Contacts of the strand formed by residues 438 - 446 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C VAL* 5.9 1.4 + - - +
146C GLU* 4.7 20.2 + - + +
150C ILE* 4.9 9.2 - - + +
409C LEU* 4.3 21.6 - - + -
410C LEU* 3.2 28.6 + - - +
411C PRO* 3.2 11.0 - - - +
434C TYR* 3.7 1.7 - - - -
435C HIS* 2.9 44.2 + - + +
436C GLY 3.0 4.7 + - - +
437C ASN* 1.3 88.0 + - - +
439C VAL* 1.3 67.9 + - - +
465C TYR 5.3 0.5 - - - +
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Residues in contact with VAL 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408C MET 3.4 5.7 - - - +
409C LEU* 3.5 7.0 - - - +
410C LEU* 2.8 43.3 + - + +
411C PRO 4.9 0.2 - - - -
412C GLN* 4.3 10.1 - - + -
415C LEU* 3.8 17.3 - - + -
432C MET* 3.7 37.7 - - + -
433C VAL 3.6 11.0 - - - +
434C TYR* 3.7 29.2 - - + +
435C HIS* 4.9 0.2 - - - -
438C GLN* 1.3 80.3 - - - +
440C ALA* 1.3 64.4 + - - +
441C LEU* 3.5 5.3 + - + +
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Residues in contact with ALA 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ILE* 5.4 1.3 - - + -
408C MET 3.5 5.6 - - - -
409C LEU* 3.9 14.1 - - + -
431C ASN 4.2 0.2 - - - +
432C MET* 3.6 4.3 - - - -
433C VAL* 2.8 42.4 + - + +
435C HIS* 3.6 29.3 + - + +
439C VAL* 1.3 71.2 - - - +
441C LEU* 1.3 62.5 + - - +
442C THR* 3.9 3.6 + - - +
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Residues in contact with LEU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406C CYS 4.4 0.2 - - - -
407C HIS* 3.5 1.4 - - - +
408C MET* 2.6 70.1 + - + +
410C LEU* 4.1 21.3 - - + -
415C LEU* 5.3 1.8 - - + -
418C VAL* 4.1 6.5 - - + -
419C ILE* 3.8 24.7 - - + -
429C GLN* 4.0 20.2 - - - +
431C ASN 4.1 4.9 - - - +
432C MET* 4.0 19.1 - - + -
439C VAL* 3.5 2.7 + - + -
440C ALA* 1.3 75.1 - - - +
442C THR* 1.3 66.5 + - - +
443C TYR* 3.7 26.5 - - + -
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Residues in contact with THR 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405C GLU* 4.0 14.4 + - - +
406C CYS 3.1 10.2 + - - -
407C HIS* 4.1 17.4 + - + -
429C GLN* 4.3 0.3 - - - +
430C THR* 3.0 38.6 + - + +
431C ASN* 3.3 50.8 + - + +
433C VAL* 6.2 0.2 - - + -
440C ALA 4.6 3.4 - - - +
441C LEU* 1.3 77.1 - - - +
443C TYR* 1.3 63.5 + - - +
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Residues in contact with TYR 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404C ALA 3.6 0.9 - - - +
405C GLU* 3.6 3.5 - - - +
406C CYS* 2.8 34.6 + - + +
408C MET* 4.4 7.7 - - + +
419C ILE* 3.9 19.5 - - + +
422C CYS* 3.7 34.1 - - + -
423C VAL* 3.9 12.8 - - + +
427C GLY* 3.6 17.3 - - - -
428C VAL 3.3 23.1 - - - -
429C GLN* 3.0 48.4 + - + +
430C THR* 4.6 0.7 - - - -
441C LEU* 3.7 22.4 - - + -
442C THR* 1.3 76.4 - - - +
444C GLU* 1.3 60.8 + - - +
445C ILE* 3.7 18.1 + - + -
434D TYR* 3.6 11.1 + - - -
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Residues in contact with GLU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C ILE* 3.8 14.7 - - + +
404C ALA 3.4 5.6 - - - +
405C GLU* 4.8 9.8 - - + +
426C ARG 4.5 0.3 - - - +
427C GLY* 3.5 1.6 - - - -
428C VAL* 2.8 42.4 + - + +
430C THR* 3.5 29.4 + - + +
443C TYR* 1.3 71.3 - - - +
445C ILE* 1.3 62.4 + - - +
446C PRO* 4.0 2.6 - - - +
473C LYS* 3.5 26.4 - - - +
474C ARG* 2.6 41.1 + - - -
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Residues in contact with ILE 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403C ILE* 4.2 1.8 - - - -
404C ALA* 2.7 40.0 + - - +
406C CYS* 3.7 22.9 - - + -
408C MET* 5.4 0.4 - - - -
422C CYS* 3.9 21.3 - - + +
425C LYS* 3.5 26.5 - - + +
427C GLY* 4.1 8.3 - - - -
443C TYR* 3.8 15.7 - - + -
444C GLU* 1.3 76.5 - - - +
446C PRO* 1.3 74.0 - - + +
447C MET 3.2 0.2 + - - -
449C GLU* 4.4 4.7 - - + -
450C VAL* 3.7 14.6 - - + +
454C PHE* 3.8 29.4 - - + -
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Residues in contact with PRO 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401C GLU* 3.3 26.0 - - - +
402C PRO 3.8 6.5 - - - +
403C ILE* 3.9 12.3 - - + -
425C LYS 3.6 4.0 - - - +
426C ARG* 3.4 56.8 - - + +
444C GLU 4.0 2.2 - - - +
445C ILE* 1.3 89.8 - - + +
447C MET* 1.3 65.2 + - - +
449C GLU* 3.0 20.4 + - + +
450C VAL* 3.1 11.1 + - - +
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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