Contacts of the strand formed by residues 378 - 383 (chain A) in PDB entry 4IX8
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 PHE 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE 4.5 0.2 - - - -
79A GLY* 3.9 22.2 - - - -
225A ASN* 3.3 40.4 - - + -
226A PRO 3.3 18.6 - - - +
228A GLY* 3.7 11.9 - - - +
256A TYR* 3.3 20.6 - + - -
286A LLP 6.2 0.4 - - - -
373A PRO* 3.6 20.5 - - - +
375A ALA 4.7 0.2 + - - -
376A SER* 3.4 16.4 + - - -
377A MET* 1.3 100.8 - - + +
379A VAL* 1.3 60.7 + - - +
422A ARG* 3.4 39.3 - - + -
423A ALA 3.4 5.8 - - - +
424A THR* 3.9 14.1 - - - -
425A VAL* 4.2 4.4 - - - +
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Residues in contact with VAL 379 (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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226A PRO 3.9 4.5 - - - -
227A CYS 4.8 2.5 - - - +
358A TYR* 4.0 19.1 - - + -
370A MET* 3.3 32.8 - - + -
371A GLU 4.0 8.5 - - - +
373A PRO* 3.9 15.5 - - + -
378A PHE* 1.3 73.9 - - - +
380A MET* 1.3 65.8 + - - +
381A LEU* 4.0 13.5 - - + -
421A LEU 3.5 0.3 - - - +
422A ARG* 3.4 6.6 - - - +
423A ALA* 2.8 54.4 + - + +
425A VAL* 4.2 8.1 - - + -
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Residues in contact with MET 380 (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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173A PRO* 3.8 31.0 - - + -
200A TRP* 3.9 24.5 + - + +
226A PRO* 3.4 38.8 + - + +
227A CYS* 3.9 12.8 + - - -
370A MET* 3.6 19.9 - - - +
371A GLU 4.5 3.6 + - - +
379A VAL* 1.3 75.0 - - - +
381A LEU* 1.3 63.5 + - - +
382A LYS* 3.8 1.7 + - - +
412A GLY* 4.5 12.3 - - - -
415A PHE* 5.3 0.9 - - + -
417A MET 4.8 0.4 - - - +
420A PHE* 3.5 33.8 - - + -
421A LEU 3.3 16.4 - - - +
422A ARG* 3.9 12.3 - - - -
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Residues in contact with LEU 381 (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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358A TYR* 4.7 3.8 - - + -
361A LEU* 4.3 19.7 - - + -
368A ILE* 4.1 22.0 - - + -
369A SER 3.7 2.0 - - - -
370A MET* 3.5 32.1 - - + -
379A VAL* 4.0 18.6 - - + -
380A MET* 1.3 73.8 - - - +
382A LYS* 1.3 61.6 + - - +
383A LEU* 3.8 1.8 + - + +
409A VAL* 5.5 4.3 - - + -
420A PHE* 3.1 7.1 - - - -
421A LEU* 2.7 61.5 + - + +
423A ALA* 4.3 17.7 - - + -
439A ILE* 5.7 6.7 - - + -
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Residues in contact with LYS 382 (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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196A PRO* 4.8 13.9 - - + -
197A SER* 6.1 0.4 - - - -
367A GLY 3.4 5.9 - - - +
368A ILE* 3.4 3.8 - - - -
369A SER* 2.8 51.1 + - - +
370A MET* 5.5 0.7 - - - -
380A MET 3.8 2.1 + - - +
381A LEU* 1.3 71.6 - - - +
383A LEU* 1.3 73.0 + - - +
384A ASN* 3.8 0.6 + - - +
419A GLY* 4.2 2.7 + - - +
420A PHE* 3.4 41.0 - - + -
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Residues in contact with LEU 383 (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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367A GLY 3.6 1.6 - - - +
368A ILE* 4.2 17.0 - - + -
381A LEU* 4.4 2.5 - - + +
382A LYS* 1.3 89.5 + - - +
384A ASN* 1.3 60.0 + - - +
385A LEU* 3.3 28.1 + - + +
388A PHE* 5.0 4.5 - - + -
394A ASP* 3.8 35.7 - - + +
397A PHE* 4.0 36.8 - - + -
419A GLY* 2.9 21.3 + - - +
421A LEU* 3.9 28.5 - - + -
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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