Contacts of the strand formed by residues 467 - 474 (chain D) in PDB entry 5E9W
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 TYR 467 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ASN* 6.3 0.2 - - - -
285D PHE* 3.2 41.0 - + - +
288D HIS* 3.7 12.2 + + - -
317D THR 4.0 1.1 - - - -
318D THR* 3.3 41.7 - - - -
319D PRO* 3.4 23.9 - - + +
320D ASN* 4.3 2.5 - - - +
360D PHE* 5.3 15.0 - + - -
362D LEU* 6.5 0.7 - - + -
370D GLU* 4.4 5.5 + - - -
394D THR* 3.8 3.6 - - - -
395D PHE* 2.9 45.6 + + + +
463D ALA 4.9 4.5 - - - -
464D THR* 3.1 15.9 + - - +
465D SER 3.9 4.7 - - - +
466D ILE* 1.3 93.5 - - + +
468D LEU* 1.3 59.9 + - - +
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Residues in contact with LEU 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D THR* 3.3 4.9 - - - -
318D THR* 2.9 58.2 + - + +
319D PRO 4.3 2.2 - - - +
320D ASN* 3.6 35.7 - - + +
321D SER 5.0 0.4 - - - +
373D VAL 6.1 0.4 - - - +
375D PHE* 4.3 27.8 - - + -
392D LYS* 4.5 15.0 - - + -
393D LYS 3.3 17.3 - - - +
394D THR* 4.2 2.7 - - + -
395D PHE* 3.4 7.0 - - - -
467D TYR* 1.3 75.2 - - - +
469D VAL* 1.3 70.3 + - - +
470D PHE* 3.9 16.6 - - + -
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Residues in contact with VAL 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D MET* 4.1 14.8 - - + +
183D LEU* 4.6 11.0 - - + -
316D GLY 3.4 9.4 - - - +
317D THR* 4.0 7.4 - - + -
391D TYR* 3.9 12.6 - - + -
392D LYS* 3.6 1.2 - - - -
393D LYS* 2.7 48.7 + - + +
395D PHE* 3.4 28.7 - - + -
398D PHE* 3.6 34.3 - - + -
468D LEU* 1.3 77.4 - - - +
470D PHE* 1.3 62.8 + - - +
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Residues in contact with PHE 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D LEU* 4.8 3.9 - - - +
287D CYS* 3.7 25.6 - - - -
314D PHE* 3.6 29.8 - + - -
315D ILE* 3.3 4.2 - - - +
316D GLY* 2.9 64.0 + - - +
317D THR 3.7 4.0 - - - -
318D THR* 4.1 18.8 - - + -
375D PHE* 3.7 31.2 - + + -
378D LEU* 4.5 6.3 - - + -
391D TYR* 3.5 10.1 - - - +
468D LEU* 3.9 16.4 - - + -
469D VAL* 1.3 76.4 - - - +
471D ALA* 1.3 64.9 + - - +
472D PHE* 3.5 19.3 - + + -
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Residues in contact with ALA 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D PHE* 3.2 39.9 - - + -
314D PHE 3.3 6.1 - - - -
315D ILE* 3.8 8.7 - - + -
389D LEU* 3.5 5.7 - - - +
390D VAL* 2.8 36.8 + - + +
391D TYR* 3.1 15.9 + - + +
470D PHE* 1.3 77.7 - - - +
472D PHE* 1.3 60.1 + - - +
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Residues in contact with PHE 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D TYR* 3.2 8.5 - - - +
314D PHE* 2.7 54.9 + + + +
375D PHE* 3.8 21.1 - + - -
378D LEU* 4.2 14.1 - - + -
379D ASN* 3.5 39.3 - - - -
382D ALA* 4.0 17.3 - - + -
387D MET* 3.6 23.6 - - + -
388D LYS* 3.3 8.1 - - - +
389D LEU* 3.7 23.3 - - + -
390D VAL* 3.8 3.6 - - - -
470D PHE* 3.5 28.5 - + + -
471D ALA* 1.3 75.3 - - - +
473D GLU* 1.3 61.7 + - - +
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Residues in contact with GLU 473 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B ASP* 5.3 6.0 - - - +
369B PRO* 5.7 9.1 - - - +
194D LYS* 2.7 28.8 + - - -
311D GLY* 3.7 6.6 - - - +
312D GLY 3.4 9.0 - - - +
313D TYR* 3.7 16.7 + - + -
387D MET* 3.3 4.2 - - - -
388D LYS* 2.8 36.3 + - + +
390D VAL* 3.6 18.8 - - + +
472D PHE* 1.3 74.8 - - - +
474D LYS* 1.3 75.5 + - - +
475D GLN* 3.3 13.5 + - - +
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Residues in contact with LYS 474 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D CYS 3.0 26.2 + - - -
306D GLU* 3.6 13.1 + - - +
308D LEU* 3.2 30.7 - - + +
309D SER 3.5 17.9 - - - +
310D PRO* 3.9 5.6 - - + -
311D GLY* 2.9 24.9 + - - -
312D GLY 2.8 14.6 + - - +
385D TYR* 2.7 31.6 + - - +
386D ASN* 3.8 10.6 - - + +
387D MET* 3.5 13.2 - - - +
473D GLU* 1.3 76.0 - - - +
475D GLN* 1.3 70.1 + - - +
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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
------------------------------------------------------------
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