Contacts of the helix formed by residues 654 - 662 (chain D) in PDB entry 1S77
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 654 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D TRP* 4.2 2.4 - - - -
623D TYR* 3.7 16.2 + - - -
628D SER* 4.3 7.9 - - - +
629D VAL* 3.8 39.9 - - + +
650D VAL* 2.9 30.7 + - - +
653D ASP* 1.3 88.3 - - + +
655D ILE* 1.3 64.6 + - - +
657D PRO* 3.5 5.2 - - - +
658D ALA* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 655 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D TRP* 3.4 42.2 - - + -
650D VAL* 3.0 7.8 + - + +
651D LEU* 3.3 8.7 - - + +
654D THR* 1.3 79.3 + - - +
656D GLN* 1.3 71.3 + - - +
658D ALA* 3.1 4.5 + - - +
659D ILE* 2.9 38.7 + - + +
667D PHE* 4.1 17.0 - - + -
670D PRO* 3.4 49.4 - - + +
673D ALA* 3.9 6.5 - - + -
674D ALA* 3.7 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 656 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D ARG* 3.9 20.8 - - - +
651D LEU* 2.5 27.6 + - + +
652D GLU* 3.0 38.0 + - - +
655D ILE* 1.3 75.4 - - - +
657D PRO* 1.3 64.7 - - + +
659D ILE* 3.4 13.9 - - - +
660D ASP* 3.2 30.7 + - - +
670D PRO* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 657 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652D GLU* 3.0 22.7 - - - +
653D ASP 3.4 21.3 - - - +
654D THR* 3.5 9.6 - - - +
655D ILE 3.3 2.5 - - - -
656D GLN* 1.3 89.1 - - + +
658D ALA* 1.3 74.0 + - - +
659D ILE 3.1 1.6 - - - -
660D ASP* 3.0 20.6 + - + +
661D SER* 3.2 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 658 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623D TYR* 3.7 28.7 - - + +
654D THR 2.9 19.5 + - - +
655D ILE* 3.1 5.5 + - - +
657D PRO* 1.3 81.0 - - - +
659D ILE* 1.3 64.0 + - - +
661D SER* 3.1 12.5 + - - -
663D LYS* 3.0 28.0 + - + -
664D GLY* 4.1 10.5 - - - +
667D PHE* 4.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 659 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655D ILE* 2.9 41.0 + - + +
656D GLN* 3.4 16.4 - - - +
658D ALA* 1.3 76.7 - - - +
660D ASP* 1.3 60.6 - - - +
662D GLY* 2.7 25.9 + - - -
664D GLY* 4.6 12.8 - - - +
665D LEU* 5.8 3.2 - - + +
667D PHE* 4.8 14.6 - - + -
670D PRO* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 660 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383D ALA* 4.3 21.5 - - + +
386D ARG* 4.3 22.2 + - - +
387D LYS* 5.4 13.0 - - + +
656D GLN* 3.2 24.8 + - - +
657D PRO* 3.0 13.8 + - + +
659D ILE* 1.3 83.1 - - - +
661D SER* 1.3 59.7 + - - +
662D GLY* 3.3 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 661 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657D PRO 3.2 7.4 + - - -
658D ALA* 3.1 13.9 + - - -
660D ASP* 1.3 77.6 - - - +
662D GLY* 1.3 57.6 + - - +
663D LYS* 2.9 46.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 662 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658D ALA 3.2 0.2 + - - -
659D ILE* 2.7 18.7 + - - -
660D ASP 3.1 1.0 - - - -
661D SER* 1.3 79.3 - - - +
663D LYS* 1.3 58.2 + - - +
664D GLY 3.2 7.8 + - - -
665D LEU* 3.6 32.5 + - - +
----------------------------------------------------------
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