Contacts of the helix formed by residues 444 - 454 (chain A) in PDB entry 4N22
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 444 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A SER 4.6 9.2 - - - +
402A VAL* 4.0 12.7 - - + +
406A ASP* 2.6 36.6 + - - +
442A ARG 3.6 2.2 + - - +
443A MET* 1.3 74.7 - - - +
445A LYS* 1.3 65.0 + - - +
446A VAL* 4.1 10.5 + - - +
447A VAL* 3.1 27.2 + - - +
448A ARG* 3.0 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 445 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLU* 4.3 17.6 + - - +
443A MET 3.4 2.2 + - - -
444A THR* 1.3 72.4 - - - +
446A VAL* 1.3 57.3 + - + +
448A ARG* 3.5 28.7 - - - +
449A ASP* 2.7 66.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 446 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASP* 4.3 7.4 - - - +
444A THR* 3.1 10.7 - - - +
445A LYS* 1.3 81.2 - - + +
447A VAL* 1.3 62.5 + - + +
449A ASP* 3.8 4.9 - - - +
450A PHE* 3.0 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ASP* 5.3 7.9 - - + +
408A PHE* 5.2 14.8 - - + -
411A LEU* 5.8 0.9 - - + -
443A MET* 3.4 29.2 - - + -
444A THR* 3.1 22.2 + - - +
446A VAL* 1.3 80.8 - - + +
448A ARG* 1.3 65.3 + - - +
450A PHE* 3.3 10.5 + - + +
451A LEU* 3.0 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A ILE* 4.6 10.5 - - + +
442A ARG* 3.4 45.0 - - - +
443A MET* 2.9 38.0 + - + +
444A THR 3.0 11.9 + - - +
445A LYS* 3.5 36.4 - - - +
447A VAL* 1.3 77.4 - - - +
449A ASP* 1.3 61.4 + - - +
451A LEU* 3.3 8.9 + - - +
452A LYS* 3.0 29.1 + - - +
461A GLU* 3.3 26.5 - - - -
701A ACT 3.6 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASP* 4.0 4.5 - - - +
260A GLU* 3.5 36.3 + - + +
445A LYS* 2.7 64.3 + - - +
446A VAL* 3.8 5.3 - - - +
448A ARG* 1.3 74.6 + - - +
450A PHE* 1.3 60.0 + - - +
452A LYS* 3.4 21.4 + - - +
453A ALA* 2.9 32.1 + - - +
701A ACT 5.3 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A PHE* 3.7 23.1 - + + -
258A PRO 4.1 6.3 - - - -
259A ASP* 3.6 22.8 + - - +
297A TRP* 3.9 43.5 - + + -
369A LEU* 4.1 21.8 - - + -
393A VAL* 6.1 3.1 - - + -
446A VAL* 3.0 20.4 + - + +
447A VAL* 3.5 9.9 - - + +
449A ASP* 1.3 75.9 - - - +
451A LEU* 1.3 77.1 + - + +
453A ALA* 3.2 6.5 + - - +
454A GLN* 2.9 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A TRP* 4.1 18.2 - - + -
369A LEU* 5.4 1.1 - - + -
411A LEU* 3.7 26.7 - - + -
429A ILE* 4.1 22.9 - - + +
431A ILE* 3.5 28.0 - - + -
443A MET* 4.4 3.1 - - - -
447A VAL* 3.0 35.8 + - + +
448A ARG 3.8 3.8 - - - +
450A PHE* 1.3 92.4 - - + +
452A LYS* 1.3 62.1 + - - +
454A GLN* 3.3 19.2 + - + +
455A GLN 4.0 2.3 + - - -
457A GLN* 5.8 0.9 + - - -
459A PRO* 3.7 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLU* 4.0 21.5 + - - -
448A ARG 3.0 9.0 + - - +
449A ASP* 3.7 21.7 + - - +
451A LEU* 1.3 77.0 - - - +
453A ALA* 1.3 62.6 + - - +
455A GLN* 3.1 21.3 + - - +
459A PRO* 4.0 14.5 - - + +
701A ACT 3.3 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 453 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A PRO* 3.4 17.2 - - + +
259A ASP* 3.4 42.2 - - - +
260A GLU* 5.1 0.7 - - - -
262A PHE 5.0 0.4 - - - +
263A SER 5.1 0.9 - - - +
449A ASP 2.9 18.6 + - - +
450A PHE 3.2 4.9 + - - +
452A LYS* 1.3 75.0 - - - +
454A GLN* 1.3 65.5 + - - +
455A GLN* 3.1 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 454 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TRP* 5.3 1.4 - - - -
257A PHE* 3.6 8.7 - - - +
258A PRO* 2.9 30.7 + - - +
296A PRO* 3.3 29.7 - - + +
297A TRP* 2.9 45.2 + - + +
429A ILE* 6.0 3.4 - - + -
450A PHE* 2.9 50.3 + - + +
451A LEU* 3.6 12.3 - - + +
452A LYS 3.1 1.4 - - - -
453A ALA* 1.3 77.7 - - - +
455A GLN* 1.3 56.2 + - - +
456A VAL* 2.8 23.3 + - + +
457A GLN* 5.6 2.0 - - + +
----------------------------------------------------------
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