Contacts of the helix formed by residues 674 - 684 (chain M) in PDB entry 2DFS
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 ASP 674 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664M PRO 2.9 17.5 + - - +
665M ASN* 4.4 11.5 - - + -
666M ASP* 5.3 3.6 + - - +
667M PHE* 5.8 3.8 - - - -
672M THR* 6.2 0.2 - - + -
673M PHE* 1.3 73.5 - - - +
675M GLU* 1.3 55.7 + - - +
676M LYS* 2.9 39.9 + - - +
677M ARG* 3.3 23.6 + - + +
678M ALA* 2.8 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 675 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M GLU 5.1 1.9 - - - +
20M GLU* 3.4 46.4 - - + +
21M VAL* 3.7 5.9 - - + +
86M LEU* 4.2 14.6 - - + +
90M LYS* 2.6 43.2 + - + +
673M PHE* 3.4 27.2 - - + +
674M ASP* 1.3 77.6 + - - +
676M LYS* 1.4 58.8 + - + +
678M ALA* 3.8 6.2 - - - +
679M VAL* 3.0 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 676 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M PRO 4.2 9.4 + - - +
19M GLU* 2.7 37.3 + - - +
20M GLU* 4.9 0.4 - - - -
21M VAL* 3.8 19.1 - - + -
674M ASP* 2.9 22.6 + - - +
675M GLU* 1.4 80.1 + - + +
677M ARG* 1.3 65.7 + - - +
679M VAL* 3.4 15.1 - - - +
680M GLN* 3.5 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 677 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213M ARG* 5.5 9.4 - - - +
663M LYS* 3.7 22.7 - - + +
664M PRO 3.9 11.7 - - - +
665M ASN* 4.2 4.0 - - - +
666M ASP* 2.6 44.4 + - - +
674M ASP* 3.3 27.2 + - + +
676M LYS* 1.3 82.5 + - - +
678M ALA* 1.3 55.6 + - - +
680M GLN* 2.8 47.7 + - - +
681M GLN* 3.0 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 678 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86M LEU* 3.8 10.3 - - + -
662M ILE* 5.0 6.2 - - + +
663M LYS 4.8 3.4 - - - -
664M PRO* 4.6 5.6 + - + +
673M PHE* 3.4 34.8 - - + -
674M ASP 2.8 19.8 + - - +
675M GLU 3.5 1.1 + - - +
677M ARG* 1.3 72.1 - - - +
679M VAL* 1.3 55.9 + - - +
681M GLN* 3.3 9.8 + - - +
682M LEU* 3.0 36.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 679 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M VAL* 4.2 19.5 - - + -
82M GLU* 3.5 41.1 - - + +
86M LEU* 4.0 14.2 - - + +
675M GLU 3.0 22.2 + - - +
676M LYS* 3.4 14.1 - - - +
678M ALA* 1.3 74.2 - - - +
680M GLN* 1.4 64.4 + - + +
682M LEU* 3.4 6.1 + - - +
683M ARG* 3.1 35.7 + - - +
688M LEU* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 680 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164M GLU* 2.9 25.1 + - - +
213M ARG* 5.8 7.0 - - - +
443M THR 5.7 3.0 + - - -
676M LYS 3.7 9.4 - - - +
677M ARG* 2.8 38.8 + - - +
679M VAL* 1.4 81.3 - - + +
681M GLN* 1.3 79.3 + - - +
683M ARG* 4.1 5.0 - - - +
684M ALA* 3.3 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 681 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164M GLU* 2.7 49.9 + - - +
167M ALA* 4.6 1.2 - - - +
661M CYS 4.6 1.7 - - - +
662M ILE* 3.8 23.5 - - + +
663M LYS* 3.0 47.8 + - - +
677M ARG* 3.0 26.6 + - - +
678M ALA 3.5 6.5 - - - +
680M GLN* 1.3 95.3 + - - +
682M LEU* 1.3 60.7 + - - +
684M ALA* 3.5 3.5 + - - +
685M CYS* 3.1 24.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 682 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82M GLU 5.9 0.2 - - - +
85M VAL* 4.3 13.0 - - + -
86M LEU* 4.5 17.5 - - + +
89M LEU* 4.3 28.0 - - + -
108M VAL* 5.0 3.1 - - + -
662M ILE* 4.1 23.8 - - + -
673M PHE* 6.2 0.7 - - + -
678M ALA* 3.0 26.7 + - + +
679M VAL* 3.4 4.7 + - + +
681M GLN* 1.3 75.6 - - - +
683M ARG* 1.4 62.4 + - - +
685M CYS* 3.3 7.4 + - - +
687M VAL* 3.3 49.2 + - + +
688M LEU* 3.9 24.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 683 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82M GLU* 4.1 15.8 + - - -
554M ALA* 3.0 32.4 - - + +
555M ASP* 2.6 42.8 + - + -
679M VAL* 3.1 25.4 + - - +
680M GLN* 4.2 5.1 - - - +
682M LEU* 1.4 73.7 - - - +
684M ALA* 1.3 57.0 + - - +
685M CYS 3.0 5.0 + - - -
686M GLY* 3.3 6.2 + - - -
688M LEU* 4.1 24.9 - - + +
689M GLU 6.0 0.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 684 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440M GLY* 4.1 2.8 - - - -
441M PHE* 3.1 59.2 + - + +
443M THR* 5.5 5.8 - - - +
554M ALA* 4.8 1.6 - - - -
680M GLN* 3.3 26.1 + - + +
681M GLN* 3.9 3.4 - - - +
683M ARG* 1.3 75.9 - - - +
685M CYS* 1.3 56.6 + - - +
686M GLY 3.6 0.4 - - - -
----------------------------------------------------------
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