Contacts of the helix formed by residues 433 - 445 (chain C) in PDB entry 3VBB
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 433 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C GLU* 2.9 35.9 + - + +
207C LEU* 4.5 6.1 - - + -
208C ILE* 3.7 33.0 - - + -
322C GLU* 2.9 31.0 + - + +
324C ILE* 4.3 12.6 - - + -
431C CYS* 3.7 11.4 - - - -
432C ALA* 1.3 71.1 - - - +
434C THR* 1.3 64.2 + - - +
436C THR* 3.6 1.0 - - - -
437C ILE* 2.7 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C TYR* 3.6 28.7 - - + +
196C LEU* 5.7 6.1 - - + -
204C GLU* 4.7 7.0 - - - +
315C ILE* 3.4 33.0 + - + +
316C PHE 4.3 3.6 + - - -
318C VAL* 4.2 3.9 - - + +
321C PHE* 3.8 26.5 - - + +
432C ALA* 3.0 2.2 + - - +
433C THR* 1.3 83.1 + - - +
435C ARG* 1.3 70.0 + - - +
437C ILE* 3.2 9.6 + - - +
438C CYS* 3.1 26.6 + - - -
224D TYR* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 435 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ARG* 6.0 1.6 - - - +
315C ILE 4.9 0.2 + - - -
316C PHE* 2.9 72.2 + - + +
317C ARG* 5.6 4.6 - - - +
321C PHE* 6.5 0.2 - - - -
323C LYS* 6.1 1.1 - - - +
383C PHE* 3.9 9.5 - - - -
391C GLU* 2.6 45.6 + - - +
392C LEU* 3.8 16.1 - - + +
432C ALA* 3.0 23.4 + - + +
434C THR* 1.3 82.0 + - - +
436C THR* 1.3 61.4 + - - +
438C CYS* 3.2 6.1 + - - +
439C ALA* 3.2 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 436 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU* 3.6 30.7 - - + -
352C TYR* 3.1 36.5 + - + -
355C LEU* 4.9 3.4 - - + -
357C ILE* 6.1 0.7 - - + -
392C LEU* 4.1 13.3 - - + +
431C CYS* 3.4 12.6 - - - -
432C ALA 3.0 17.5 + - - -
433C THR 3.7 2.5 - - - -
435C ARG* 1.3 73.3 - - - +
437C ILE* 1.3 67.3 + - - +
439C ALA* 3.1 2.9 + - + +
440C ILE* 2.9 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 437 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C LEU* 5.9 3.4 - - + -
200C LEU* 4.3 16.4 - - + +
203C LEU* 3.3 44.6 - - + -
204C GLU* 4.0 16.4 - - + +
207C LEU* 3.4 21.5 - - + -
315C ILE* 4.1 18.2 - - + -
433C THR 2.7 32.2 + - - +
434C THR* 3.4 8.7 - - - +
436C THR* 1.3 73.6 - - - +
438C CYS* 1.3 57.9 + - - +
440C ILE* 3.2 5.2 + - + +
441C LEU* 2.9 38.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 438 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C HIS* 3.5 39.6 - - + +
174C VAL* 5.4 1.8 - - - -
315C ILE* 3.4 34.3 - - - -
316C PHE* 4.2 15.3 - - + -
383C PHE* 3.6 9.4 - - + -
434C THR 3.1 13.0 + - - -
435C ARG 3.6 8.1 - - - +
436C THR 3.2 0.4 - - - -
437C ILE* 1.3 77.4 - - - +
439C ALA* 1.3 56.5 + - - +
441C LEU* 3.9 4.7 - - - +
442C GLU* 3.2 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 439 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C ILE* 4.1 16.4 - - + -
383C PHE* 3.4 33.1 - - + -
392C LEU* 4.0 18.2 - - + -
435C ARG 3.2 6.9 + - - +
436C THR* 3.1 8.1 + - + +
438C CYS* 1.3 73.6 - - - +
440C ILE* 1.3 65.8 + - + +
442C GLU* 3.5 0.9 + - - +
443C ASN* 3.1 34.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 440 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C LEU* 4.6 15.5 - - + -
207C LEU* 4.2 12.1 - - + -
355C LEU* 4.8 9.6 - - + -
357C ILE* 3.9 20.6 - - + -
436C THR* 2.9 34.0 + - + +
437C ILE* 3.5 11.2 - - + +
439C ALA* 1.3 76.3 - - - +
441C LEU* 1.3 59.3 + - + +
444C TYR* 2.9 33.5 + - + +
450C ILE* 5.2 3.6 - - + -
453C PRO* 3.9 31.0 - - + -
456C LEU* 4.1 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 441 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C HIS* 4.6 4.7 - - + +
173C LEU* 3.4 31.3 - - + +
174C VAL* 4.0 29.6 - - + +
177C VAL* 5.2 2.2 - - + -
200C LEU* 4.4 11.9 - - + -
203C LEU* 4.2 20.4 - - + -
437C ILE* 2.9 29.7 + - + +
438C CYS* 3.9 9.0 - - - +
440C ILE* 1.3 76.3 - - + +
442C GLU* 1.3 64.1 + - - +
445C GLN* 3.0 28.9 + - - +
450C ILE* 3.4 30.3 - - + +
468C ILE* 5.9 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 442 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C LYS* 3.9 5.5 - - - +
168C TYR 4.2 0.7 - - - +
169C SER* 3.2 6.2 - - - -
170C HIS* 2.7 37.8 + - + +
173C LEU* 3.7 1.8 - - - -
383C PHE* 2.9 32.1 - - + +
384C PRO* 3.9 18.9 - - + +
385C GLY 3.0 17.7 + - - +
386C SER* 2.7 27.9 + - - -
438C CYS 3.2 18.1 + - - +
439C ALA 4.2 2.2 - - - +
440C ILE 3.5 0.2 - - - -
441C LEU* 1.3 78.8 - - - +
443C ASN* 1.3 61.3 + - - +
445C GLN* 2.8 25.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 443 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C VAL* 5.1 1.0 - - - +
166C LYS* 2.9 27.0 + - - -
356C GLY 4.9 1.8 - - - +
357C ILE* 3.8 15.1 - - + +
358C PRO* 3.5 30.5 - - + +
382C TRP 3.1 18.6 + - - -
384C PRO* 2.6 33.7 - - - +
439C ALA* 3.1 26.3 + - - +
440C ILE 4.2 0.9 - - - +
442C GLU* 1.3 80.5 - - - +
444C TYR* 1.3 69.2 + - + +
445C GLN 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 444 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354C SER 5.0 0.7 + - - -
355C LEU 2.7 34.9 + - - -
356C GLY* 3.8 16.9 - - - -
357C ILE* 4.4 5.4 - - + -
440C ILE* 2.9 25.4 + - + +
441C LEU 3.8 0.7 - - - -
443C ASN* 1.3 83.2 - - + +
445C GLN* 1.3 63.4 + - - +
446C THR* 3.7 0.5 - - - +
450C ILE* 4.3 5.4 - - + -
451C THR* 3.0 65.8 + - + +
452C VAL 4.5 1.3 - - - -
453C PRO* 3.5 36.6 - - + +
454C GLU 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 445 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C LYS* 3.6 28.6 + - + +
167C LYS* 3.5 9.5 - - - +
168C TYR* 2.7 62.8 - - + +
173C LEU* 3.9 16.5 - - + +
385C GLY* 5.1 0.2 - - - -
441C LEU 3.0 11.5 + - - +
442C GLU* 2.8 26.9 - - - +
443C ASN 3.4 2.2 - - - -
444C TYR* 1.3 78.2 - - - +
446C THR* 1.3 68.7 + - - +
449C GLY 4.0 5.4 - - - -
450C ILE* 4.1 4.3 - - + -
470C PHE* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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