Contacts of the helix formed by residues 187 - 197 (chain C) in PDB entry 2W7U
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 THR 187 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLY* 3.7 26.0 - - - +
141C THR* 3.8 16.0 - - + +
185C TYR* 3.1 12.0 + - + +
186C PHE* 1.3 75.0 - - - +
188C PRO* 1.3 70.8 - - + +
189C GLN* 3.8 9.4 + - - +
190C LEU* 3.0 26.0 + - - +
191C LYS* 2.8 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 188 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C TYR* 6.1 0.9 - - + -
186C PHE 4.5 1.3 - - - +
187C THR* 1.3 89.6 - - + +
189C GLN* 1.3 55.5 + - - +
191C LYS* 3.8 19.1 - - + +
192C GLU* 3.0 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 189 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C TYR* 5.3 7.3 + - - +
187C THR* 3.1 9.5 - - - +
188C PRO* 1.3 79.2 - - - +
190C LEU* 1.3 64.5 + - + +
192C GLU* 3.5 9.2 + - - +
193C PHE* 3.4 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C TYR* 3.5 45.1 - - + +
77C GLU* 4.5 7.0 - - + -
79C LEU* 4.3 11.3 - - + +
141C THR* 3.8 15.3 - - + -
184C VAL* 3.8 21.8 - - + -
185C TYR 3.4 25.4 - - - +
186C PHE* 4.2 14.1 - - + -
187C THR* 3.0 18.8 + - - +
189C GLN* 1.3 77.6 - - + +
191C LYS* 1.3 64.2 + - - +
193C PHE* 3.2 5.7 + - - +
194C ILE* 3.1 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 3.8 40.5 - - + +
104C ALA 3.0 25.2 + - - +
105C ASP* 4.3 11.7 + - - +
106C GLY* 4.8 1.0 - - - +
165C LEU 6.0 0.2 - - - +
186C PHE* 3.7 34.1 + - + +
187C THR 2.8 14.5 + - - +
188C PRO* 3.8 20.2 - - + +
190C LEU* 1.3 76.0 - - - +
192C GLU* 1.3 57.1 + - - +
194C ILE* 3.9 8.5 - - - +
195C GLN* 3.1 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C PRO 3.0 16.9 + - - +
189C GLN* 3.7 9.8 - - - +
190C LEU 3.2 0.4 - - - -
191C LYS* 1.3 76.6 - - - +
193C PHE* 1.3 58.8 + - - +
195C GLN* 3.9 4.7 - - + +
196C ASN* 3.0 49.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 3.8 9.9 - - + -
72C GLU 3.3 22.2 - - - -
73C TYR* 3.5 45.1 - + + -
74C PRO* 4.2 11.4 - - + -
79C LEU* 4.4 7.4 - - + -
81C ILE* 3.6 26.2 - - + -
189C GLN 3.4 9.6 + - - +
190C LEU 3.2 8.8 + - - +
192C GLU* 1.3 77.5 - - - +
194C ILE* 1.3 63.9 + - - +
196C ASN* 3.5 6.5 + - + +
197C ASN* 2.9 47.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 3.9 27.6 - - + -
33C THR* 5.1 1.1 - - + +
35C VAL* 3.9 19.5 - - + -
79C LEU* 4.4 10.8 - - + -
81C ILE* 4.0 23.0 - - + +
103C PHE* 3.9 14.6 - - + -
186C PHE* 4.0 38.4 - - + -
190C LEU 3.1 20.6 + - - +
191C LYS* 3.9 5.4 - - - +
193C PHE* 1.3 77.0 - - - +
195C GLN* 1.3 61.9 + - - +
197C ASN* 3.1 13.3 + - - +
198C ILE* 3.2 16.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 195 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 3.9 19.2 - - - -
191C LYS 3.1 17.3 + - - +
192C GLU* 3.9 6.5 - - + +
193C PHE 3.3 0.2 - - - -
194C ILE* 1.3 76.0 - - - +
196C ASN* 1.3 64.3 + - - +
197C ASN 3.3 0.3 + - - -
198C ILE* 3.4 42.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 196 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192C GLU* 3.0 36.1 + - - +
193C PHE* 3.7 9.9 - - + +
195C GLN* 1.3 78.8 - - - +
197C ASN* 1.3 65.7 + - - +
198C ILE 3.5 3.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 197 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C THR* 3.8 2.2 + - - +
71C VAL* 3.8 24.7 - - - +
81C ILE* 3.9 21.5 - - + +
83C HIS* 2.6 36.3 + - + -
193C PHE* 2.9 50.9 + - - +
194C ILE 3.1 9.0 + - - +
196C ASN* 1.3 82.4 - - - +
198C ILE* 1.3 57.5 + - - +
----------------------------------------------------------
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