Contacts of the strand formed by residues 131 - 134 (chain B) in PDB entry 2LDX
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 LYS 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LYS 3.1 15.5 + - - +
90B LEU* 3.3 13.5 - - + +
91B VAL 3.0 22.7 + - - +
129B ASP 5.2 0.7 - - - +
130B CYS* 1.3 79.0 - - - +
132B ILE* 1.3 63.6 + - - +
133B ILE* 5.0 1.2 - - - +
155B GLY 3.8 0.2 - - - -
156B ARG* 3.4 19.7 - - + +
158B ILE* 2.9 27.0 - - + +
262B ILE* 3.0 55.4 - - + +
296B GLU 4.0 9.9 - - - +
297B SER 4.8 0.9 - - - -
298B GLY* 3.1 35.5 + - - +
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B VAL* 2.9 24.2 - - + +
93B ILE* 3.3 35.0 - - + -
120B VAL* 4.9 9.2 - - + -
123B VAL* 5.3 2.7 - - + -
124B ILE* 5.1 5.4 - - + -
130B CYS* 3.5 20.0 - - - -
131B LYS* 1.3 71.9 - - - +
133B ILE* 1.3 71.7 - - - +
134B VAL* 4.2 5.2 - - + -
146B VAL* 5.4 2.7 - - + -
150B SER* 4.9 5.8 - - - -
152B PHE* 3.5 30.1 - - + -
156B ARG 3.0 12.8 + - - +
157B VAL* 4.1 12.3 - - + -
158B ILE* 2.6 37.8 + - - +
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Residues in contact with ILE 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LEU* 3.3 45.5 - - + -
91B VAL 3.2 7.7 + - - +
92B ILE* 3.4 8.7 - - + -
93B ILE 3.4 11.8 + - - -
131B LYS* 5.0 2.7 - - - +
132B ILE* 1.3 86.4 - - - +
134B VAL* 1.3 68.8 + - - +
135B VAL* 4.0 5.6 - - + -
158B ILE* 3.4 9.0 - - + +
159B GLY 5.0 1.6 - - - +
160B SER* 4.5 13.0 - - - +
255B VAL* 4.1 39.0 - - + +
258B LEU* 4.3 11.2 - - + -
259B ALA* 4.2 1.6 - - - +
262B ILE* 3.6 18.8 - - + -
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 4.2 8.5 - - + +
116B MET* 4.6 6.5 - - + -
132B ILE* 4.2 14.4 - - + -
133B ILE* 1.3 78.7 - - - +
135B VAL* 1.3 61.3 + - - +
136B THR* 4.0 18.6 - - - +
139B VAL* 4.1 8.4 - - - +
142B LEU* 4.3 6.1 - - + -
143B THR* 4.0 24.5 - - - +
146B VAL* 3.5 33.0 - - + -
157B VAL* 5.2 1.3 - - + -
158B ILE 2.8 17.3 + - - +
159B GLY* 3.6 0.9 - - - -
160B SER* 3.1 27.9 + - - -
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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