Contacts of the strand formed by residues 147 - 149 (chain A) in PDB entry 2PK9
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 LEU 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASN* 2.6 33.8 + - - +
89A LEU* 4.6 5.2 - - + -
113A PHE* 3.7 46.7 - - + +
116A GLN* 3.2 19.6 - - + +
117A LEU* 3.8 33.9 - - + +
139A LEU* 4.1 35.4 - - + -
140A LEU 3.4 8.5 - - - +
141A ILE* 4.3 11.4 - - + -
146A GLN* 1.3 72.5 - - - +
148A LYS* 1.3 69.4 + - - +
149A LEU* 4.6 0.7 - - + -
202A MET* 5.7 0.2 - - - -
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Residues in contact with LYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS 5.7 0.2 + - - -
63A GLU* 3.5 14.5 + - - +
64A ASN* 3.5 18.8 - - - -
65A ILE 4.3 2.9 - - - +
66A VAL* 3.6 23.8 - - + +
83A GLU* 2.7 37.1 + - - +
85A MET* 3.7 14.6 - - + -
140A LEU* 2.9 36.5 + - - +
142A ASN* 4.0 13.1 - - - +
144A ARG* 5.5 2.0 - - - +
146A GLN* 3.5 33.0 + - - +
147A LEU* 1.3 83.8 - - - +
149A LEU* 1.3 64.8 + - - +
150A GLY 3.5 0.5 + - - -
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Residues in contact with LEU 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN 3.2 15.7 + - - +
65A ILE* 3.6 5.2 - - + -
66A VAL* 3.0 22.7 + - - +
117A LEU* 3.5 46.2 - - + +
120A GLY 4.0 2.5 - - - -
121A LEU* 3.7 42.4 - - + +
124A CYS* 4.0 12.3 - - - -
131A HIS* 4.7 5.8 - - + -
134A LEU* 4.2 7.4 - - + -
138A ASN 3.6 7.4 - - - +
139A LEU* 3.8 8.5 - - + -
147A LEU* 4.6 1.1 - - + -
148A LYS* 1.3 70.7 - - - +
150A GLY* 1.3 58.2 + - - +
152A PHE* 3.6 21.1 - - + -
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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