Contacts of the strand formed by residues 157 - 162 (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 GLN 157 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146M ALA* 3.4 20.6 - - + +
149M GLN* 3.1 43.6 + - - +
150M MET* 3.2 5.1 - - + +
153M ASP* 5.5 0.4 - - - +
155M ARG* 3.2 16.9 + - - +
156M ASN* 1.3 84.8 - - - +
158M SER* 1.3 64.0 + - - +
159M ILE 4.3 0.2 - - - -
223M TYR* 4.0 1.9 + - - -
432M PHE* 3.0 8.5 + - - +
433M ILE* 3.3 19.0 - - + -
434M GLY 2.8 25.7 + - - -
654M THR* 4.0 3.1 - - - +
655M THR* 2.8 35.1 + - - +
657M HIS* 3.4 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 158 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157M GLN* 1.3 72.3 - - - +
159M ILE* 1.3 58.7 + - - +
160M ILE* 3.6 6.3 + - - -
223M TYR* 2.8 24.5 + - - -
434M GLY 3.3 5.6 - - - -
651M LEU* 3.6 21.2 - - - +
654M THR* 2.7 25.9 + - - +
655M THR 3.1 10.3 + - - -
656M PRO* 3.2 7.4 - - - +
657M HIS* 2.8 29.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M ILE* 5.4 4.0 - - + -
142M VAL* 4.3 13.7 - - + +
143M ALA* 4.4 10.8 - - - -
146M ALA* 4.3 6.7 - - + -
158M SER* 1.3 71.5 - - - +
160M ILE* 1.3 56.7 + - - +
161M VAL* 3.7 18.6 + - + -
176M ALA* 4.5 12.8 - - + -
180M PHE* 3.9 31.9 - - + -
433M ILE* 4.3 10.3 - - + -
434M GLY 2.7 12.0 + - - +
435M VAL* 3.3 11.6 - - + +
436M LEU* 2.8 31.1 + - - +
657M HIS* 3.6 22.9 - - + +
659M VAL* 4.3 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158M SER* 4.2 12.8 - - - +
159M ILE* 1.3 72.3 - - - +
161M VAL* 1.3 64.7 + - - +
162M SER* 5.0 6.2 + - - +
436M LEU* 3.9 26.2 - - + -
438M ILE* 4.6 11.7 - - + -
461M LEU* 4.4 13.0 - - + -
464M GLN* 3.9 18.8 - - - +
651M LEU* 4.3 20.0 - - + -
656M PRO* 4.0 9.6 - - + -
657M HIS 2.7 14.9 + - - +
658M TYR* 3.6 31.2 - - + -
659M VAL 3.0 26.5 + - - +
660M ARG* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139M ILE* 5.7 1.3 - - + -
159M ILE* 4.1 13.9 - - + -
160M ILE* 1.3 74.9 - - - +
162M SER* 1.3 62.3 + - - +
169M LYS* 3.7 41.6 - - + +
172M SER* 4.1 12.3 - - - -
173M ALA* 5.1 2.5 - - + +
435M VAL* 4.0 25.6 - - + -
436M LEU 2.9 21.2 + - - +
437M ASP* 3.9 2.9 - - + -
438M ILE* 3.3 18.2 + - - +
659M VAL* 3.5 13.9 - - + -
661M CYS* 3.8 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 162 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160M ILE* 4.1 7.3 + - - +
161M VAL* 1.3 75.6 - - - +
163M GLY* 1.3 53.9 + - - +
169M LYS* 3.8 5.2 - - - -
438M ILE* 3.4 13.0 - - - -
439M TYR 3.6 17.7 - - - -
440M GLY* 5.0 2.2 - - - -
458M ASN* 5.6 1.3 - - - -
461M LEU* 6.2 1.1 - - - -
659M VAL 3.0 8.4 + - - -
660M ARG* 3.1 37.3 + - - -
661M CYS* 2.8 33.8 + - - +
685M CYS* 5.0 0.7 - - - -
----------------------------------------------------------
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