Contacts of the helix formed by residues 59 - 65 (chain L) in PDB entry 2CHT
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 ALA 59 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212J TSA 3.5 33.8 - - + +
47L LEU* 3.4 20.9 - - + +
58L PRO* 1.3 78.2 - - - +
60L LYS* 1.3 61.3 + - - +
61L ALA 2.9 2.1 + - - -
62L VAL* 3.0 20.3 + - - +
63L ARG* 4.1 2.9 + - - +
73L VAL* 3.7 10.1 - - + +
75L CYS* 3.3 23.6 - - - -
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Residues in contact with LYS 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212J TSA 3.1 17.7 + - - +
17L GLU* 4.2 23.0 + - - -
21L LEU* 3.8 21.0 - - + +
56L VAL* 3.6 19.5 - - + -
57L PHE* 2.9 17.4 + - + +
59L ALA* 1.3 76.7 - - - +
61L ALA* 1.3 59.4 + - - +
63L ARG* 3.2 48.1 - - - +
64L GLU* 4.5 1.0 + - - +
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Residues in contact with ALA 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L LEU* 3.7 20.9 - - - +
24L THR* 3.7 26.7 - - + -
25L LYS* 3.9 16.9 - - + +
28L LEU* 4.6 2.5 - - + -
58L PRO 2.9 16.7 + - - +
60L LYS* 1.3 74.1 - - - +
62L VAL* 1.3 62.5 + - - +
63L ARG 3.0 4.7 - - - -
64L GLU* 2.9 23.3 + - - +
65L LEU* 4.2 4.0 + - - +
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Residues in contact with VAL 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28L LEU* 3.6 24.2 - - + -
45L MET* 3.7 25.6 - - + -
47L LEU* 4.4 8.5 - - + -
58L PRO 5.0 1.1 - - - +
59L ALA* 3.0 12.5 + - - +
61L ALA* 1.3 74.6 - - - +
63L ARG* 1.3 56.8 + - + +
65L LEU* 2.9 33.9 + - + +
68L TRP* 3.9 39.7 - - + +
71L VAL* 5.0 4.3 - - + +
73L VAL* 3.9 17.0 - - + -
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Residues in contact with ARG 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J ARG* 3.4 33.2 - - - +
212J TSA 4.5 8.3 - - - +
59L ALA 4.3 4.9 - - - +
60L LYS* 3.2 52.6 - - - +
61L ALA 3.0 0.2 + - - -
62L VAL* 1.3 77.7 - - + +
64L GLU* 1.3 54.1 + - - +
65L LEU 3.2 8.3 + - - +
68L TRP 6.3 0.4 - - - -
69L GLN* 6.3 2.7 - - - +
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Residues in contact with GLU 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L LEU* 6.1 0.7 - - - +
25L LYS* 3.1 41.7 + - + +
60L LYS 5.5 0.9 - - - +
61L ALA* 2.9 13.7 + - - +
63L ARG* 1.3 75.1 - - - +
65L LEU* 1.3 64.3 + - - +
66L SER* 3.6 6.1 + - - -
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Residues in contact with LEU 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L LYS* 4.5 8.3 - - + +
28L LEU* 3.7 36.1 - - + -
29L GLU* 3.7 33.4 - - + +
32L ILE* 4.1 16.8 - - + -
61L ALA 4.5 2.9 - - - +
62L VAL* 2.9 18.8 + - + +
63L ARG 4.2 4.9 - - - +
64L GLU* 1.3 83.8 - - - +
66L SER* 1.3 65.2 + - - +
67L GLY 3.3 0.3 + - - -
68L TRP* 3.0 42.6 + - + +
69L GLN 4.5 1.2 + - - -
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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