Contacts of the strand formed by residues 438 - 446 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108E VAL 5.3 6.5 + - - -
146E GLU* 5.5 5.5 + - - -
150E ILE* 5.4 7.5 - - + +
409E LEU* 3.6 29.7 - - + +
410E LEU* 3.9 6.7 + - - +
411E PRO* 3.9 23.6 - - - +
434E TYR* 3.4 5.9 - - - -
435E HIS* 2.7 50.0 + - + +
437E ASN* 1.3 85.7 + - - +
439E VAL* 1.3 65.2 + - - +
440E ALA 4.3 0.2 - - - -
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Residues in contact with VAL 439 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E MET 3.4 3.6 - - - +
409E LEU* 3.5 6.6 - - - +
410E LEU* 2.9 45.2 + - + +
411E PRO 4.4 0.9 - - - +
412E GLN* 3.7 27.4 - - + -
415E LEU* 3.7 18.2 - - + -
432E MET* 3.7 39.5 - - + -
433E VAL 3.4 4.7 - - - +
434E TYR* 3.9 8.3 - - + -
438E GLN* 1.3 78.0 - - - +
440E ALA* 1.3 61.4 + - - +
441E LEU* 3.4 15.0 + - + +
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Residues in contact with ALA 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E MET 3.6 6.3 - - - -
409E LEU* 4.1 13.0 - - + -
431E ASN* 3.7 1.6 + - - +
432E MET* 3.5 5.9 + - - -
433E VAL* 2.6 40.3 + - + +
435E HIS* 3.5 30.0 + - + +
438E GLN 4.3 0.2 - - - -
439E VAL* 1.3 69.1 - - - +
441E LEU* 1.3 63.3 + - - +
442E THR* 3.6 5.9 + - - +
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Residues in contact with LEU 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407E HIS* 3.8 0.2 - - - -
408E MET* 2.6 68.0 + - + +
410E LEU* 3.9 19.3 - - + -
415E LEU* 4.6 5.8 - - + -
418E VAL* 3.8 13.5 - - + -
419E ILE* 3.7 21.8 - - + -
429E GLN* 3.8 18.2 - - - +
431E ASN 3.8 3.8 - - - +
432E MET* 4.5 9.0 - - + +
439E VAL* 3.4 12.4 + - + +
440E ALA* 1.3 72.8 - - - +
442E THR* 1.3 59.4 + - - +
443E TYR* 3.5 31.0 - - + -
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Residues in contact with THR 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405E GLU* 3.9 17.2 - - - +
406E CYS 3.2 9.3 + - - -
407E HIS* 3.9 19.3 - - + -
429E GLN* 4.0 0.3 - - - -
430E THR* 2.9 35.0 + - + +
431E ASN* 3.0 58.0 + - + +
440E ALA* 4.2 3.4 - - + +
441E LEU* 1.3 75.6 - - - +
443E TYR* 1.3 62.6 + - - +
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Residues in contact with TYR 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E ALA 3.6 0.3 - - - +
405E GLU* 3.5 3.8 - - - +
406E CYS* 2.8 39.7 + - - +
408E MET* 4.2 5.4 - - + +
419E ILE* 3.1 26.2 - - + +
422E CYS* 3.6 34.5 - - + -
423E VAL* 4.0 12.9 - - + +
427E GLY* 3.9 9.9 - - - -
428E VAL 3.5 26.0 - - - -
429E GLN* 3.1 48.0 + - + +
430E THR* 4.6 0.9 - - - -
441E LEU* 3.5 22.4 - - + -
442E THR* 1.3 76.2 + - - +
444E GLU* 1.3 59.5 + - - +
445E ILE* 3.9 18.6 - - + -
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Residues in contact with GLU 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E ILE* 4.0 12.2 - - + +
404E ALA 3.3 7.9 - - - +
405E GLU* 4.6 9.9 - - + +
426E ARG 4.2 0.3 - - - +
427E GLY* 3.4 1.9 - - - -
428E VAL* 2.7 54.6 + - + +
430E THR* 3.7 22.1 + - - +
443E TYR* 1.3 73.9 - - - +
445E ILE* 1.3 60.9 + - - +
446E PRO* 4.2 2.4 - - - +
473E LYS* 3.5 30.2 + - + -
474E ARG* 3.1 26.8 + - - -
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Residues in contact with ILE 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403E ILE* 4.4 2.0 - - - -
404E ALA* 2.7 41.0 + - - +
406E CYS* 3.7 19.3 - - + -
408E MET* 5.5 0.2 - - - -
422E CYS* 3.7 21.5 - - + -
425E LYS* 3.5 31.9 - - + +
427E GLY* 4.1 9.9 - - - -
443E TYR* 4.0 13.5 - - + -
444E GLU* 1.3 77.3 - - - +
446E PRO* 1.3 75.6 - - - +
449E GLU* 4.3 2.9 - - + -
450E VAL* 4.0 12.8 - - + +
454E PHE* 3.7 30.5 - - + -
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Residues in contact with PRO 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401E GLU* 3.1 29.6 - - - +
402E PRO 3.6 6.3 - - - +
403E ILE* 4.0 13.9 - - + -
425E LYS 3.8 3.1 - - - +
426E ARG* 3.3 54.5 - - - +
444E GLU 4.2 2.0 - - - +
445E ILE* 1.3 88.2 - - + +
447E MET* 1.3 65.6 + - - +
449E GLU* 3.0 21.1 + - + +
450E VAL* 3.3 6.1 + - - +
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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