Contacts of the strand formed by residues 195 - 202 (chain A) in PDB entry 1XSK
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 LYS 195 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU 4.3 0.3 - - - +
166A GLY* 3.3 5.3 - - - -
167A GLU* 2.4 74.0 + - + +
193A ALA* 4.0 3.4 - - - +
194A TYR* 1.3 80.8 - - - +
196A ASN* 1.3 60.9 + - - +
197A ILE* 4.7 4.3 - - + -
465A ALA 3.7 2.0 - - - -
466A ARG 2.8 36.7 + - - +
468A ALA* 3.8 21.5 - - + +
478A HIS* 3.5 35.4 - - + -
479A TRP 3.1 14.9 + - - -
480A GLY* 4.4 0.2 - - - -
500A ILE* 3.7 24.2 - - + -
505A PHE* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 5.5 0.2 + - - -
165A LEU 4.3 2.9 - - - -
168A ARG* 2.8 35.4 + - - +
180A GLU 3.3 8.0 - - - +
181A THR* 3.6 10.9 - - - -
182A TRP 3.0 38.7 + - - +
183A ASN* 2.9 32.3 + - - +
193A ALA* 3.3 15.3 + - - +
195A LYS* 1.3 71.9 - - - +
197A ILE* 1.3 74.1 + - - +
198A PRO* 4.5 3.3 - - - +
438A ASN* 4.8 6.2 + - - +
468A ALA 3.9 7.8 + - - +
469A SER* 4.0 5.9 + - - -
470A VAL 4.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A LEU* 3.1 26.3 + - - +
166A GLY* 3.8 20.4 - - - +
181A THR* 3.9 2.8 - - - +
195A LYS* 4.4 3.8 - - + +
196A ASN* 1.3 88.5 - - - +
198A PRO* 1.3 58.4 - - - +
199A PHE* 2.7 27.8 + - + +
254A TYR* 3.5 24.9 - - - +
468A ALA* 4.7 2.0 - - + -
469A SER* 3.6 9.4 - - - +
470A VAL* 3.5 31.4 - - + +
473A GLN* 5.4 0.2 - - - +
503A SER* 4.4 10.5 - - - +
505A PHE* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 3.3 31.9 - - + +
165A LEU* 4.4 0.2 - - + -
181A THR* 3.7 23.6 - - + +
196A ASN 4.5 2.5 - - - +
197A ILE* 1.3 78.8 - - - +
199A PHE* 1.3 57.4 + - - +
208A VAL 3.7 1.7 - - - +
209A LEU* 3.5 4.9 - - + -
210A VAL* 3.0 47.6 + - + +
212A HIS 4.2 3.6 - - - +
216A VAL* 4.1 11.9 - - + -
218A PHE* 3.9 20.5 - - + -
470A VAL* 3.7 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLY* 4.1 0.2 - - - -
165A LEU* 2.8 27.9 + - - +
197A ILE* 2.7 24.2 + - + +
198A PRO* 1.3 75.4 - - - +
200A TYR* 1.3 81.3 + - - +
201A MET* 4.0 7.2 - - + -
207A GLY* 4.0 2.5 - - - -
208A VAL 3.3 26.2 - - - -
209A LEU* 4.0 5.4 - - + -
242A ILE* 4.0 9.9 - - + -
250A VAL* 3.9 21.5 - - + -
251A LEU* 4.3 11.2 - - + -
254A TYR* 3.7 42.4 - + + -
502A LEU 3.5 24.7 - - - -
503A SER* 4.2 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 3.5 27.0 - - - +
155A ASP 5.6 0.2 + - - -
162A VAL* 3.6 22.9 - - + -
163A TYR 3.3 13.2 - - - +
165A LEU* 4.1 11.7 - - + -
199A PHE* 1.3 81.2 - - - +
201A MET* 1.3 66.6 + - - +
202A THR* 4.0 18.4 - - + -
206A TYR* 4.5 6.5 + + - -
207A GLY* 3.1 2.4 - - - -
208A VAL* 2.8 68.7 + - + +
218A PHE* 4.0 17.9 - + - -
220A VAL* 6.5 0.2 - - + -
228A VAL* 3.6 43.9 - - + +
230A PHE* 4.3 6.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 3.5 3.1 - - - +
163A TYR* 2.9 40.9 + - + +
199A PHE* 4.0 9.4 - - + -
200A TYR* 1.3 76.9 - - - +
202A THR* 1.3 69.0 + - - +
206A TYR 3.4 11.7 - - - +
207A GLY* 3.8 5.2 - - - -
247A PRO* 3.2 50.3 - - + +
250A VAL* 4.0 11.9 - - + -
251A LEU* 4.2 16.4 - - - -
502A LEU* 4.0 41.5 - - + +
592A MET* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A LEU* 4.5 1.3 - - + -
160A GLU* 3.0 30.8 + - - +
161A THR 3.0 14.8 - - - +
162A VAL* 4.3 7.6 - - + -
163A TYR* 4.4 5.2 - - - -
200A TYR* 4.0 17.7 - - + -
201A MET* 1.3 88.5 - - - +
203A ASN* 1.3 59.6 + - - +
204A ARG* 2.9 22.3 + - - +
205A GLY* 3.5 9.4 + - - -
206A TYR* 3.1 30.8 + - + +
247A PRO* 4.6 1.7 - - - +
592A MET* 4.5 5.4 - - - +
----------------------------------------------------------
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