Contacts of the strand formed by residues 253 - 259 (chain A) in PDB entry 1L8A
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 253 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A ALA* 3.7 30.1 - - + +
202A ILE* 3.8 23.8 - - + -
205A ALA* 3.7 10.5 - - + -
224A VAL* 3.5 16.4 - - + +
226A ALA* 5.0 0.4 - - + -
245A ALA* 4.0 14.6 - - + -
250A LEU* 3.2 11.2 + - + +
251A ASP 3.4 2.2 - - - -
252A ASN* 1.3 81.4 - - - +
254A VAL* 1.3 69.9 + - - +
255A PHE* 4.0 16.6 - - + -
287A TRP* 3.5 27.4 - - + -
383A ALA* 3.7 4.1 - - + +
384A THR* 3.3 21.8 + - - +
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Residues in contact with VAL 254 (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 THR* 3.8 20.4 - - + -
224A VAL 2.8 8.9 + - - -
225A TYR* 3.5 22.5 - - + +
226A ALA 3.0 25.5 + - - -
251A ASP 5.9 1.3 - - - +
253A LEU* 1.3 81.1 - - - +
255A PHE* 1.3 74.0 + - - +
256A VAL* 3.8 9.6 + - + +
376A ALA* 4.3 24.0 - - + +
377A GLN* 6.0 0.7 - - - -
384A THR* 3.3 10.1 - - - +
386A ILE* 3.9 25.6 - - + -
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Residues in contact with PHE 255 (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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198A PRO* 3.4 33.2 - - + -
202A ILE* 3.7 13.9 - - + -
226A ALA* 3.6 24.2 - - + -
228A LEU* 3.6 22.4 - - + -
233A MET* 4.5 0.2 - - + -
238A SER 4.0 13.5 - - - -
242A ILE* 4.0 3.6 - - + -
253A LEU* 4.0 15.5 - - + -
254A VAL* 1.3 78.2 - - - +
256A VAL* 1.3 57.4 + - - +
257A ILE* 3.9 1.3 - - + -
282A PHE* 3.6 30.7 - + - -
287A TRP* 3.6 29.3 - + + -
384A THR 2.9 6.1 + - - -
385A VAL* 3.2 12.1 - - + -
386A ILE* 2.7 32.4 + - - -
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Residues in contact with VAL 256 (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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116A ILE* 4.0 14.4 - - + -
225A TYR* 4.3 1.8 - - + -
226A ALA 2.8 14.8 + - - +
227A PHE* 3.5 38.7 - - + -
228A LEU 2.8 26.9 + - - +
254A VAL* 3.9 13.2 - - + +
255A PHE* 1.3 75.9 - - - +
257A ILE* 1.3 64.2 + - - +
258A ASN* 3.6 0.8 + - + +
373A PHE* 3.7 37.0 - - + -
386A ILE* 3.6 14.1 - - + +
388A ALA* 5.1 1.8 - - + -
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Residues in contact with ILE 257 (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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228A LEU* 3.5 16.8 - - + +
229A GLY 3.9 6.3 - - - +
230A ASP* 3.8 29.8 - - + +
233A MET* 3.8 30.5 - - + -
255A PHE* 4.6 0.4 - - + -
256A VAL* 1.3 74.1 - - - +
258A ASN* 1.3 60.9 + - - +
259A CYS* 3.0 20.2 + - - -
278A LEU* 4.1 5.4 - - + -
282A PHE* 4.1 10.5 - - + -
385A VAL* 3.7 20.4 - - + -
386A ILE 2.9 7.7 + - - -
387A LEU* 3.6 24.7 - - + -
388A ALA* 3.0 22.6 + - - -
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Residues in contact with ASN 258 (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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109A SER 4.3 1.2 + - - -
112A SER* 2.9 24.2 + - - -
113A SER* 3.5 26.0 + - - -
116A ILE* 4.8 3.8 - - + -
140A GLN* 4.6 6.0 - - - +
228A LEU 2.8 19.0 + - - +
229A GLY* 4.0 0.4 - - - -
230A ASP* 3.3 21.1 + - - +
256A VAL* 3.6 2.5 + - + +
257A ILE* 1.3 69.1 - - - +
259A CYS* 1.3 57.5 + - - +
260A ASN* 3.2 14.8 + - - +
388A ALA* 3.9 5.6 - - - -
390A THR* 2.6 34.7 + - - +
887B TPP 3.8 12.0 + - - +
888B MG 3.8 2.9 - - - -
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Residues in contact with CYS 259 (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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230A ASP* 3.2 9.6 - - - +
257A ILE* 3.0 30.2 + - - -
258A ASN* 1.3 69.8 - - - +
260A ASN* 1.3 56.5 + - - +
261A LEU* 3.1 6.3 + - - +
274A ILE* 4.9 1.3 - - + -
275A ILE* 3.6 35.4 - - + -
278A LEU* 4.1 9.2 - - - -
387A LEU* 3.9 22.0 - - - -
388A ALA 2.6 17.4 + - - +
389A HIS* 3.5 11.6 - - - -
390A THR* 3.2 16.8 + - - -
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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