Contacts of the helix formed by residues 81 - 85 (chain A) in PDB entry 3KDM
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 GLN 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A PRO* 5.4 3.1 - - - -
63A ARG* 3.5 33.4 + - - +
79A GLY 2.9 15.9 + - - +
80A LEU* 1.3 74.5 - - - +
82A ALA* 1.3 68.3 + - - +
83A GLY* 3.1 5.4 + - - +
84A ASP* 2.9 28.7 + - - +
110A ILE* 3.6 11.0 - - - +
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Residues in contact with ALA 82 (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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14A PRO* 5.8 2.4 - - - +
81A GLN* 1.3 72.3 - - - +
83A GLY* 1.3 55.5 + - - +
84A ASP 3.1 1.4 + - - -
85A GLU* 2.7 45.8 - - - +
110A ILE* 4.1 8.5 - - + +
172A SER* 3.1 20.2 - - - +
173A LYS* 3.5 19.7 - - - +
175A SER* 4.1 6.1 - - - +
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Residues in contact with GLY 83 (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 GLN* 4.4 2.3 + - - -
41A HIS* 3.2 26.9 + - - -
81A GLN* 3.0 5.9 + - - +
82A ALA* 1.3 78.5 - - - +
84A ASP* 1.3 61.5 + - - +
85A GLU* 3.3 1.3 - - - -
172A SER* 3.4 17.4 + - - -
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Residues in contact with ASP 84 (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 GLN* 4.4 2.8 + - - +
63A ARG* 2.8 46.0 + - - -
64A PHE* 3.7 16.2 - - - -
77A ILE* 3.7 2.0 - - + +
80A LEU* 3.5 21.5 - - + +
81A GLN* 2.9 28.4 + - - +
83A GLY* 1.3 79.0 - - - +
85A GLU* 1.3 65.9 + - - +
86A ALA* 3.1 3.4 + - - +
88A TYR* 2.6 33.9 + - - +
108A VAL* 4.0 4.7 - - + +
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Residues in contact with GLU 85 (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 HIS* 3.0 24.6 + - - -
42A PRO* 5.5 0.5 - - - +
81A GLN 4.2 0.4 + - - -
82A ALA* 2.7 23.5 - - - +
83A GLY 3.3 0.6 - - - +
84A ASP* 1.3 74.6 - - - +
86A ALA* 1.3 57.3 + - - +
108A VAL* 3.8 12.8 - - - +
110A ILE* 2.9 25.2 - - + +
170A GLN* 3.2 29.2 - - + +
171A ASP 2.4 34.2 - - - +
172A SER* 3.1 7.2 - - - -
175A SER* 2.7 28.8 + - - -
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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