Contacts of the helix formed by residues 485 - 496 (chain A) in PDB entry 5I73
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 GLY 485 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TRP* 5.1 1.3 - - - -
237A LEU* 4.9 2.0 - - - +
480A THR* 3.3 28.6 - - - +
482A THR* 3.5 7.4 + - - -
483A PHE 3.3 7.7 + - - -
484A GLY* 1.3 74.4 - - - +
486A ALA* 1.3 62.8 + - - +
487A TYR 3.1 2.2 - - - -
488A VAL* 2.9 22.1 + - - +
489A VAL* 3.0 18.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TRP* 4.2 11.8 - - + -
232A TYR* 5.3 1.1 - - - +
237A LEU* 3.8 34.1 - - + +
239A ILE* 4.3 4.7 - - + +
484A GLY 3.8 0.2 - - - -
485A GLY* 1.3 76.4 - - - +
487A TYR* 1.3 56.3 + - - +
489A VAL* 3.1 13.7 + - - +
490A LYS* 2.9 25.8 + - - +
565A LEU* 3.7 25.8 - - + +
566A PHE* 5.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.4 39.3 + - + +
242A SER* 4.1 9.9 + - - -
243A LYS 5.7 0.9 - - - -
244A GLY* 3.6 38.4 - - - -
245A LEU* 3.6 19.1 - - + -
484A GLY* 4.2 15.7 - - - +
485A GLY 3.1 0.4 - - - -
486A ALA* 1.3 77.1 - - - +
488A VAL* 1.3 56.3 + - - +
490A LYS 3.4 0.2 + - - -
491A LEU* 2.9 29.3 + - - +
565A LEU* 3.8 22.2 + - + -
566A PHE* 4.8 4.0 + - - +
568A TYR* 3.6 38.2 - + - +
570A TYR* 3.1 26.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 5.6 0.4 - - - -
245A LEU* 4.3 9.0 - - + -
248A LEU* 4.2 16.6 - - + -
479A VAL* 4.4 28.5 - - + +
480A THR* 4.9 9.6 - - - +
484A GLY 3.5 21.3 - - - +
485A GLY* 2.9 6.7 + - - +
487A TYR* 1.3 73.6 - - - +
489A VAL* 1.3 61.2 + - - +
491A LEU* 4.2 7.4 - - + -
492A LEU* 2.9 62.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.8 29.9 - - + -
178A THR* 4.3 2.5 - - - +
179A ILE* 4.6 15.0 - - + -
182A TRP* 4.2 15.5 - - + -
403A PRO* 6.4 2.0 - - + -
480A THR* 3.5 23.6 - - + -
485A GLY 3.0 14.8 + - - +
486A ALA* 3.1 15.7 + - + +
488A VAL* 1.3 74.9 - - - +
490A LYS* 1.3 60.4 + - + +
492A LEU* 4.3 0.5 - - - +
493A GLU* 2.9 46.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 5.5 3.6 - - - +
401A ALA 4.6 14.5 + - - -
402A GLY* 6.1 2.0 - - - -
403A PRO* 6.3 2.5 - - - -
486A ALA 2.9 7.5 + - - +
489A VAL* 1.3 77.4 - - + +
491A LEU* 1.3 57.0 + - - +
493A GLU* 3.8 7.5 - - - +
494A GLU* 2.9 62.3 + - + +
563A LEU* 4.6 12.9 - - + +
564A ARG 4.3 18.0 + - - +
565A LEU* 4.2 23.1 - - + -
570A TYR* 3.1 27.8 - - + +
705A 68P 5.2 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 3.9 21.8 - - + -
487A TYR 2.9 17.5 + - - +
488A VAL* 4.0 7.0 - - + +
489A VAL 3.4 0.2 - - - -
490A LYS* 1.3 77.1 - - - +
492A LEU* 1.3 68.3 + - + +
495A TYR* 2.9 64.8 + - + +
496A ALA* 3.5 2.1 + - - +
563A LEU* 4.3 9.4 - - + -
570A TYR* 4.4 6.0 + - + -
574A SER* 3.6 23.6 - - - +
577A LEU* 3.6 32.8 - - + -
578A GLY* 4.5 5.6 - - - +
581A ILE* 5.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 4.5 25.4 - - + +
174A SER* 4.6 10.8 - - - -
175A TYR* 4.3 17.5 - - + -
480A THR* 5.4 1.8 - - - +
488A VAL* 2.9 42.8 + - + +
489A VAL 4.3 0.9 - - - +
491A LEU* 1.3 88.3 - - + +
493A GLU* 1.3 58.9 + - - +
496A ALA* 3.3 10.6 + - + +
497A THR* 2.9 35.6 + - + +
581A ILE* 3.9 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A TRP* 5.6 1.3 - - - -
104A ARG* 3.0 31.4 + - - -
175A TYR* 3.6 29.2 - - + +
179A ILE* 5.5 1.4 - - - +
489A VAL* 2.9 33.5 + - - +
490A LYS* 3.9 7.4 - - + +
492A LEU* 1.3 77.9 - - - +
494A GLU* 1.3 59.2 + - + +
497A THR* 3.4 14.0 + - - -
498A GLY* 4.0 6.8 + - - -
701A 68P 5.4 0.6 + - + -
705A 68P 3.7 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 4.8 3.5 + - - +
490A LYS* 2.9 36.9 + - - +
493A GLU* 1.3 81.0 - - + +
495A TYR* 1.3 61.8 + - + +
496A ALA 3.6 0.9 - - - -
499A PRO* 3.9 3.9 - - - +
556A PHE* 3.6 19.1 - - - -
561A PRO* 3.2 31.8 - - + +
563A LEU* 3.4 25.4 - - + +
705A 68P 3.2 55.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A LEU* 2.9 33.6 + - + +
494A GLU* 1.3 83.7 - - + +
496A ALA* 1.3 59.7 + - - +
499A PRO* 3.9 13.2 - - - +
556A PHE* 4.2 6.1 - + - -
560A PRO* 4.4 12.3 + - + +
561A PRO* 2.5 37.8 + - + -
562A GLN* 4.2 2.6 + - - -
563A LEU* 3.5 31.9 + - + +
570A TYR* 5.9 0.2 - - + -
574A SER* 4.1 7.6 - - - -
575A ILE* 3.6 50.0 - - + +
578A GLY* 3.4 25.2 - - - +
579A TYR* 3.8 9.5 + - - -
582A GLY* 5.3 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 5.8 1.1 - - + -
491A LEU 3.5 1.3 + - - +
492A LEU* 3.3 22.9 + - + +
494A GLU 3.6 0.4 - - - -
495A TYR* 1.3 78.9 - - - +
497A THR* 1.3 72.3 + - + +
498A GLY 3.4 1.4 + - - -
499A PRO* 3.6 9.9 - - - +
500A ALA* 3.5 15.8 - - - +
578A GLY* 3.7 20.0 - - - +
581A ILE* 4.1 23.1 - - + -
582A GLY* 4.1 8.8 - - - +
----------------------------------------------------------
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