - - + +
39B ILE* 5.8 4.2 - - - +
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Residues in contact with LEU 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 GLU* 3.7 24.9 - - + +
44A GLU* 3.6 13.9 - - - +
46A ARG* 1.3 85.6 - - - +
48A SER* 1.3 64.4 + - - +
49A LEU 3.1 5.4 + - - +
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Residues in contact with SER 48 (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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44A GLU* 3.1 16.4 + - - +
45A LEU* 2.9 26.3 + - - +
47A LEU* 1.3 77.0 - - - +
49A LEU* 1.3 64.7 + - - +
50A GLU* 3.3 3.8 + - - +
178A ARG* 4.8 8.2 + - - -
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Residues in contact with LEU 49 (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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45A LEU* 3.6 15.7 - - + +
46A ARG 3.0 16.5 + - - +
47A LEU 3.7 4.1 - - - +
48A SER* 1.3 76.0 - - - +
50A GLU* 1.3 68.1 + - - +
51A ARG* 3.5 8.0 + - - +
56A LEU* 4.6 10.3 - - + -
60A GLN* 5.9 2.2 - - - +
167A PHE* 4.7 6.3 - - + -
170A PHE* 3.8 23.1 - - + -
171A LEU* 3.7 29.4 - - + -
174A LYS* 4.2 19.5 - - + -
178A ARG* 3.7 26.0 - - - +
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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