Contacts of the helix formed by residues 194 - 200 (chain A) in PDB entry 2XFN
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 194 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ASP* 3.4 13.5 - - - -
189A VAL* 3.0 21.9 + - - -
190A LYS* 3.8 5.5 + - - +
193A GLY* 1.3 79.0 - - - +
195A THR* 1.3 66.9 + - - -
196A THR 3.4 2.5 - - - -
197A ARG 3.3 2.0 + - - -
198A ILE* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 4.4 3.8 - - - -
119A TRP* 3.8 38.8 + - + +
122A MET* 3.8 26.2 - - + -
123A ASP* 2.7 37.5 + - - +
168A PHE* 4.2 7.2 - - + -
189A VAL* 3.9 14.1 - - + -
194A GLY* 1.3 72.2 - - - +
196A THR* 1.3 69.6 + - - +
198A ILE* 3.4 3.9 - - - +
199A ILE* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 4.4 14.9 - - + +
103A PHE* 3.8 17.7 - - - -
123A ASP* 4.8 0.7 + - - -
194A GLY 3.4 0.4 - - - -
195A THR* 1.3 81.0 + - - +
197A ARG* 1.3 62.9 + - - +
199A ILE* 3.6 6.1 - - - +
200A SER* 2.6 41.8 + - - +
203A ASN* 5.9 1.1 - - - +
477A ILE* 3.7 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A PRO* 4.1 15.7 - - - +
64A THR* 3.8 23.2 - - - +
192A CYS 3.4 22.4 - - - +
193A GLY* 3.9 13.6 + - - +
194A GLY 3.3 6.4 + - - +
196A THR* 1.3 79.0 - - - +
198A ILE* 1.3 61.4 + - - +
199A ILE 3.4 0.3 + - - -
200A SER 3.7 0.2 + - - -
203A ASN* 2.9 47.3 + - - +
204A GLY* 3.3 9.7 - - - -
205A GLY* 3.0 26.7 + - - -
432A TRP* 3.8 11.2 - - + -
474A ALA* 4.2 9.7 - - - +
475A GLN 2.9 22.0 + - - -
476A PRO* 4.3 1.8 - - - +
477A ILE* 3.5 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 3.8 17.9 - - + -
172A CYS* 3.9 21.0 - - + -
188A TYR* 4.1 17.7 - - + -
189A VAL* 4.3 12.1 - - + -
192A CYS* 3.8 28.7 - - + -
194A GLY 3.0 16.3 + - - +
195A THR* 3.4 12.3 - - - +
197A ARG* 1.3 80.2 - - - +
199A ILE* 1.3 68.9 + - + +
205A GLY* 4.6 1.6 + - - -
206A GLN* 3.1 21.1 + - - +
432A TRP* 4.5 7.2 - - + -
435A TYR* 3.3 25.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 3.3 24.7 - - + +
103A PHE* 3.1 44.4 - - + -
168A PHE* 2.9 43.7 - - + -
171A LEU* 6.5 1.3 - - + -
172A CYS* 5.1 2.2 - - - -
195A THR 3.0 13.7 - - - +
196A THR 3.6 5.6 - - - +
198A ILE* 1.3 78.9 - - + +
200A SER* 1.3 67.1 + - - +
206A GLN* 3.8 7.5 + - - +
326A TYR* 4.3 2.8 + - - -
1501A XCG 3.3 41.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PRO* 4.0 13.9 - - - +
196A THR* 2.6 34.9 + - - +
197A ARG 3.7 0.4 + - - -
198A ILE 3.4 1.0 - - - -
199A ILE* 1.3 79.6 - - - +
201A THR* 1.3 60.1 + - - +
202A THR 3.4 19.0 + - - -
203A ASN* 4.2 2.5 - - - -
204A GLY* 3.2 17.4 - - - -
205A GLY 3.2 1.4 + - - -
206A GLN* 3.1 24.1 + - - -
1501A XCG 4.1 6.5 - - - -
----------------------------------------------------------
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