Contacts of the strand formed by residues 430 - 440 (chain D) in PDB entry 3DBL
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 THR 430 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D ARG 4.2 7.2 - - - -
153D TRP* 4.3 3.1 - - - +
156D GLY* 3.7 6.4 - - - -
201D GLU* 4.5 10.1 - - - +
345D ALA* 5.4 2.0 - - + +
376D MET* 4.6 12.3 - - + -
427D ASP* 3.0 20.1 + - + +
429D THR* 1.3 94.5 - - + +
431D PRO* 1.3 71.7 - - - +
432D GLN* 2.9 42.5 + - + +
434D VAL* 5.4 7.0 - - + -
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Residues in contact with PRO 431 (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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153D TRP* 3.1 57.4 - - + +
156D GLY* 3.7 3.8 - - - +
157D MET* 3.5 36.3 - - + +
160D SER* 5.6 1.1 - - - -
430D THR* 1.3 87.2 - - - +
432D GLN* 1.3 60.1 + - - +
433D THR* 5.1 1.0 + - - -
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Residues in contact with GLN 432 (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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156D GLY* 3.7 22.7 + - - +
159D ILE* 3.4 24.3 - - - +
160D SER* 3.9 13.6 - - - +
344D PRO 5.7 0.4 - - - -
345D ALA* 3.4 37.5 + - - +
425D VAL 4.5 1.9 - - - +
426D ALA* 4.8 6.1 - - - +
430D THR* 2.9 34.8 + - + +
431D PRO* 1.3 85.1 - - - +
433D THR* 1.3 62.9 + - - +
434D VAL* 3.7 7.0 + - + +
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Residues in contact with THR 433 (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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424D ALA* 3.9 26.7 - - + -
425D VAL 3.6 17.9 + - - +
426D ALA* 4.7 9.1 - - + +
431D PRO 5.1 1.0 + - - -
432D GLN* 1.3 75.0 - - - +
434D VAL* 1.3 60.9 + - - +
435D LEU* 3.3 19.0 + - + +
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Residues in contact with VAL 434 (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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344D PRO* 3.0 44.0 - - + +
351D GLN* 6.0 0.4 - - + -
376D MET* 3.5 29.8 - - + -
423D LEU 4.0 0.2 - - - +
425D VAL* 3.1 42.5 + - + +
430D THR* 5.4 6.5 - - + -
432D GLN* 3.7 6.6 + - + +
433D THR* 1.3 70.7 - - - +
435D LEU* 1.3 70.5 + - - +
436D PHE* 4.2 15.4 - - + -
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Residues in contact with LEU 435 (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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350D PRO* 3.6 33.2 - - + +
351D GLN 3.3 13.3 + - - -
422D GLU* 3.9 22.4 - - + +
423D LEU 3.6 3.4 - - - +
424D ALA* 4.1 24.7 - - + -
433D THR* 3.3 19.5 + - + +
434D VAL* 1.3 77.6 - - - +
436D PHE* 1.3 75.5 + - - +
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Residues in contact with PHE 436 (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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344D PRO* 5.5 0.2 - - + -
350D PRO* 4.7 1.1 - - - -
351D GLN* 3.5 39.3 - - + +
353D ILE* 3.9 29.2 - - + -
364D VAL* 6.4 0.9 - - + -
368D LEU* 3.4 34.1 - - + -
374D LEU* 4.4 13.0 - - + -
376D MET* 5.0 3.4 - - + -
422D GLU* 2.9 6.1 - - - -
423D LEU* 2.6 47.0 + - + +
425D VAL* 3.7 34.5 - - + -
434D VAL* 4.2 22.9 - - + -
435D LEU* 1.3 84.9 - - - +
437D LYS* 1.3 61.5 + - - +
438D LEU 3.8 1.0 + - - -
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Residues in contact with LYS 437 (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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349D LEU* 5.2 6.5 - - - +
350D PRO* 3.9 27.9 + - + +
351D GLN 2.7 9.4 + - - +
352D ASN* 3.4 28.1 + - - +
353D ILE 3.2 20.6 + - - -
420D GLY 5.9 1.8 - - - -
421D GLN* 4.0 5.6 - - - +
422D GLU* 3.6 36.8 - - + +
436D PHE* 1.3 70.5 - - - +
438D LEU* 1.3 62.9 + - - +
439D HIS* 3.6 17.7 + - + +
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Residues in contact with LEU 438 (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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353D ILE* 4.2 22.4 - - + -
355D PHE* 4.2 22.7 - - + +
364D VAL* 5.9 1.3 - - + -
412D LEU* 4.5 4.3 - - + -
417D LEU* 4.2 22.7 - - + -
418D VAL 4.4 7.4 - - - +
419D ASP* 3.4 11.3 - - - +
420D GLY* 3.7 13.5 + - - -
421D GLN* 3.1 19.9 + - + +
423D LEU* 4.3 22.2 - - + -
436D PHE 3.8 2.8 + - - -
437D LYS* 1.3 71.9 - - - +
439D HIS* 1.3 73.0 + - - +
440D PHE* 3.3 40.8 - - + -
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Residues in contact with HIS 439 (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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352D ASN* 3.4 25.0 + - + -
353D ILE 3.1 14.2 + - - +
354D GLN* 3.5 26.9 - - - +
355D PHE 3.3 21.1 + - - +
419D ASP* 4.0 3.6 + - - -
420D GLY* 5.3 8.7 - - - -
437D LYS* 3.7 25.7 + - + +
438D LEU* 1.3 78.8 + - - +
440D PHE* 1.3 65.8 + - - +
441D THR* 3.4 11.5 + - + -
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Residues in contact with PHE 440 (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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355D PHE 3.1 11.9 - - - -
357D PRO* 3.2 33.7 - - + -
412D LEU* 3.5 29.8 - - + -
413D LYS* 4.3 10.5 - - + -
417D LEU 3.1 28.5 - - - -
418D VAL 3.5 16.4 - - - -
419D ASP* 3.0 39.0 + - + +
438D LEU* 3.3 28.3 - - + -
439D HIS* 1.3 69.3 - - - +
441D THR* 1.3 68.4 + - - +
442D SER 4.2 0.4 - - - -
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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