Contacts of the helix formed by residues 425 - 437 (chain C) in PDB entry 1P4V
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 425 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C PRO* 4.5 12.9 + - + +
349C ARG* 4.7 1.7 + - - -
353C TYR* 3.6 33.2 - - + +
354C GLY* 3.7 19.4 + - - +
423C LEU 3.3 1.4 + - - -
424C LEU* 1.3 76.9 - - - +
426C ALA* 1.3 65.8 + - - +
427C GLU* 3.7 9.2 + - - +
428C SER* 3.2 27.9 + - - -
429C GLU* 3.0 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 426 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425C THR* 1.3 74.1 - - - +
427C GLU* 1.3 57.9 + - - +
429C GLU* 3.3 12.0 + - - +
430C LYS* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 427 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346C PRO 4.5 5.2 - - - +
347C THR* 5.2 3.5 - - - +
349C ARG* 3.3 33.0 + - - +
425C THR* 3.7 7.4 + - - +
426C ALA* 1.3 79.7 - - - +
428C SER* 1.3 56.5 + - - +
430C LYS* 3.3 6.9 + - - +
431C GLU* 2.9 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 428 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C ARG* 2.8 25.8 + - - +
354C GLY 2.9 22.3 + - - -
355C GLY 3.8 4.1 + - - -
356C ARG* 5.6 0.2 - - - -
357C PRO* 4.2 12.5 - - - +
424C LEU* 3.6 20.4 - - - +
425C THR* 3.2 17.6 + - - -
427C GLU* 1.3 77.0 - - - +
429C GLU* 1.3 58.4 + - - +
431C GLU* 3.9 1.3 - - - +
432C TRP* 2.9 30.8 + - - +
475C TYR* 4.9 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 429 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C LEU* 3.7 28.0 - - + +
425C THR 3.0 17.6 + - - +
426C ALA* 3.6 10.3 - - - +
428C SER* 1.3 75.4 - - - +
430C LYS* 1.3 64.6 + - - +
432C TRP* 3.3 9.0 + - + +
433C LYS* 3.0 56.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 430 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C ALA 2.9 17.8 + - - +
427C GLU* 3.4 8.3 - - - +
429C GLU* 1.3 78.4 + - - +
431C GLU* 1.3 65.8 + - + +
433C LYS* 3.4 7.3 + - - +
434C GLU* 3.0 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 431 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349C ARG* 2.6 30.3 + - - +
356C ARG* 2.9 31.6 + - - -
427C GLU* 2.9 29.3 + - + +
428C SER 3.9 3.1 - - - +
430C LYS* 1.3 77.8 - - + +
432C TRP* 1.3 57.0 + - - +
434C GLU* 3.2 8.6 + - - +
435C TRP* 2.8 28.9 + - - +
475C TYR* 3.6 11.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 432 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C PRO* 4.0 13.7 - - + -
358C ASP 3.9 5.8 - - - -
359C ARG 2.8 24.7 + - - -
360C ASP* 3.2 28.3 - - - -
361C GLY* 3.3 14.4 - - - -
424C LEU* 5.2 5.2 - - + -
428C SER 2.9 19.2 + - - +
429C GLU* 3.5 14.4 - - + +
430C LYS 3.2 0.2 - - - -
431C GLU* 1.3 75.3 - - - +
433C LYS* 1.3 95.8 + - + +
435C TRP* 2.9 7.4 + + - +
436C LEU* 2.9 46.9 + - + +
475C TYR* 3.7 30.7 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 433 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429C GLU* 3.0 52.3 + - + +
430C LYS* 3.8 5.6 - - + +
432C TRP* 1.3 93.0 - - + +
434C GLU* 1.3 62.6 + - - +
436C LEU* 3.3 27.0 + - + +
437C LYS* 3.7 15.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 434 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LYS* 3.0 14.7 + - + +
431C GLU* 3.4 12.8 - - - +
433C LYS* 1.3 75.6 - - - +
435C TRP* 1.3 62.3 + - - +
437C LYS* 3.0 46.5 + - - +
438C THR* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 435 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ARG* 3.4 51.8 - - + -
431C GLU 2.8 13.1 + - - +
432C TRP* 2.9 10.3 + + - +
434C GLU* 1.3 76.1 - - - +
436C LEU* 1.3 80.3 + - + +
437C LYS 3.1 1.0 + - - -
438C THR* 3.3 6.1 + - - -
439C SER* 2.9 54.6 + - - -
440C GLN* 3.0 24.1 + - + +
441C TYR* 4.0 8.4 - - - +
442C LYS 5.4 0.2 - - - +
475C TYR* 3.3 53.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359C ARG 3.6 21.8 - - - +
432C TRP* 2.9 47.5 + - + +
433C LYS* 3.4 21.3 - - + +
434C GLU 3.2 0.4 - - - -
435C TRP* 1.3 89.6 - - + +
437C LYS* 1.3 65.2 + - - +
438C THR* 3.1 1.8 + - - -
439C SER* 3.1 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 437 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433C LYS* 4.1 12.8 - - - +
434C GLU* 3.0 46.4 - - - +
435C TRP 3.1 0.2 - - - -
436C LEU* 1.3 79.1 - - - +
438C THR* 1.3 68.1 + - + +
----------------------------------------------------------
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