Contacts of the strand formed by residues 451 - 465 (chain S) in PDB entry 6O81
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 TRP 451 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B ASP 5.5 1.0 + - - -
263B ASN* 4.5 5.9 - - - +
264B PHE* 4.8 3.1 - - + -
265B ASP* 3.4 45.5 - - + -
78S THR* 6.0 7.2 - - - -
79S ILE* 6.1 5.2 - - + -
139S ASP* 3.6 14.9 - - - +
140S ILE* 4.7 6.1 + - + +
403S VAL* 4.8 11.2 - - + -
404S LEU 4.7 1.3 - - - -
405S MET* 3.7 58.3 - - + +
444S SER* 5.0 6.1 - - - -
445S ARG* 3.9 11.7 - - - -
446S ARG* 3.1 56.3 - - + +
450S HIS* 1.3 71.1 - - - +
452S ARG* 1.3 59.7 + - - +
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Residues in contact with ARG 452 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139S ASP* 3.8 12.8 - - + -
381S LEU* 5.5 5.3 - - - +
384S VAL* 3.5 28.9 - - - +
444S SER* 3.8 3.6 - - - -
445S ARG* 2.8 40.1 + - - +
447S VAL* 4.4 19.0 - - + +
448S GLU 5.8 0.2 - - - +
450S HIS* 3.7 27.9 + - + +
451S TRP* 1.3 77.1 - - - +
453S LEU* 1.3 64.9 + - - +
454S ILE* 4.6 0.2 - - - +
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Residues in contact with LEU 453 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139S ASP* 4.0 14.5 + - + +
142S MET* 5.8 3.4 - - + -
143S ALA* 4.6 22.7 - - + +
381S LEU* 5.8 4.7 - - - +
382S LEU 5.8 0.9 + - - -
442S ALA* 6.0 1.3 - - + -
443S LEU 4.6 2.5 - - - +
444S SER* 3.9 9.8 - - - +
452S ARG* 1.3 78.0 - - - +
454S ILE* 1.3 59.5 + - - +
455S GLY 4.9 4.3 - - - +
456S TRP* 5.5 13.9 - - + +
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Residues in contact with ILE 454 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377S LEU* 3.5 8.4 - - + +
378S LEU* 2.9 31.8 + - - +
395S VAL* 4.6 18.0 - - + +
443S LEU* 2.9 13.6 + - + +
444S SER 4.6 0.2 - - - -
445S ARG* 4.6 26.2 - - + +
452S ARG 3.7 0.8 + - - +
453S LEU* 1.3 75.8 - - - +
455S GLY* 1.3 60.8 + - - +
456S TRP* 5.8 1.6 - - - -
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Residues in contact with GLY 455 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376S PHE 3.4 14.4 - - - -
377S LEU* 4.1 2.9 - - - -
378S LEU 4.5 1.1 - - - -
442S ALA* 3.6 2.4 - - - +
443S LEU* 2.9 34.8 + - - +
453S LEU* 3.8 2.9 - - - +
454S ILE* 1.3 81.7 - - - +
456S TRP* 1.3 79.8 + - - -
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Residues in contact with TRP 456 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ASN* 6.5 0.9 - - + -
576B LEU* 5.9 9.2 - - + -
142S MET 5.1 2.2 + - - -
143S ALA* 5.4 3.2 - - - +
146S LEU* 3.4 40.0 - - + +
177S ILE* 4.5 23.3 - - + -
374S SER 3.6 1.1 - - - +
376S PHE* 3.1 37.4 + - + +
378S LEU* 5.1 15.0 - - + -
382S LEU* 6.1 4.7 - - + -
440S LYS* 6.2 3.1 - - + -
441S ILE 3.6 8.7 - - - +
442S ALA* 4.1 13.0 - - + +
443S LEU* 5.8 1.8 - - - -
453S LEU* 5.5 12.8 - - + +
454S ILE 6.0 0.7 - - - -
455S GLY* 1.3 89.7 + - - -
457S GLY* 1.3 60.3 + - - +
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Residues in contact with GLY 457 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373S ILE* 5.1 3.4 - - - -
374S SER* 3.3 17.5 - - - -
376S PHE* 5.1 1.8 - - - -
440S LYS* 3.4 8.4 - - - +
441S ILE* 2.9 34.7 + - - -
456S TRP* 1.3 79.4 - - - +
458S GLN* 1.3 60.3 + - - -
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Residues in contact with GLN 458 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373S ILE* 4.0 2.5 - - - -
374S SER* 3.0 32.2 + - - +
438S GLY* 4.6 8.5 - - - +
439S GLU 3.8 7.6 - - - +
440S LYS* 5.4 0.9 - - - -
457S GLY* 1.3 74.9 - - - +
459S ILE* 1.3 65.3 + - - +
460S ARG* 3.2 3.1 + - - +
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Residues in contact with ILE 459 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371S LEU* 5.5 8.7 - - + -
372S GLU 4.9 1.1 - - - +
373S ILE* 4.0 12.5 - - + +
436S GLU 5.2 3.1 - - - +
437S VAL* 3.0 31.7 - - - +
438S GLY* 3.6 8.7 - - - -
439S GLU 3.4 16.7 + - - +
441S ILE* 5.3 7.0 - - + +
458S GLN* 1.3 70.8 - - - +
460S ARG* 1.3 61.0 + - - +
461S ARG 5.0 6.1 - - - +
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Residues in contact with ARG 460 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372S GLU* 2.8 16.7 + - + +
373S ILE* 4.7 4.3 - - - -
374S SER* 5.2 1.8 - - - +
437S VAL 4.9 2.6 - - - +
458S GLN 3.2 6.6 + - - +
459S ILE* 1.3 72.9 - - - +
461S ARG* 1.3 64.6 + - + +
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Residues in contact with ARG 461 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371S LEU* 3.5 5.2 - - - +
372S GLU* 2.9 40.1 + - + +
437S VAL 5.5 2.5 - - - -
459S ILE* 3.7 5.3 - - - +
460S ARG* 1.3 80.3 + - + +
462S GLY* 1.3 59.6 + - - +
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Residues in contact with GLY 462 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368S PHE* 4.8 14.5 - - - -
370S GLU 3.3 10.3 - - - -
371S LEU* 4.3 3.1 - - - -
461S ARG* 1.3 78.5 - - - +
463S VAL* 1.3 61.1 + - - -
464S THR* 3.7 4.0 + - - -
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Residues in contact with VAL 463 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367S ILE 3.9 0.2 - - - +
368S PHE* 3.4 3.4 - - - +
369S THR* 3.0 29.2 + - - -
370S GLU* 2.9 29.5 + - + +
462S GLY* 1.3 70.9 - - - -
464S THR* 1.3 63.9 + - - +
465S ILE* 5.3 0.2 - - - +
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Residues in contact with THR 464 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366S GLU* 4.0 12.6 - - - -
367S ILE 3.5 5.2 - - - -
368S PHE* 3.7 25.6 - - - -
462S GLY 3.7 4.2 + - - -
463S VAL* 1.3 74.6 - - - +
465S ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 465 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309S LEU 5.1 10.3 - - - +
310S MET* 6.1 1.1 - - - -
311S CYS* 5.1 6.8 - - + +
366S GLU* 4.6 0.8 - - - +
367S ILE* 2.9 37.4 + - + +
369S THR* 6.2 3.6 - - - -
463S VAL 5.3 0.7 - - - +
464S THR* 1.3 79.1 - - - +
466S LYS* 1.3 62.3 + - - +
467S PRO 4.2 0.7 - - - -
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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