Contacts of the strand formed by residues 112 - 117 (chain J) in PDB entry 2AK4
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 THR 112 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6J GLN* 3.1 25.6 - - + +
7J THR 4.6 2.7 - - - +
8J PRO* 3.0 27.5 - - - +
9J LYS 3.2 6.1 - - - -
10J PHE* 5.4 0.2 - - - -
11J GLN* 5.6 1.2 - - - +
21J LEU* 3.4 41.8 - - + +
34J TRP* 4.9 1.8 - - + -
88J SER 3.9 0.2 - - - +
89J VAL* 3.4 3.8 - - - -
90J TYR* 2.9 33.0 + - - +
111J GLY* 1.3 73.7 - - - -
113J ARG* 1.3 66.1 + - - +
114J LEU* 3.7 3.6 + - - +
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Residues in contact with ARG 113 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9J LYS 2.8 8.7 + - - +
10J PHE* 3.4 32.8 - - + -
11J GLN* 2.9 25.1 + - - +
87J THR* 4.8 12.1 - - - +
88J SER* 3.9 6.4 + - - +
89J VAL* 3.9 29.9 - - + +
111J GLY 4.3 0.6 - - - -
112J THR* 1.3 71.8 + - - +
114J LEU* 1.3 62.0 + - - +
115J THR* 4.3 5.1 + - - -
156J ASP* 2.8 46.4 + - - -
157J HIS* 3.2 21.7 + - + -
179J PRO* 5.9 1.6 - - - +
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Residues in contact with LEU 114 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J GLN* 3.5 11.0 - - + +
13J LEU* 4.2 12.3 - - + -
19J MET* 3.5 42.0 - - + -
21J LEU* 5.0 2.7 - - + -
79J LEU* 4.1 11.0 - - + -
86J GLN 3.2 27.8 - - - +
87J THR* 3.3 6.8 - - - +
88J SER 3.0 32.4 + - - +
90J TYR* 3.9 20.4 - - + -
112J THR* 3.7 5.3 + - - +
113J ARG* 1.3 75.4 + - - +
115J THR* 1.3 65.1 + - - +
116J VAL* 3.6 24.2 - - + -
157J HIS* 4.5 0.4 - - - -
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Residues in contact with THR 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J GLN 3.0 8.2 + - - -
12J VAL* 3.4 5.4 - - + +
13J LEU* 2.8 27.4 + - - +
87J THR* 3.8 17.5 - - + +
113J ARG* 4.3 3.8 + - - -
114J LEU* 1.3 75.1 + - - +
116J VAL* 1.3 65.6 + - - +
117J THR* 4.6 1.1 - - - +
154J TYR* 3.5 30.5 - - + +
155J PRO* 3.4 25.0 - - + +
156J ASP* 4.3 1.2 + - - -
157J HIS* 2.9 25.9 - - - -
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Residues in contact with VAL 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J LEU* 3.3 11.0 - - + +
15J THR* 3.9 20.9 - - - +
79J LEU* 4.9 0.2 - - + -
82J ALA* 3.8 30.7 - - + -
83J ALA 3.6 35.7 - - - +
84J PRO* 3.6 14.5 - - - +
86J GLN* 4.5 2.2 - - + -
87J THR* 3.0 19.1 + - - +
114J LEU* 3.6 25.4 - - + -
115J THR* 1.3 74.9 - - - +
117J THR* 1.3 62.9 + - - +
154J TYR* 4.4 1.9 + - - -
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Residues in contact with THR 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J VAL* 4.4 14.6 - - + -
13J LEU 2.9 16.6 + - - +
14J LYS* 3.4 4.9 - - - -
15J THR* 2.9 27.8 + - - -
84J PRO* 5.3 1.3 - - - -
115J THR* 3.9 1.1 - - - -
116J VAL* 1.3 74.7 - - - +
118J GLU* 1.3 67.1 + - - +
119J ASP 3.3 21.3 - - - +
120J LEU* 4.5 5.6 - - + +
122J ASN* 3.4 16.5 + - - +
123J VAL* 4.7 1.6 - - + -
154J TYR* 3.4 38.7 + - + -
188J ASP* 4.6 4.3 - - - +
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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