Contacts of the strand formed by residues 368 - 379 (chain A) in PDB entry 3D8F
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 LYS 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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366A GLY 2.6 33.3 + - - +
367A ILE* 1.3 73.3 - - - +
369A CYS* 1.3 59.5 + - - +
370A PHE* 3.7 20.5 - - + -
425A GLN* 3.9 0.7 - - - +
426A LEU* 2.9 38.8 + - + +
494A SER* 3.7 38.4 + - - +
497A GLU* 3.1 29.5 + - - +
498A ILE* 3.9 18.6 - - + +
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Residues in contact with CYS 369 (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 ILE* 3.9 15.1 + - + +
368A LYS* 1.3 74.7 - - - +
370A PHE* 1.3 73.0 + - - +
423A LEU* 3.5 41.3 - - - -
424A LEU 3.9 3.1 - - - -
425A GLN* 4.1 15.9 - - + -
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Residues in contact with PHE 370 (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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368A LYS* 3.7 28.5 - - + -
369A CYS* 1.3 83.7 - - - +
371A ALA* 1.3 63.0 + - - +
372A VAL* 3.3 4.0 + - + +
423A LEU* 3.4 5.0 - - - -
424A LEU* 2.9 45.1 + - + +
426A LEU* 3.7 20.2 - - + -
484A CYS* 6.0 0.9 - - + -
486A ALA* 5.8 6.7 - - + -
490A ASN* 3.8 26.5 - - + -
491A ILE* 3.3 42.2 - - + -
494A SER* 3.4 22.7 - - - -
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Residues in contact with ALA 371 (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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370A PHE* 1.3 70.8 - - - +
372A VAL* 1.3 61.4 + - - +
421A ASP* 6.5 0.7 - - + -
422A LEU 3.7 7.0 - - - +
423A LEU* 4.8 8.8 - - + +
484A CYS* 3.6 2.8 - - - +
485A GLU* 3.1 52.1 + - + +
486A ALA 4.7 0.7 + - - -
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Residues in contact with VAL 372 (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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370A PHE 3.9 2.5 - - - +
371A ALA* 1.3 79.7 - - - +
373A ARG* 1.3 57.9 + - - +
421A ASP* 3.7 7.6 - - - +
422A LEU* 2.8 55.2 + - + +
424A LEU* 3.6 43.3 - - + +
433A LEU* 4.5 1.3 - - + -
482A PHE* 4.2 24.0 - - + -
483A ARG 3.7 5.4 - - - +
484A CYS* 4.1 22.4 - - + -
485A GLU 4.9 0.2 - - - +
491A ILE* 4.3 7.2 - - + -
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Residues in contact with ARG 373 (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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372A VAL* 1.3 74.7 - - - +
374A SER* 1.3 70.0 + - - +
375A LEU* 4.0 7.3 - - + +
420A LYS* 3.7 25.2 + - - +
421A ASP* 3.6 22.4 + - - +
422A LEU* 4.6 2.0 - - - -
482A PHE* 3.2 9.8 - - - -
483A ARG* 3.0 50.3 + - + +
485B GLU* 3.2 36.8 + - - -
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Residues in contact with SER 374 (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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373A ARG* 1.3 79.1 - - - +
375A LEU* 1.3 66.2 + - - +
376A GLY* 3.3 14.7 + - - -
420A LYS 5.4 0.2 + - - -
422A LEU* 3.8 25.8 - - - +
433A LEU* 5.8 1.3 - - - -
481A VAL 4.3 2.1 + - - -
482A PHE* 3.8 19.8 - - - -
371B ALA* 3.7 11.8 - - - +
423B LEU* 5.8 3.1 - - - +
485B GLU* 5.2 0.7 - - - +
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Residues in contact with LEU 375 (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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373A ARG* 4.0 12.3 - - - +
374A SER* 1.3 80.9 + - - +
376A GLY* 1.3 56.4 + - - +
401A LEU* 3.9 22.4 - - + +
402A SER* 3.4 29.8 - - - +
464A ASP* 5.6 0.2 - - - -
481A VAL* 3.2 33.7 + - + +
483A ARG* 3.7 34.8 - - + +
369B CYS 3.9 1.4 - - - +
370B PHE* 4.0 1.7 - - - -
371B ALA* 3.0 30.9 + - - +
485B GLU* 3.8 34.4 - - + +
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Residues in contact with GLY 376 (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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374A SER* 3.3 11.9 + - - -
375A LEU* 1.3 79.0 - - - +
377A TRP* 1.3 66.0 + - - +
401A LEU* 3.4 7.1 - - - +
480A HIS* 3.7 4.6 + - - +
481A VAL 3.1 23.9 + - - +
369B CYS* 3.1 17.3 - - - -
371B ALA* 4.3 2.9 - - - +
423B LEU* 5.2 4.5 - - - -
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Residues in contact with TRP 377 (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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376A GLY* 1.3 75.1 - - - +
378A VAL* 1.3 82.6 + - - +
379A GLU* 3.6 17.5 - - - -
401A LEU* 3.5 2.0 - - - +
476A MET* 3.7 12.8 - - + -
478A LYS* 3.4 45.5 - - + +
479A CYS 3.3 15.5 - - - +
480A HIS* 3.8 29.2 - + + +
367B ILE* 3.1 40.2 - - + -
369B CYS* 2.8 54.3 + - + +
423B LEU* 5.4 3.2 - - + +
425B GLN* 3.8 18.8 - - - +
427B GLU* 5.9 0.4 - - - -
439B GLN* 5.7 3.0 + - - +
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Residues in contact with VAL 378 (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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377A TRP* 1.3 87.1 - - - +
379A GLU* 1.3 78.0 + - - +
380A MET* 3.5 3.8 + - - +
397A CYS* 3.8 30.3 - - - +
400A GLN* 4.8 7.2 - - + +
401A LEU* 3.6 32.3 - - + -
478A LYS* 3.8 0.2 - - - -
479A CYS* 3.1 26.2 + - - +
367B ILE 3.6 4.3 - - - +
368B LYS* 3.7 31.2 - - + -
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Residues in contact with GLU 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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377A TRP* 3.6 8.3 - - + -
378A VAL* 1.3 82.3 - - - +
380A MET* 1.3 74.5 + - - +
381A THR* 5.2 6.1 - - - +
384A GLU* 4.5 1.9 - - - +
397A CYS* 5.2 0.2 - - - -
476A MET* 3.1 31.6 - - + +
477A LEU 3.5 6.5 - - - +
366B GLY* 3.8 18.1 - - - -
367B ILE* 2.9 54.0 + - - +
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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