Contacts of the strand formed by residues 368 - 379 (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 LYS 368 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377C TRP* 3.7 4.7 - - - -
378C VAL* 4.0 22.0 - - + -
400C GLN* 3.7 24.4 + - - +
366D GLY 3.3 31.9 - - - +
367D ILE* 1.3 83.2 - - - +
369D CYS* 1.3 60.0 + - - +
370D PHE* 3.6 31.6 - - + -
425D GLN* 3.3 2.4 - - - -
426D LEU* 3.0 35.4 + - + -
493D THR* 6.1 1.0 - - - +
494D SER* 3.0 33.3 + - - +
497D GLU* 4.6 11.9 + - - +
498D ILE* 6.4 1.3 - - + -
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Residues in contact with CYS 369 (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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375C LEU 3.8 0.7 - - - +
376C GLY* 3.3 8.1 - - - -
377C TRP* 2.8 69.4 + - + +
378C VAL* 4.9 0.2 - - - +
401C LEU* 4.1 3.0 - - - +
368D LYS* 1.3 75.9 - - - +
370D PHE* 1.3 60.3 + - - +
423D LEU* 3.7 35.4 - - - -
424D LEU 3.7 4.0 - - - -
425D GLN* 3.6 25.4 - - + -
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Residues in contact with PHE 370 (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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375C LEU 4.0 3.4 - - - -
400C GLN* 3.8 19.3 - - - -
401C LEU* 3.4 27.4 - - + -
368D LYS* 3.6 28.9 - - + -
369D CYS* 1.3 74.3 - - - +
371D ALA* 1.3 61.3 + - - +
372D VAL* 3.5 10.6 + - + +
423D LEU* 4.6 2.2 - - - -
424D LEU* 3.0 43.4 + - + +
426D LEU* 4.4 18.2 - - + -
484D CYS* 5.8 0.9 - - + -
486D ALA* 4.4 12.6 - - + -
490D ASN* 4.4 6.3 - - + -
491D ILE* 3.8 44.6 - - + -
494D SER* 3.9 14.1 - - - -
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Residues in contact with ALA 371 (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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374C SER 3.5 19.1 - - - +
375C LEU* 3.1 23.8 + - - +
369D CYS 3.9 0.6 + - - -
370D PHE* 1.3 70.0 - - - +
372D VAL* 1.3 63.0 + - - +
422D LEU 3.6 8.5 - - - +
423D LEU* 4.3 12.4 - - + +
484D CYS* 3.9 0.3 - - - +
485D GLU* 3.2 36.1 + - + +
486D ALA 5.0 0.2 + - - -
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Residues in contact with VAL 372 (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* 3.6 16.4 - - + +
371D ALA* 1.3 81.2 - - - +
373D ARG* 1.3 60.9 + - - +
420D LYS 3.9 0.2 - - - +
421D ASP* 3.7 2.6 - - - +
422D LEU* 2.8 43.7 + - + +
424D LEU* 4.0 29.6 - - + -
433D LEU* 5.0 0.7 - - + -
482D PHE* 3.9 35.2 - - + -
483D ARG 3.5 7.6 - - - +
484D CYS* 3.7 24.2 - - - -
485D GLU* 5.8 0.2 - - - -
491D ILE* 4.5 0.2 - - + -
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Residues in contact with ARG 373 (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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373C ARG* 4.8 15.0 - - - +
420C LYS 5.5 2.0 - - - +
372D VAL* 1.3 71.8 - - - +
374D SER* 1.3 68.3 + - - +
375D LEU* 3.4 10.4 + - - +
419D GLY* 3.4 35.1 + - - +
420D LYS 3.2 7.2 - - - +
421D ASP* 2.9 36.6 + - - +
482D PHE* 3.2 3.5 - - - -
483D ARG* 2.7 51.7 + - + +
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Residues in contact with SER 374 (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* 4.1 1.4 + - - +
373D ARG* 1.3 72.4 - - - +
375D LEU* 1.3 61.7 + - - +
376D GLY* 3.3 7.2 + - - -
416D TRP* 2.8 23.3 + - - -
417D GLY 3.0 22.3 + - - -
418D GLU* 3.2 0.9 - - - -
419D GLY* 2.7 30.1 + - - -
420D LYS 2.7 14.2 + - - -
422D LEU* 4.2 10.0 - - - +
480D HIS* 6.0 0.9 - - - +
481D VAL 4.0 3.7 + - - -
482D PHE* 3.8 18.7 - - - -
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Residues in contact with LEU 375 (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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373D ARG* 3.4 10.5 + - - +
374D SER* 1.3 77.4 - - - +
376D GLY* 1.3 58.5 + - - +
398D ILE 6.0 0.2 - - - +
401D LEU* 4.2 39.6 - - + +
402D SER* 5.3 0.2 - - - -
418D GLU* 3.0 25.7 - - - +
419D GLY 4.8 0.7 - - - +
464D ASP* 4.4 11.4 - - - +
481D VAL* 2.9 34.7 + - + +
482D PHE 4.1 0.9 - - - +
483D ARG* 3.9 46.9 - - + +
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Residues in contact with GLY 376 (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* 3.3 9.6 + - - -
375D LEU* 1.3 81.3 - - - +
377D TRP* 1.3 65.4 + - - +
401D LEU* 4.3 4.5 - - - -
417D GLY* 4.9 2.2 - - - -
418D GLU* 3.5 23.0 - - - +
480D HIS* 3.5 3.3 - - - +
481D VAL* 3.0 28.7 + - - +
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Residues in contact with TRP 377 (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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376D GLY* 1.3 75.3 - - - +
378D VAL* 1.3 87.5 + - - +
379D GLU* 3.8 20.2 - - + -
401D LEU* 4.6 5.7 - - - +
416D TRP* 5.8 2.0 - + - -
417D GLY* 6.4 1.8 - - - -
418D GLU* 4.7 3.2 + - - +
476D MET* 4.2 15.9 - - + -
478D LYS* 3.5 41.7 - - + +
479D CYS 3.5 11.0 - - - +
480D HIS* 3.3 35.0 - + + +
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Residues in contact with VAL 378 (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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377D TRP* 1.3 84.6 - - - +
379D GLU* 1.3 76.3 + - + +
397D CYS* 3.8 46.7 - - + +
400D GLN* 4.0 28.0 - - - +
401D LEU* 4.3 16.4 - - + -
478D LYS* 3.4 3.8 - - - -
479D CYS* 2.8 32.1 + - - +
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Residues in contact with GLU 379 (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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377D TRP* 3.7 11.4 - - + -
378D VAL* 1.3 91.7 - - + +
380D MET* 1.3 71.6 + - - +
384D GLU* 4.9 1.2 - - - +
397D CYS* 4.4 0.9 - - - -
476D MET* 3.4 43.0 - - + +
477D LEU 3.8 4.3 - - - +
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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