Contacts of the helix formed by residues 446 - 457 (chain P) in PDB entry 6NR8
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 GLU 446 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416P GLU 4.2 1.0 - - - +
417P ILE* 3.4 28.4 - - - +
420P ALA* 3.6 20.5 - - + +
442P ALA 4.0 11.9 - - - +
443P GLU* 3.4 13.6 + - - +
444P ALA 3.2 1.0 - - - -
445P PHE* 1.3 72.9 - - - +
447P ALA* 1.3 58.2 + - - +
448P ILE 3.2 2.5 - - - -
449P PRO* 3.3 21.5 - - - +
450P ARG* 3.0 46.8 + - - +
464P ILE* 3.9 21.0 - - + +
467P LEU* 5.5 0.2 - - - +
468P TYR* 4.0 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 447 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106P VAL* 3.7 35.9 - - + +
110P ALA* 3.7 6.1 - - + -
444P ALA 3.5 13.0 + - - +
445P PHE 3.1 1.4 - - - -
446P GLU* 1.3 77.0 - - - +
448P ILE* 1.3 57.2 + - + +
450P ARG* 3.2 29.0 - - - +
451P ALA* 2.6 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 448 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P TYR* 6.5 1.6 - - + -
103P PHE* 3.6 43.5 - - + +
106P VAL* 3.7 26.0 - - + -
107P PHE* 4.8 6.5 - - + -
412P GLY* 4.1 6.5 - - - -
413P GLY* 3.6 27.4 - - - +
416P GLU* 3.9 6.1 - - + -
444P ALA 5.1 1.3 - - - +
445P PHE* 3.7 11.9 - - - +
446P GLU 3.2 1.0 - - - -
447P ALA* 1.3 81.0 - - + +
449P PRO* 1.3 62.7 - - + +
451P ALA* 3.3 4.0 + - + +
452P LEU* 3.1 43.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 449 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413P GLY* 4.2 13.7 - - - +
416P GLU* 4.9 0.9 - - + -
417P ILE* 4.7 1.3 - - + -
445P PHE 3.7 6.1 - - - +
446P GLU* 3.3 38.4 - - + +
448P ILE* 1.3 89.8 - - + +
450P ARG* 1.3 61.4 + - - -
452P LEU* 4.0 6.2 - - + +
453P ALA* 3.2 23.6 + - - +
460P ALA* 4.5 2.9 - - - +
463P VAL* 4.7 15.5 - - + +
464P ILE* 4.6 8.7 - - + +
467P LEU* 4.3 22.7 - - + -
477P ASN* 4.4 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 450 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C TRP* 6.4 0.2 - - - -
110P ALA* 4.0 11.5 - - - +
114P LEU* 5.3 4.6 - - - +
443P GLU* 3.0 32.1 + - - +
446P GLU* 3.0 31.7 + - - +
447P ALA* 3.2 36.2 + - - +
449P PRO* 1.3 74.8 - - - +
451P ALA* 1.3 63.1 + - - +
453P ALA* 3.6 1.6 + - - +
454P GLU* 3.1 39.8 + - - +
460P ALA* 3.7 25.5 - - + +
464P ILE* 3.8 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 451 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P THR 4.2 7.4 - - - +
44P ARG* 2.8 28.3 - - - +
47P TYR* 5.2 1.8 - - + +
106P VAL* 4.5 15.3 - - + -
447P ALA 2.6 19.7 + - - +
448P ILE* 3.3 10.2 + - + +
450P ARG* 1.3 74.7 - - - +
452P LEU* 1.3 57.3 + - + +
454P GLU* 3.2 5.9 + - - -
455P ASN* 2.6 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P TYR* 4.7 4.3 - - + +
48P GLY* 4.2 17.5 - - - -
49P PRO* 3.7 29.6 - - + -
412P GLY* 4.1 5.8 - - - +
448P ILE* 3.1 37.4 + - + +
449P PRO* 4.5 4.7 - - + +
451P ALA* 1.3 80.3 - - + +
453P ALA* 1.3 60.9 + - - +
455P ASN* 3.6 7.7 - - - +
456P SER* 3.0 30.3 + - - -
477P ASN* 3.5 20.6 - - - +
478P VAL 3.3 27.1 - - - +
479P GLY* 4.7 1.4 - - - +
480P LEU* 3.9 6.3 - - + +
492P MET* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 453 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449P PRO 3.2 20.9 + - - +
450P ARG 4.0 2.5 - - - +
452P LEU* 1.3 77.5 - - - +
454P GLU* 1.3 55.9 + - - +
456P SER 3.3 1.2 + - - -
457P GLY 2.8 6.9 + - - -
458P VAL* 2.7 56.2 + - + +
459P LYS 3.5 16.2 - - - +
460P ALA* 3.8 11.4 - - + -
463P VAL* 4.2 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 454 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119O GLN* 4.9 2.1 - - - +
41P GLN* 4.5 6.8 - - - +
44P ARG* 3.4 46.7 + - + +
45P THR* 3.8 10.6 + - - -
450P ARG* 3.1 30.5 + - - +
451P ALA* 4.4 0.2 - - - -
453P ALA* 1.3 74.2 - - + +
455P ASN* 1.3 65.6 + - - +
457P GLY* 3.3 11.9 + - - +
458P VAL 4.4 5.8 - - - +
460P ALA* 5.7 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 455 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119O GLN* 3.3 22.5 - - - +
44P ARG 3.2 5.4 + - - +
45P THR* 2.6 34.4 + - - +
47P TYR 2.8 25.4 - - - +
50P ASN 2.8 27.1 + - - +
52P MET* 3.7 7.5 - - - +
451P ALA 2.6 20.5 + - - +
452P LEU* 3.6 8.3 - - - +
453P ALA 3.3 0.2 - - - -
454P GLU* 1.3 73.5 - - - +
456P SER* 1.3 56.5 + - - +
480P LEU* 3.6 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 456 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O PRO* 3.9 1.4 - - - +
119O GLN* 3.2 18.3 + - - -
120O ILE* 3.7 21.7 - - - +
123O ARG* 5.6 1.1 + - - +
452P LEU 3.0 16.6 + - - -
453P ALA 3.7 4.5 - - - -
455P ASN* 1.3 76.2 - - - +
457P GLY* 1.3 61.0 + - - +
458P VAL* 3.8 15.3 - - - -
479P GLY 3.9 2.4 + - - -
480P LEU* 3.4 17.9 - - - +
484P ALA* 3.3 30.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 457 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117O HIS 3.9 23.6 - - - +
118O PRO* 4.1 8.6 - - - +
119O GLN* 4.3 2.2 - - - -
430O LYS* 4.7 2.3 + - - -
453P ALA 2.8 4.3 + - - -
454P GLU* 3.3 14.7 + - - -
455P ASN 3.7 0.2 + - - -
456P SER* 1.3 79.3 - - - +
458P VAL* 1.3 63.1 + - - +
----------------------------------------------------------
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