Contacts of the strand formed by residues 159 - 162 (chain A) in PDB entry 3LDH
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 ARG 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A PRO* 2.6 58.9 + - - +
133A CYS 3.4 11.3 + - - +
134A LEU* 2.9 37.5 - - + +
135A LYS* 3.1 4.0 + - - +
155A LEU* 2.8 27.9 - - + +
156A PRO* 3.0 22.3 + - - +
157A MET 2.3 15.2 + - - -
158A HIS* 1.3 93.1 - - + +
160A ILE* 1.3 61.8 + - + +
161A ILE* 3.6 3.8 - - - +
296A GLY* 2.7 30.4 + - - +
297A ILE* 4.0 2.7 - - - +
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Residues in contact with ILE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LYS* 4.1 14.8 - - + +
146A ASN* 3.4 22.4 - - - +
150A TRP* 3.1 42.2 - - + +
153A SER* 5.5 0.9 - - - +
155A LEU* 3.8 25.1 - - + +
157A MET 2.4 36.2 + - - +
159A ARG 1.3 70.4 - - - +
161A ILE* 1.3 73.0 + - - +
272A SER 3.8 6.3 - - - +
273A THR* 5.1 6.0 - - + +
286A PHE* 3.2 28.5 - - + -
298A SER* 5.3 0.2 - - - -
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Residues in contact with ILE 161 (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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134A LEU* 5.5 0.2 - - + -
135A LYS 2.2 33.5 + - - +
136A GLU* 3.0 22.4 - - + +
137A LEU* 3.2 4.0 + - - +
146A ASN* 3.5 4.3 - - - -
158A HIS 3.9 11.2 - - - +
159A ARG 3.6 6.5 - - - +
160A ILE* 1.3 125.7 - - - +
162A GLY* 1.3 58.5 + - - +
163A SER* 4.3 4.3 - - - +
257A LEU* 5.9 4.9 - - + -
261A ILE* 4.0 26.2 - - + -
271A VAL* 2.2 47.6 - - + -
272A SER 4.6 0.9 - - - -
273A THR* 6.4 0.2 - - + -
293A LEU* 5.0 8.1 - - + -
298A SER* 4.2 13.5 - - - -
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Residues in contact with GLY 162 (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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136A GLU* 4.4 0.4 - - - -
137A LEU* 2.3 40.3 + - - +
142A GLY 4.3 3.8 - - - -
146A ASN* 3.0 35.0 + - - -
161A ILE* 1.3 74.7 - - - +
163A SER* 1.3 65.7 + - - +
164A GLY 3.7 0.9 - - - -
271A VAL* 4.2 0.4 - - - +
272A SER* 3.7 7.9 + - - -
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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