Contacts of the strand formed by residues 426 - 434 (chain A) in PDB entry 3DL2
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 PHE 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297A GLU* 3.0 42.4 + - - +
300A THR* 3.5 26.9 - - + -
301A TYR* 3.7 26.0 - + + -
304A TRP* 3.6 51.6 - + + -
311A ALA* 4.6 4.7 - - + -
314A VAL 3.6 19.5 - - - -
412A SER* 4.0 3.6 - - - -
413A ALA* 3.2 16.4 - - - +
414A LEU* 3.4 39.5 - - + -
425A VAL* 1.3 77.0 - - - +
427A LEU* 1.3 62.5 + - - +
462A ILE* 4.4 1.6 - - - +
466A GLN* 5.0 1.6 - - - +
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A GLU* 4.5 2.0 - - + -
347A GLY* 3.7 26.0 - - - +
348A GLU* 3.8 5.2 - - + +
412A SER* 3.9 4.0 - - - -
413A ALA 2.9 24.7 + - - +
415A ALA* 4.1 12.5 - - + +
421A ILE* 3.6 30.7 - - + -
425A VAL* 3.9 6.3 + - + -
426A PHE* 1.3 77.0 - - - +
428A SER* 1.3 64.1 + - - +
429A LEU* 3.3 7.1 + - + +
455A LEU* 3.7 29.6 - - + +
458A SER* 3.9 11.4 - - - -
459A ALA* 4.3 6.7 - - + +
462A ILE* 3.7 27.4 - - + -
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Residues in contact with SER 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A GLU* 5.4 0.2 - - - +
318A GLY* 4.1 4.0 - - - -
319A CYS* 2.9 36.3 + - - -
346A ILE* 3.2 8.7 - - - +
347A GLY* 2.8 45.2 + - - -
410A SER* 2.7 34.2 + - - -
411A VAL 3.2 10.0 + - - -
412A SER* 4.0 1.8 + - - +
427A LEU* 1.3 71.0 - - - +
429A LEU* 1.3 63.3 + - - +
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ILE* 5.3 2.0 - - + -
410A SER* 3.9 3.8 - - - -
411A VAL 2.9 21.6 + - - +
413A ALA* 4.4 7.6 - - + +
414A LEU 4.3 4.9 - - - +
415A ALA* 4.1 20.4 - - + -
418A TYR* 4.0 29.8 - - + -
419A TYR* 3.7 33.4 - - + +
427A LEU 3.8 10.1 - - - +
428A SER* 1.3 81.7 - - - +
430A PRO* 1.3 75.5 - - + +
431A CYS* 3.1 15.4 + - - -
441A VAL* 4.2 20.2 - - + -
455A LEU* 4.8 7.6 - - + -
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Residues in contact with PRO 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A TRP* 4.1 21.3 - - + -
346A ILE* 3.7 18.8 - - + -
356A THR* 5.3 0.2 - - + -
408A VAL* 3.8 14.4 - - + -
409A HIS 3.6 5.4 - - - +
410A SER* 4.0 4.0 - - - -
419A TYR* 5.8 1.8 - - - +
429A LEU* 1.3 87.9 - - + +
431A CYS* 1.3 57.5 + - - +
441A VAL* 3.7 5.9 - - + +
442A ILE* 3.0 53.3 + - + +
444A THR* 4.0 22.4 - - + -
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Residues in contact with CYS 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A LYS 3.5 0.5 - - - +
408A VAL* 3.2 3.8 - - - +
409A HIS* 2.7 42.9 + - - +
411A VAL* 4.0 14.4 - - + -
413A ALA* 3.9 20.6 - - - -
429A LEU* 3.1 15.9 + - - -
430A PRO* 1.3 75.5 - - - +
432A ILE* 1.3 63.2 + - - +
433A LEU* 3.6 4.8 + - + +
438A VAL* 3.9 20.9 - - + -
440A GLU 3.3 7.2 - - - +
441A VAL* 3.8 24.5 - - - -
442A ILE* 5.4 0.2 - - - -
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Residues in contact with ILE 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A LYS* 3.5 37.9 - - + +
407A LYS 3.6 4.5 - - - -
408A VAL* 4.0 12.6 - - + -
431A CYS* 1.3 70.9 - - - +
433A LEU* 1.3 60.1 + - - +
438A VAL* 3.6 4.7 - - - -
439A SER* 2.9 46.6 + - - +
440A GLU* 2.8 38.1 + - + +
442A ILE* 3.8 26.0 - - + -
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Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ILE* 4.0 27.6 - - + -
397A MET* 4.5 11.2 - - + +
400A SER* 3.8 8.7 - - - +
401A ILE* 4.4 18.6 - - + -
406A LYS* 3.0 26.4 + - - -
407A LYS 3.1 14.4 + - - +
409A HIS* 3.7 35.4 - - + -
411A VAL* 4.2 6.7 - - + -
431A CYS* 4.2 12.1 - - + +
432A ILE* 1.3 77.7 - - - +
434A GLY* 1.3 58.5 + - - +
437A GLY* 3.4 7.9 - - - +
438A VAL* 3.8 29.8 - - + -
439A SER* 5.1 0.7 - - - -
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Residues in contact with GLY 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A SER 3.8 9.6 - - - -
401A ILE* 3.3 22.1 - - - +
404A ASN* 3.3 15.5 - - - -
406A LYS* 4.7 2.0 - - - -
433A LEU* 1.3 75.3 - - - +
435A THR* 1.3 66.6 + - - -
436A ASN 3.3 3.1 - - - -
437A GLY* 2.9 18.9 + - - -
439A SER* 5.2 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