Contacts of the strand formed by residues 421 - 425 (chain A) in PDB entry 1I43
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 421 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A PRO* 3.5 32.1 - - + -
213A PHE* 3.6 28.0 - - + -
338A TYR* 4.4 6.3 - - + -
363A SER* 4.0 23.3 - - - -
364A PHE 3.8 14.1 - - - +
365A GLU* 4.4 7.0 - - + +
398A GLN* 3.6 12.3 - - - +
399A PRO* 3.6 30.6 - - + +
416A GLY 5.6 0.2 - - - +
417A ILE* 4.2 10.5 - - + -
418A MET* 3.1 21.9 + - + +
420A ASN* 1.3 79.7 - - - +
422A VAL* 1.3 69.6 + - - +
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A SER* 3.3 3.5 - - - -
364A PHE* 2.8 63.5 + - + +
366A VAL* 4.4 9.4 - - + -
373A THR* 3.3 33.2 - - + -
376A PHE* 4.4 6.7 - - + -
377A VAL* 4.4 9.9 - - + -
396A VAL* 4.0 23.6 - - + -
397A ASP 3.6 6.3 - - - +
398A GLN* 4.2 6.5 - - + -
399A PRO* 4.5 0.2 - - - -
420A ASN 3.6 3.4 - - - +
421A LEU* 1.3 78.9 - - - +
423A ARG* 1.3 62.3 + - - +
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Residues in contact with ARG 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ASN* 3.6 22.6 + - - -
212A PRO* 4.5 9.3 - - + +
239A PHE* 4.7 4.0 - - + -
361A ALA* 5.1 11.2 - - + -
362A VAL 3.9 2.7 - - - +
363A SER* 3.4 20.0 - - - +
386A ALA 5.0 0.8 + - - -
387A PRO 4.9 1.0 - - - -
388A SER 3.6 22.8 + - - +
389A PHE* 3.9 19.8 - - - +
395A ILE* 3.8 2.3 - - - +
396A VAL* 3.5 5.2 - - - -
397A ASP* 3.0 63.4 + - - +
399A PRO* 3.9 14.5 - - + +
421A LEU* 5.7 0.2 - - + -
422A VAL* 1.3 73.4 - - - +
424A PHE* 1.3 67.9 + - - +
425A SER* 4.0 2.3 + - - +
600A PMC 3.3 44.4 + - - -
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Residues in contact with PHE 424 (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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360A GLY 3.9 0.3 - - - +
361A ALA* 3.5 1.9 - - - +
362A VAL* 2.7 45.9 + - - +
364A PHE* 3.9 22.0 - + + -
376A PHE* 5.5 0.9 - + - -
380A LEU* 4.2 9.2 - - + -
383A PRO* 3.7 28.0 - - + -
394A SER* 4.1 9.6 - - - -
395A ILE 3.7 2.5 - - - -
396A VAL* 3.4 25.1 - - + -
422A VAL 3.9 0.8 + - - -
423A ARG* 1.3 75.1 - - - +
425A SER* 1.3 66.2 + - - +
426A PHE* 3.4 50.0 + + + -
434A LEU* 4.6 6.3 - - + -
438A ILE* 3.9 31.0 - - + -
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Residues in contact with SER 425 (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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262A PHE* 5.7 0.9 - - - -
360A GLY 4.1 5.1 - - - -
361A ALA* 4.5 5.2 - - - +
388A SER 4.6 0.7 - - - -
389A PHE* 3.2 26.7 - - - +
390A GLY* 3.0 27.2 + - - -
391A GLY 4.8 0.7 + - - -
393A GLU 5.0 2.1 + - - -
394A SER* 3.3 3.5 - - - -
395A ILE* 2.9 43.2 + - - +
423A ARG* 4.0 4.6 + - - -
424A PHE* 1.3 72.9 - - - +
426A PHE* 1.3 64.7 + - - +
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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