Contacts of the strand formed by residues 234 - 242 (chain A) in PDB entry 2DFS
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 ILE 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A PHE* 3.9 11.9 - - + +
181A ALA* 3.9 27.1 - - + +
184A SER* 3.4 21.8 + - - +
186A SER* 4.5 4.0 - - - -
187A ALA* 3.6 38.9 - - + +
191A ASN* 5.2 2.7 - - - -
192A VAL* 4.2 32.3 - - + +
226A ILE* 4.2 14.6 - - + -
227A GLY 3.9 4.0 - - - -
228A PHE* 3.6 22.8 - - + -
233A ARG* 1.4 74.5 - - + +
235A ILE* 1.3 61.8 + - - +
236A GLY 5.3 0.2 - - - +
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Residues in contact with ILE 235 (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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187A ALA* 5.2 2.7 - - - -
190A ALA* 4.7 7.6 - - - +
192A VAL* 4.3 9.0 - - - +
227A GLY* 3.1 20.6 + - - +
228A PHE 4.2 0.7 - - - +
229A ASP* 4.1 14.4 - - + +
231A ARG* 5.5 2.2 - - - +
233A ARG* 3.7 20.9 - - - +
234A ILE* 1.3 78.9 - - - +
236A GLY* 1.3 61.5 + - - +
424A HIS 5.1 0.5 - - - +
425A SER* 2.7 29.1 + - - +
427A VAL* 3.5 45.8 - - + +
428A LYS 4.0 4.3 - - - +
429A GLN* 3.8 28.7 - - + +
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Residues in contact with GLY 236 (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* 4.1 16.9 - - - +
226A ILE* 3.8 5.7 - - - +
227A GLY* 2.9 23.0 + - - +
234A ILE* 5.8 0.2 - - - +
235A ILE* 1.3 83.7 + - - +
237A ALA* 1.3 62.5 + - - +
423A LEU 3.5 12.3 - - - -
425A SER* 4.2 8.3 - - - -
429A GLN* 5.9 0.4 - - - -
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Residues in contact with ALA 237 (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* 4.2 6.1 - - + -
196A VAL* 4.3 1.3 - - + -
224A ILE* 4.1 6.1 - - + -
225A GLU 3.1 13.9 - - - +
226A ILE* 4.0 17.5 - - + -
227A GLY 4.4 1.1 - - - +
236A GLY* 1.3 74.6 - - - +
238A ASN* 1.3 62.6 + - - +
420A ASN* 4.4 0.2 - - - +
423A LEU* 3.0 54.2 + - + +
424A HIS* 4.0 7.7 + - - +
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Residues in contact with ASN 238 (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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223A TYR 3.6 1.0 - - - +
224A ILE* 3.4 5.0 - - - -
225A GLU* 2.7 67.5 + - + +
237A ALA* 1.3 76.0 - - - +
239A MET* 1.3 69.6 + - - +
240A ARG* 3.3 22.8 - - - +
420A ASN* 3.5 10.6 + - - +
423A LEU* 4.9 0.9 - - - -
424A HIS* 3.4 25.8 - - + +
429A GLN* 6.0 1.8 - - - +
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Residues in contact with MET 239 (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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199A SER* 3.7 23.3 - - - +
203A MET* 3.6 41.5 - - + +
222A LYS* 4.4 8.5 - - + -
223A TYR 3.4 3.4 - - - -
224A ILE* 3.7 25.4 - - + -
238A ASN* 1.3 77.3 + - - +
240A ARG* 1.3 73.0 + - - +
241A THR* 4.4 1.3 - - + -
416A VAL* 3.8 20.6 - - + +
419A VAL* 3.8 22.2 - - + -
420A ASN* 2.8 35.6 + - - +
423A LEU* 4.9 6.2 - - + +
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Residues in contact with ARG 240 (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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221A GLY 4.0 0.3 - - - +
222A LYS* 3.7 2.8 - - - -
223A TYR* 2.8 41.5 + - + +
225A GLU* 2.6 42.9 + - - +
238A ASN* 3.3 17.7 - - - +
239A MET* 1.3 78.6 - - - +
241A THR* 1.3 62.8 + - - +
242A TYR* 3.2 36.3 - - + -
416A VAL* 5.2 0.7 - - - -
650A THR* 4.5 7.0 - - - +
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Residues in contact with THR 241 (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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203A MET* 4.0 4.5 - - + -
220A PHE* 4.0 21.3 - - + -
221A GLY 3.5 4.5 - - - -
222A LYS* 5.2 0.2 - - - -
239A MET* 4.4 7.4 - - + -
240A ARG* 1.3 77.8 - - - +
242A TYR* 1.3 71.5 + - - +
412A PHE* 3.7 28.6 - - + -
413A ASN* 4.6 6.6 + - - -
416A VAL* 3.9 32.0 - - + +
643A SER* 4.8 0.2 + - - -
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Residues in contact with TYR 242 (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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220A PHE* 3.5 4.9 - - - +
221A GLY* 2.9 38.7 + - - +
223A TYR* 4.1 13.6 - + + -
240A ARG* 3.2 42.6 - - + -
241A THR* 1.3 81.6 - - - +
243A LEU* 1.4 75.7 + - + +
244A LEU* 3.3 4.7 + - - -
436A LEU* 5.2 0.9 - - + -
643A SER* 3.5 26.7 - - - +
646A LEU* 4.0 9.6 - - + -
647A LEU* 3.6 47.3 - - + -
650A THR* 3.1 24.1 + - - +
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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