Contacts of the helix formed by residues 192 - 199 (chain A) in PDB entry 3PEJ
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 VAL 192 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.8 37.7 - - + -
88A ILE* 5.4 4.6 - - + +
165A ILE* 4.8 9.9 - - + -
170A THR* 3.9 31.9 - - + +
174A LEU* 4.2 7.9 - - + -
187A ILE* 3.0 28.1 + - + +
190A PHE* 4.2 4.3 - - + +
191A GLY* 1.4 82.7 - - - +
193A GLY* 1.3 63.5 + - - +
194A PHE 3.1 5.6 + - - -
195A TYR* 3.1 32.3 + - + +
196A SER 4.3 1.2 + - - -
1001A BC2 3.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU* 3.6 31.3 - - - +
106A ASN* 4.9 2.7 - - - -
187A ILE* 3.1 21.3 + - - -
188A GLY* 4.4 1.3 - - - -
191A GLY 3.7 0.4 - - - -
192A VAL* 1.3 77.5 - - - +
194A PHE* 1.4 55.9 + - - +
196A SER* 2.6 31.7 + - - -
1001A BC2 3.0 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LEU* 4.1 17.9 - - + +
106A ASN* 4.0 9.5 - - - +
193A GLY* 1.4 71.3 - - - +
195A TYR* 1.3 77.0 + + + +
196A SER* 3.1 5.8 + - - -
197A ALA* 3.1 23.5 + - + +
198A PHE* 4.6 8.3 - + - -
204A VAL* 3.6 28.5 - - + -
206A VAL* 3.7 26.0 - - + -
218A TRP* 3.6 29.4 - + - -
220A SER* 4.6 7.4 - - - -
243A ILE* 4.2 9.0 - - + -
1001A BC2 2.7 56.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A TYR* 2.7 34.6 + - - -
81A VAL* 3.7 30.7 - - + -
84A LEU* 4.2 24.5 - - + -
85A MET* 4.5 15.4 - - + +
88A ILE* 4.5 10.3 - - + +
89A VAL* 5.7 0.3 - - - +
162A LEU* 3.7 4.5 - - - +
165A ILE* 3.5 30.9 - - + +
192A VAL* 3.1 29.8 + - + +
194A PHE* 1.3 87.6 - + - +
196A SER* 1.4 53.8 + - - +
197A ALA 3.1 5.8 - - - -
198A PHE* 3.1 42.1 + + - +
218A TRP* 4.4 0.7 - + - -
220A SER* 5.6 2.0 - - - -
1001A BC2 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.8 18.5 - - - +
92A LEU* 5.3 1.3 - - - -
98A VAL* 5.4 0.9 - - - -
99A PHE* 3.4 26.1 + - - +
102A GLU* 3.6 7.8 - - - +
103A LEU* 5.7 0.9 - - - +
187A ILE* 4.1 19.3 - - - -
192A VAL 4.3 1.0 + - - -
193A GLY 2.6 22.5 + - - -
194A PHE 3.1 0.5 + - - -
195A TYR* 1.4 71.4 - - - +
197A ALA* 1.4 60.2 + - - +
198A PHE 3.1 5.6 - - - -
199A LEU* 3.1 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 4.1 13.2 - - - +
103A LEU* 4.7 10.1 - - + +
194A PHE* 3.1 16.9 + - + +
195A TYR 3.1 0.2 - - - -
196A SER* 1.4 77.1 + - - +
198A PHE* 1.4 58.2 + - + +
199A LEU 3.2 2.2 + - - -
200A VAL* 3.3 6.1 + - - +
201A ALA* 2.9 28.8 + - - +
204A VAL* 3.8 24.9 - - + -
245A LEU* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 3.5 40.4 - - + -
89A VAL* 3.6 14.8 - - + +
194A PHE* 4.6 8.3 - + - -
195A TYR* 3.1 32.9 + + - +
196A SER 3.1 1.6 - - - -
197A ALA* 1.4 76.0 - - + +
199A LEU* 1.3 59.8 + - - +
200A VAL 3.4 0.7 - - - -
201A ALA 3.2 20.3 - - - +
202A ASP 4.2 4.9 - - - -
204A VAL* 3.7 24.9 - - + -
220A SER* 3.7 34.1 - - - -
221A THR 3.7 18.4 - - - -
222A ALA* 3.8 16.6 - - + +
248A LYS* 3.4 14.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 4.3 7.0 - - + -
89A VAL* 3.7 30.3 - - + +
92A LEU* 3.5 47.3 - - + +
93A TYR* 3.9 2.5 - - - +
96A LYS* 3.4 61.6 + - + +
98A VAL* 4.7 4.3 - - + -
99A PHE* 4.8 0.7 - - + -
196A SER* 3.1 33.9 + - - +
198A PHE* 1.3 78.4 - - - +
200A VAL* 1.4 58.1 + - + +
248A LYS* 3.4 12.5 + - - +
250A ASP* 4.5 0.9 - - - +
251A ALA* 5.2 0.2 - - - +
----------------------------------------------------------
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