Contacts of the strand formed by residues 388 - 394 (chain A) in PDB entry 2ILU
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 VAL 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A ARG* 3.7 19.3 + - - +
289A GLU* 4.6 0.9 - - - +
337A VAL* 4.0 18.6 - - + -
341A VAL* 3.8 26.0 - - + -
365A TYR* 4.1 9.0 - - + -
368A THR* 3.5 10.3 - - - +
370A LEU* 3.7 33.7 - - + -
379A ILE* 5.0 4.3 - - + -
384A THR* 3.6 25.4 - - + +
386A GLY 2.9 8.6 + - - -
387A PRO* 1.3 76.2 - - - +
389A LEU* 1.3 66.4 + - - +
390A PRO* 3.8 10.2 - - + +
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Residues in contact with LEU 389 (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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273A ILE* 3.9 20.2 - - + +
277A ARG* 3.2 46.2 - - + +
288A ALA 4.2 10.1 - - - +
289A GLU 5.0 0.2 - - - -
291A VAL* 3.8 22.4 - - + -
305A LEU* 4.3 20.9 - - + -
309A MET* 4.7 13.9 - - - -
368A THR 2.9 15.1 + - - +
369A LEU* 3.3 15.0 - - + +
370A LEU 3.1 20.8 + - - -
387A PRO 4.7 3.8 - - - +
388A VAL* 1.3 75.2 - - - +
390A PRO* 1.3 66.1 - - - +
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Residues in contact with PRO 390 (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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255A LYS* 4.4 8.5 - - - +
289A GLU 3.0 29.4 - - - +
290A ARG* 4.2 1.1 - - - -
291A VAL* 3.1 21.7 + - - +
370A LEU* 3.4 12.3 - - + +
373A VAL* 4.0 26.0 - - + -
379A ILE* 4.6 13.0 - - + -
380A MET* 4.0 19.9 - - - +
384A THR* 5.5 0.7 - - - +
388A VAL* 3.8 9.2 - - + +
389A LEU* 1.3 85.2 - - + +
391A VAL* 1.3 61.7 + - - +
392A VAL* 4.0 2.3 + - - +
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Residues in contact with VAL 391 (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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291A VAL* 3.4 20.0 - - + +
293A VAL* 3.8 16.4 - - + -
298A TYR* 3.5 36.3 + - + +
301A PHE* 5.0 1.1 - - + -
302A VAL* 4.7 5.4 - - + -
305A LEU* 4.4 12.8 - - + -
369A LEU* 3.6 28.9 - - + -
370A LEU 2.7 9.7 + - - -
371A LEU* 3.5 16.2 - - + -
372A ASP* 3.9 3.8 + - - -
373A VAL* 3.9 15.2 + - - +
389A LEU 3.9 1.3 - - - +
390A PRO* 1.3 77.7 - - - +
392A VAL* 1.3 60.2 + - - +
393A ALA 4.0 0.5 + - - -
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Residues in contact with VAL 392 (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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291A VAL 3.1 6.4 + - - +
292A TYR* 3.4 27.4 - - + -
293A VAL 3.2 20.8 + - - -
373A VAL* 3.1 41.1 - - + +
374A ARG* 4.1 3.6 - - - +
375A GLN 4.3 11.4 - - - +
380A MET* 3.6 28.3 - - + -
390A PRO 4.0 0.6 - - - +
391A VAL* 1.3 75.0 - - - +
393A ALA* 1.3 74.5 + - - +
394A PHE 3.9 0.2 + - - -
403A MET* 4.6 7.6 - - - -
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Residues in contact with ALA 393 (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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293A VAL 3.1 11.0 - - - +
295A LYS* 4.0 26.0 + - + +
298A TYR* 4.0 24.5 - - + -
373A VAL 4.7 1.0 + - - -
391A VAL 4.0 2.4 + - - -
392A VAL* 1.3 86.9 - - - +
394A PHE* 1.3 61.5 + - - +
403A MET* 4.8 2.3 - - - +
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Residues in contact with PHE 394 (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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259A ILE* 3.8 3.8 - - + -
260A VAL 4.1 1.8 - - - -
261A MET* 3.6 23.6 - - - -
292A TYR* 3.4 33.9 - - + -
293A VAL* 2.9 27.1 + - - -
294A GLN* 3.0 56.4 - - + +
295A LYS* 3.4 10.6 + - - +
392A VAL 4.8 0.4 - - - +
393A ALA* 1.3 75.9 - - - +
395A ASP* 1.3 62.4 + - - +
396A THR 3.3 35.4 - - - -
399A ASP* 4.4 0.4 - - + -
400A ALA* 3.5 23.1 - - + -
403A MET* 3.5 25.6 - - + -
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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