Contacts of the strand formed by residues 438 - 446 (chain D) in PDB entry 3CB4
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 GLN 438 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108D VAL 5.4 6.0 - - - +
146D GLU* 5.9 3.4 + - - -
150D ILE* 4.9 9.6 - - + -
409D LEU* 3.7 26.9 - - + +
410D LEU* 3.6 23.9 + - - +
411D PRO* 4.1 9.5 - - - +
412D GLN* 4.4 1.0 - - - +
434D TYR* 4.8 0.2 - - - -
435D HIS* 2.8 46.2 + - + +
437D ASN* 1.3 88.1 + - - +
439D VAL* 1.3 64.5 + - - +
440D ALA 3.4 2.1 + - - -
465D TYR 5.0 1.9 - - - +
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Residues in contact with VAL 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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408D MET 3.7 0.2 - - - +
409D LEU* 3.6 2.6 - - - -
410D LEU* 2.7 41.7 + - + +
412D GLN* 3.6 33.7 - - + -
415D LEU* 3.7 17.7 - - + -
432D MET* 3.7 34.8 - - + -
433D VAL 3.6 8.5 - - - +
434D TYR* 3.7 18.6 - - + +
437D ASN 4.0 0.2 - - - -
438D GLN* 1.3 70.7 - - - +
440D ALA* 1.3 60.8 + - - +
441D LEU* 3.4 17.8 + - + +
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Residues in contact with ALA 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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150D ILE* 5.8 0.4 - - + -
408D MET 3.4 6.5 - - - -
409D LEU* 3.9 16.6 - - + -
432D MET* 3.8 2.9 - - - -
433D VAL* 2.6 40.9 + - + +
435D HIS* 3.6 26.2 - - + +
438D GLN 3.4 1.2 + - - -
439D VAL* 1.3 69.8 - - - +
441D LEU* 1.3 63.2 + - - +
442D THR* 3.8 5.5 + - - +
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Residues in contact with LEU 441 (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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406D CYS 4.3 0.7 - - - -
407D HIS* 3.5 1.0 - - - +
408D MET* 2.6 69.6 + - + +
409D LEU* 5.6 0.2 - - - +
410D LEU* 3.8 21.8 - - + -
415D LEU* 5.0 0.9 - - + +
418D VAL* 4.2 7.0 - - + -
419D ILE* 3.7 24.9 - - + -
429D GLN* 4.2 14.8 - - - +
431D ASN 4.3 4.0 - - - +
432D MET* 4.4 10.5 - - + +
439D VAL* 3.4 15.6 + - + -
440D ALA* 1.3 74.3 - - - +
442D THR* 1.3 60.7 + - - +
443D TYR* 3.6 31.9 - - + -
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Residues in contact with THR 442 (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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405D GLU* 4.3 7.8 + - - +
406D CYS 3.2 8.3 + - - -
407D HIS* 3.8 24.8 - - + -
429D GLN* 4.0 1.0 - - - +
430D THR* 3.0 37.5 + - + +
431D ASN* 3.2 54.5 + - + +
440D ALA 4.3 4.9 - - - +
441D LEU* 1.3 78.3 - - - +
443D TYR* 1.3 60.6 + - - +
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Residues in contact with TYR 443 (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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415C LEU* 3.9 5.5 - - - +
405D GLU* 3.6 1.0 - - - -
406D CYS* 2.7 42.6 + - - +
408D MET* 5.3 3.3 - - + +
419D ILE* 3.2 30.3 - - + +
422D CYS* 3.6 35.0 - - + -
423D VAL* 3.8 14.6 - - + +
427D GLY* 3.7 12.8 - - - -
428D VAL 3.3 25.4 - - - -
429D GLN* 3.3 36.8 + - + +
430D THR* 4.9 0.9 - - - -
441D LEU* 3.6 34.5 - - + -
442D THR* 1.3 75.2 + - - +
444D GLU* 1.3 58.4 + - - +
445D ILE* 3.8 18.2 - - + -
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Residues in contact with GLU 444 (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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403D ILE* 4.2 15.6 - - + +
404D ALA 3.6 2.5 - - - -
405D GLU* 4.5 14.8 - - + +
427D GLY* 3.4 1.0 - - - -
428D VAL* 2.6 52.9 + - + +
430D THR* 3.7 25.5 + - + +
443D TYR* 1.3 71.5 - - - +
445D ILE* 1.3 59.2 + - - +
446D PRO* 4.2 2.4 - - - +
473D LYS* 3.6 25.2 - - + -
474D ARG* 2.7 31.9 + - - -
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Residues in contact with ILE 445 (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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403D ILE* 4.3 1.8 - - - -
404D ALA* 2.8 41.7 + - - +
406D CYS* 3.8 22.2 - - + -
408D MET* 5.3 0.7 - - - -
422D CYS* 4.0 13.7 - - + -
425D LYS* 3.4 28.0 - - + +
427D GLY* 3.9 9.9 - - - -
443D TYR* 3.8 23.8 - - + -
444D GLU* 1.3 78.1 - - - +
446D PRO* 1.4 73.2 - - + +
447D MET 3.3 0.2 + - - -
449D GLU* 4.3 5.4 - - + -
450D VAL* 3.9 13.9 - - + +
454D PHE* 3.9 26.5 - - + -
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Residues in contact with PRO 446 (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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401D GLU* 3.3 28.5 - - - +
402D PRO 3.6 6.3 - - - +
403D ILE* 3.8 14.8 - - + -
425D LYS 3.9 2.9 - - - +
426D ARG* 3.4 53.6 - - + +
444D GLU 4.2 1.8 - - - +
445D ILE* 1.4 91.1 - - + +
447D MET* 1.3 60.7 + - - +
449D GLU* 2.9 24.4 + - + +
450D VAL* 3.2 9.7 + - - +
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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