Contacts of the strand formed by residues 284 - 289 (chain A) in PDB entry 2RD0
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 ASN 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-25A TYR* 5.2 1.2 + - - -
193A VAL* 3.3 11.4 - - - +
195A TRP* 3.6 12.0 - - - +
254A VAL* 4.0 0.3 - - - -
255A CYS* 3.0 38.8 + - + +
272A TYR* 3.2 13.8 + - - +
282A MET* 2.5 30.5 - - - +
283A PRO* 1.3 73.7 - - - +
285A LEU* 1.3 67.9 + - - +
793A LEU* 3.0 46.4 + - + +
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Residues in contact with LEU 285 (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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192A VAL* 3.9 24.9 - - + -
193A VAL 3.2 6.1 + - - +
194A ILE* 4.4 5.4 - - + -
195A TRP* 2.9 30.9 + - - -
220A VAL* 5.3 3.6 - - + -
252A LEU* 3.7 31.0 - - + -
253A LYS 3.2 5.8 - - - +
254A VAL* 4.1 4.9 - - - -
255A CYS* 3.4 2.2 - - - -
261A PHE* 3.4 40.4 - - + -
267A LEU* 4.6 8.3 - - + -
272A TYR* 3.5 19.1 - - + -
273A ILE* 4.5 8.1 - - + -
283A PRO* 4.7 0.2 - - + -
284A ASN* 1.3 86.6 - - - +
286A MET* 1.3 61.6 + - - +
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Residues in contact with MET 286 (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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195A TRP* 3.8 8.5 - - + +
197A ILE* 4.5 20.2 - - - +
251A ILE 3.3 5.2 - - - +
252A LEU* 3.4 6.7 - - - -
253A LYS* 2.7 72.3 + - + +
255A CYS* 4.2 10.8 - - - -
285A LEU* 1.3 74.9 - - - +
287A LEU* 1.3 76.2 + - - +
288A MET* 3.4 8.9 + - + +
787A ASP* 5.1 0.9 - - - +
788A ILE* 4.5 20.6 - - + -
789A MET* 3.5 28.3 - - + +
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Residues in contact with LEU 287 (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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194A ILE* 3.3 36.1 - - + +
195A TRP 3.1 15.3 + - - +
196A VAL* 3.8 25.0 - - + +
197A ILE 5.4 1.4 + - - -
221A ILE* 3.8 26.5 - - + -
224A ALA* 4.7 6.3 - - + -
225A ILE* 4.3 25.1 - - + -
228A LYS* 6.3 0.9 - - + -
250A TYR* 3.9 23.6 - - + -
251A ILE 3.7 3.6 - - - +
252A LEU* 3.7 10.1 - - + -
286A MET* 1.3 80.4 - - - +
288A MET* 1.3 60.3 + - - +
289A ALA 4.3 0.2 + - - -
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Residues in contact with MET 288 (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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250A TYR* 3.2 6.7 - - - -
251A ILE* 2.9 40.2 + - + +
253A LYS* 4.1 20.9 - - + -
260A TYR* 4.0 26.9 - - + -
286A MET* 3.4 11.4 + - + +
287A LEU* 1.3 73.0 - - - +
289A ALA* 1.3 71.3 + - - +
290A LYS* 3.2 0.9 + - - -
292A SER* 3.4 40.4 - - - +
293A LEU* 4.1 11.2 - - + +
296A GLN* 3.9 15.0 - - - +
788A ILE* 6.4 2.2 - - + -
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Residues in contact with ALA 289 (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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249A LYS* 3.5 8.3 - - + +
250A TYR* 3.7 18.8 - - + -
288A MET* 1.3 73.9 - - - +
290A LYS* 1.3 66.8 + - - +
291A GLU* 4.2 7.9 - - + +
292A SER* 2.5 37.6 + - - +
293A LEU 3.1 5.7 + - - -
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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