Contacts of the strand formed by residues 190 - 198 (chain C) in PDB entry 3NSH
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 TYR 190 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ILE* 3.9 17.8 - - + +
186C ASP 3.9 3.6 - - - -
187C HIS* 3.2 62.0 + - + +
188C SER 3.4 2.9 + - - -
189C LEU* 1.3 80.0 - - - +
191C THR* 1.3 79.7 + - - +
192C GLY 3.4 17.7 - - - -
193C SER* 4.8 0.4 - - - -
194C LEU* 3.9 27.6 - - + +
348C TYR* 3.3 34.8 - + + -
361C ALA* 3.7 11.4 - - + -
362C VAL 3.2 14.6 - - - +
364C ALA* 4.1 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C TYR* 1.3 88.2 - - - +
192C GLY* 1.3 68.7 + - - +
193C SER 4.6 0.2 - - - +
361C ALA* 4.1 1.0 - - - +
362C VAL* 3.0 41.0 + - - +
363C SER 4.8 1.1 + - - +
364C ALA* 5.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C TYR* 3.4 15.9 - - - -
191C THR* 1.3 78.6 - - - +
193C SER* 1.3 60.7 + - - -
362C VAL* 6.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C TYR* 4.8 0.2 - - - -
191C THR 4.6 0.5 - - - +
192C GLY* 1.3 75.0 - - - -
194C LEU* 1.3 67.6 + - - +
195C TRP* 3.6 26.2 + - - +
360C PHE 3.6 3.8 - - - +
361C ALA* 3.6 17.7 - - - +
362C VAL 5.1 0.2 + - - -
376C VAL* 4.6 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ILE* 4.4 13.0 - - + -
190C TYR* 3.9 28.7 - - + +
192C GLY 4.1 1.0 + - - -
193C SER* 1.3 77.3 - - - +
195C TRP* 1.3 61.2 + - - +
196C TYR* 3.6 35.0 - - + +
348C TYR* 4.2 4.7 - - + +
350C VAL* 3.8 22.2 - - + -
359C GLY* 3.7 19.1 - - - +
360C PHE 3.5 22.7 - - - -
361C ALA* 3.7 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C SER* 3.6 26.6 + - - -
194C LEU* 1.3 75.9 - - - +
196C TYR* 1.3 62.2 + - - +
300C GLN* 3.6 35.4 - - + -
301C SER 4.2 0.2 - - - -
302C PHE* 3.6 38.6 - + + -
358C ILE 3.5 1.2 - - - +
359C GLY* 3.0 2.6 - - - -
360C PHE 2.7 35.1 + - - -
376C VAL* 3.5 33.9 + - + -
378C GLY 3.3 38.1 - - - +
379C PRO* 3.4 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C ILE* 4.0 15.4 - - - +
194C LEU* 3.6 40.7 - - + +
195C TRP* 1.3 77.4 - - - +
197C THR* 1.3 60.1 + - - +
295C GLY* 3.8 2.4 - - - -
296C GLU* 3.6 37.5 + - - +
300C GLN 4.8 1.7 - - - +
302C PHE* 3.4 11.8 - - - -
350C VAL* 4.7 4.8 - - + +
352C ASP* 4.2 9.9 + - + -
357C ARG* 3.5 57.8 + - + -
358C ILE 3.2 2.5 - - - -
359C GLY* 3.4 26.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C TYR* 1.3 75.5 - - - +
198C PRO* 1.4 65.7 + - - +
207C VAL* 3.8 30.2 - - + +
208C ILE 4.6 3.3 + - - -
293C LEU* 3.9 18.3 - - + +
294C MET* 2.5 30.3 + - - +
296C GLU* 4.7 0.7 - - - -
302C PHE* 3.9 11.4 - - - -
357C ARG* 3.3 3.5 - - - -
358C ILE* 2.8 44.7 + - + +
360C PHE* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 198 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C THR* 1.4 90.4 + - - +
199C ILE* 1.3 67.4 + - - +
200C ARG* 3.4 5.9 + - - +
206C GLU 3.6 4.9 - - - +
207C VAL* 3.9 13.7 - - - +
208C ILE* 5.1 1.0 + - - +
294C MET* 3.2 43.0 - - + +
295C GLY 3.6 15.7 - - - +
296C GLU* 4.0 13.7 - - + +
356C LYS 3.5 10.8 - - - +
357C ARG* 4.1 2.7 - - + -
----------------------------------------------------------
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