Contacts of the strand formed by residues 477 - 484 (chain D) 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 LEU 477 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379D GLU* 3.8 6.1 - - - +
380D MET* 3.0 43.5 + - + +
381D THR 3.8 2.2 - - - -
382D GLU* 3.4 48.2 - - + +
385D LEU* 3.7 15.3 - - + -
451D ARG* 4.1 20.9 - - + +
468D VAL* 5.1 3.6 - - + -
469D ALA 3.9 3.8 - - - -
470D ARG* 3.8 46.1 - - + +
476D MET* 1.3 71.5 - - - +
478D LYS* 1.3 62.0 + - - +
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Residues in contact with LYS 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D TRP* 3.5 55.5 - - + +
378D VAL 3.4 5.6 - - - -
380D MET* 4.6 2.0 - - - +
416D TRP* 6.0 1.4 - - - -
467D TYR 4.0 0.5 - - - +
468D VAL* 3.3 6.5 - - - +
469D ALA 3.0 34.7 + - - +
471D ASP* 2.6 41.8 + - + +
474D THR* 4.5 5.8 + - - +
476D MET* 3.2 26.7 - - + +
477D LEU* 1.3 76.2 - - - +
479D CYS* 1.3 59.9 + - - +
480D HIS* 3.8 24.1 + - + +
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Residues in contact with CYS 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377D TRP* 3.5 2.0 - - - -
378D VAL* 2.8 30.8 + - - +
380D MET* 3.6 23.1 - - - -
394D VAL* 4.3 8.3 - - - -
397D CYS* 3.4 32.5 - - - -
466D ALA* 4.0 23.6 - - - -
467D TYR 3.6 4.5 - - - -
468D VAL* 3.6 14.1 - - + -
478D LYS* 1.3 72.5 - - - +
480D HIS* 1.3 63.0 + - - +
481D VAL* 3.8 7.8 - - - +
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Residues in contact with HIS 480 (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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374D SER* 6.0 0.7 - - - +
376D GLY 3.5 8.6 + - - +
377D TRP* 3.3 31.8 - + + +
416D TRP* 3.5 35.5 - + + -
443D HIS* 5.9 0.4 + - - -
465D PHE 3.9 0.3 - - - +
466D ALA* 3.3 4.3 - - - -
467D TYR* 3.1 59.5 + + + -
469D ALA* 4.6 6.4 + - - +
471D ASP* 6.0 0.4 + - - -
478D LYS* 3.8 34.3 + - + +
479D CYS* 1.3 73.8 - - - +
481D VAL* 1.3 60.1 + - - +
482D PHE* 4.0 23.5 - - + -
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Residues in contact with VAL 481 (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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374D SER* 4.0 1.0 + - - -
375D LEU* 2.9 42.5 + - + +
376D GLY 3.0 8.0 + - - +
397D CYS 4.2 11.0 - - - +
398D ILE* 4.2 29.2 - - + +
401D LEU* 3.7 29.4 - - + -
464D ASP* 4.6 2.9 - - + -
465D PHE 3.4 9.6 - - - +
466D ALA* 4.3 9.2 - - + -
479D CYS* 3.8 13.9 - - - +
480D HIS* 1.3 80.4 - - - +
482D PHE* 1.3 74.0 + - - +
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Residues in contact with PHE 482 (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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372D VAL* 3.9 33.2 - - + -
373D ARG 3.2 7.9 - - - +
374D SER* 3.8 24.5 - - - -
375D LEU* 4.1 4.7 - - - +
416D TRP* 4.9 5.4 - + - -
424D LEU* 4.3 9.2 - - + -
433D LEU* 3.6 31.0 - - + -
464D ASP* 3.4 5.9 - - - +
465D PHE* 2.9 51.1 + + + +
467D TYR* 3.3 41.7 - + - -
480D HIS* 4.0 19.5 - - + -
481D VAL* 1.3 78.0 - - - +
483D ARG* 1.3 59.4 + - - +
484D CYS* 3.7 4.1 + - - -
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Residues in contact with ARG 483 (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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372D VAL* 3.5 1.1 - - - -
373D ARG* 2.7 47.8 + - + +
375D LEU* 3.9 26.3 - - + +
401D LEU 4.9 1.4 + - - -
402D SER* 3.1 30.9 + - - +
463D ARG* 4.0 34.9 - - - +
464D ASP* 3.8 21.2 + - - +
482D PHE* 1.3 70.8 - - - +
484D CYS* 1.3 63.1 + - - +
485D GLU* 4.1 0.7 + - - +
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Residues in contact with CYS 484 (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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370D PHE* 5.9 0.4 - - + -
371D ALA 3.9 6.5 - - - +
372D VAL* 3.7 21.8 - - + -
463D ARG* 2.8 43.0 + - - +
465D PHE* 3.8 31.6 - - - -
482D PHE* 4.2 2.0 - - - -
483D ARG* 1.3 76.5 - - - +
485D GLU* 1.3 60.1 + - - +
486D ALA* 3.1 24.5 - - + +
488D ALA* 4.5 4.9 - - - -
491D ILE* 3.8 13.0 - - + -
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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