Contacts of the helix formed by residues 417 - 432 (chain B) in PDB entry 5M64
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 ILE 417 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 5.0 10.1 - - + -
99B VAL* 4.2 30.7 - - + -
102B VAL* 5.6 7.6 - - + -
137B LEU* 5.3 7.6 - - + -
139B LEU* 5.3 12.6 - - + -
158B CYS* 5.3 8.1 - - + -
413B LEU* 3.0 38.4 + - + +
414B LYS* 4.1 6.1 - - - +
415B GLU 3.2 0.6 - - - -
416B LYS* 1.3 79.9 - - - +
418B ASP* 1.3 71.9 + - - +
419B GLU 3.1 2.5 - - - -
420B TYR* 3.1 26.8 + - + +
421B LEU* 3.8 1.7 + - - +
457B ILE* 4.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 418 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 3.4 34.0 - - - +
99B VAL* 5.2 3.6 - - - +
414B LYS* 3.5 19.3 + - - +
415B GLU* 3.6 13.4 + - - +
416B LYS 3.6 0.2 - - - -
417B ILE* 1.3 79.3 - - - +
419B GLU* 1.3 59.2 + - - +
420B TYR 3.2 0.4 - - - -
421B LEU* 2.9 14.6 + - + +
422B GLN* 2.8 37.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 419 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B GLU 4.3 2.2 + - - +
416B LYS* 3.2 36.9 - - + +
417B ILE* 5.5 0.2 - - - -
418B ASP* 1.3 77.4 - - - +
420B TYR* 1.3 67.7 + - - +
422B GLN* 3.3 10.9 + - - +
423B ASN* 2.9 28.9 + - - +
454B ASN* 4.2 22.8 + - - +
457B ILE* 4.3 17.2 - - - +
460B LYS* 5.0 13.6 + - - +
473B GLN* 6.0 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 420 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 5.4 8.7 - - + -
139B LEU* 5.4 8.1 - - + -
141B LEU* 3.6 32.0 - - + +
156B ARG* 5.7 0.7 - - - +
158B CYS* 5.9 3.6 - - - -
417B ILE* 3.1 17.0 + - + +
419B GLU* 1.3 91.6 - - - +
421B LEU* 1.3 62.9 + - + +
423B ASN* 3.2 4.0 + - - +
424B ILE* 3.0 62.7 + - + +
450B LEU* 4.0 19.9 - - - +
453B VAL* 3.6 17.9 - - + -
454B ASN* 3.8 7.2 - - - +
455B GLU* 3.2 36.2 + - - -
457B ILE* 5.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 3.6 42.2 - - + +
97B VAL* 3.7 27.1 - - + +
98B SER* 4.5 7.6 - - - +
99B VAL* 4.9 14.8 - - + -
417B ILE 3.8 0.8 + - - +
418B ASP* 2.9 20.8 + - + +
420B TYR* 1.3 82.3 - - + +
422B GLN* 1.3 63.3 + - + +
424B ILE* 3.2 24.4 - - + +
425B ILE* 3.2 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 422 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 3.0 29.5 + - - +
265B ARG* 4.8 14.1 - - - +
338B PHE 5.7 1.6 + - - -
339B GLN* 3.2 23.6 + - - +
418B ASP* 2.8 30.1 + - + +
419B GLU* 3.7 10.5 - - - +
421B LEU* 1.3 73.0 - - + +
423B ASN* 1.3 58.0 + - - +
425B ILE* 3.3 11.6 - - - +
426B ALA* 3.1 27.5 + - - +
429B ARG* 5.6 1.6 + - - -
473B GLN* 6.1 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 423 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B GLU* 2.9 18.7 + - - +
420B TYR 3.8 1.1 - - - +
421B LEU 3.2 0.4 - - - -
422B GLN* 1.3 77.2 - - - +
424B ILE* 1.3 60.3 + - - +
426B ALA* 3.9 6.2 - - - +
427B GLN* 3.0 29.1 + - - +
452B ARG 5.3 0.4 + - - -
453B VAL* 3.3 21.5 - - + +
454B ASN* 2.7 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 424 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL* 3.7 18.8 - - + -
141B LEU* 5.2 2.0 - - + -
143B TRP* 5.4 5.2 - - + -
420B TYR* 3.0 51.7 + - + +
421B LEU* 3.2 39.0 - - + +
423B ASN* 1.3 77.9 - - - +
425B ILE* 1.3 62.4 + - + +
427B GLN* 3.3 6.7 + - - +
428B VAL* 3.0 34.3 + - + +
449B VAL* 5.2 5.3 - - + +
450B LEU* 6.0 0.7 - - - -
453B VAL* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 425 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 3.4 36.6 - - + +
72B VAL 5.5 4.3 - - - +
73B ILE* 3.7 27.6 - - + +
95B LEU* 5.9 2.2 - - + -
97B VAL* 4.3 16.4 - - + -
339B GLN* 5.2 2.2 - - - +
421B LEU* 3.2 31.6 + - + +
422B GLN* 3.3 20.2 - - - +
424B ILE* 1.3 77.2 - - + +
426B ALA* 1.3 62.2 + - + +
428B VAL* 3.9 6.0 - - - +
429B ARG* 3.1 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B GLN 3.1 22.1 + - - +
423B ASN* 3.9 9.9 - - - +
424B ILE 3.3 0.2 - - - -
425B ILE* 1.3 76.3 - - - +
427B GLN* 1.3 58.9 + - - +
429B ARG* 3.5 27.9 - - - +
430B MET* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 427 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ASN* 3.0 23.9 + - - +
424B ILE* 3.6 8.3 - - - +
425B ILE 3.3 0.2 - - - -
426B ALA* 1.3 75.9 - - - +
428B VAL* 1.3 57.7 + - - +
430B MET* 3.5 19.4 - - - +
431B ASP* 3.0 65.0 + - - +
449B VAL* 4.0 19.1 - - + +
452B ARG* 3.6 40.0 - - + +
453B VAL* 5.3 4.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 428 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 3.8 23.8 - - + -
74B PHE 4.6 1.3 - - - +
75B ASP* 3.9 11.2 - - - +
95B LEU* 3.8 25.1 - - + -
143B TRP* 5.4 6.7 - - + -
424B ILE* 3.0 22.8 + - + +
425B ILE* 3.9 6.1 - - - +
426B ALA 3.3 0.2 - - - -
427B GLN* 1.3 76.9 - - - +
429B ARG* 1.3 59.7 + - - +
431B ASP* 3.2 7.3 + - - +
432B ILE* 3.0 27.3 + - + +
445B TYR* 5.5 9.9 - - + +
449B VAL* 4.4 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 429 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 3.7 21.8 - - + +
74B PHE 6.1 0.7 - - - -
339B GLN* 5.1 19.6 + - - +
422B GLN* 5.6 1.4 + - - -
425B ILE* 3.1 26.9 + - - +
426B ALA* 3.5 29.9 - - - +
428B VAL* 1.3 76.0 - - - +
430B MET* 1.3 57.1 + - - +
432B ILE* 3.3 15.6 - - + +
433B ASN* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 430 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B ALA 2.9 20.0 + - - +
427B GLN* 3.5 26.7 - - - +
429B ARG* 1.3 78.1 - - - +
431B ASP* 1.3 84.1 + - - +
432B ILE 3.2 0.2 - - - -
433B ASN* 3.3 25.8 + - - +
434B ARG* 3.7 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 431 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLN* 3.0 49.4 + - - +
428B VAL* 3.2 5.5 + - - +
430B MET* 1.3 86.7 - - - +
432B ILE* 1.3 60.4 + - - +
434B ARG* 3.6 6.3 + - - +
435B GLY 3.0 29.3 + - - +
437B ALA* 4.2 12.7 - - + +
445B TYR* 5.0 7.6 + - - +
449B VAL* 4.0 12.0 - - - +
452B ARG* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 432 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE 5.5 2.9 - - - +
75B ASP* 4.2 20.2 - - + +
76B GLY* 3.4 36.1 - - - +
77B LYS* 5.9 2.5 - - + -
428B VAL 3.0 11.5 + - - +
429B ARG* 3.3 27.4 - - + +
431B ASP* 1.3 75.1 - - - +
433B ASN* 1.3 72.2 + - - +
435B GLY* 3.5 11.6 + - - +
437B ALA* 4.1 22.2 - - + +
----------------------------------------------------------
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