Contacts of the helix formed by residues 159 - 166 (chain A) in PDB entry 4PEI
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 ASN 159 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU* 2.7 34.1 + - - +
139A LYS* 4.1 27.9 - - + +
158A ARG* 1.3 71.0 - - - +
160A TYR* 1.3 64.9 + - - +
161A VAL 3.0 1.4 + - - -
162A ILE* 3.0 33.8 + - - +
163A GLN* 3.2 20.5 + - - +
213A ILE* 3.7 15.9 - - + +
295A LEU* 5.9 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TYR* 5.0 2.8 - - - -
115A VAL* 3.7 19.2 - - + +
116A CYS* 5.3 2.2 - - - -
138A GLU 4.5 0.6 + - - -
142A TYR* 3.5 25.1 - + - -
158A ARG* 3.1 32.6 + - + +
159A ASN* 1.3 86.2 - - - +
161A VAL* 1.3 69.8 + - + +
162A ILE 3.0 1.1 + - - -
163A GLN* 3.1 18.6 + - - +
164A MET* 3.2 29.2 + - + +
286A PHE* 3.7 27.8 - + - -
293A PRO* 3.3 34.1 - - + -
295A LEU* 4.4 24.4 - - + +
299A ILE* 4.7 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.6 32.3 - - + +
116A CYS* 3.8 22.4 - - + -
129A VAL* 4.0 11.7 - - + -
157A THR* 4.1 7.0 - - + -
158A ARG 3.5 18.6 - - - +
159A ASN 3.0 2.0 + - - -
160A TYR* 1.3 88.3 - - + +
162A ILE* 1.3 65.9 + - - +
164A MET* 3.0 14.8 + - - +
165A LEU* 3.0 20.8 + - + +
213A ILE* 3.7 22.7 - - + -
217A ILE* 3.9 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ASN* 3.0 30.5 + - - +
160A TYR 3.0 0.8 - - - -
161A VAL* 1.3 79.1 - - - +
163A GLN* 1.3 76.9 + - - +
165A LEU* 4.0 0.3 - - - +
166A SER* 3.1 36.6 + - - -
212A PRO 5.6 0.2 - - - -
213A ILE* 3.9 39.0 - - + +
216A VAL* 3.9 34.3 - - + -
217A ILE* 4.2 18.3 - - + +
220A THR* 5.8 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 163 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ASN* 3.2 31.8 + - - +
160A TYR* 3.1 9.7 + - - +
162A ILE* 1.3 97.9 - - - +
164A MET* 1.3 60.3 + - - +
165A LEU 3.4 0.7 + - - -
166A SER* 3.6 13.6 + - - -
167A ASN* 5.0 1.0 + - - -
299A ILE* 3.7 29.6 - - + +
300A SER* 4.5 21.0 - - - +
303A LEU* 3.3 16.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A CYS* 4.1 8.3 - - - -
160A TYR* 3.2 32.0 + - + +
161A VAL* 3.0 9.1 + - - +
163A GLN* 1.3 77.6 - - - +
165A LEU* 1.3 58.9 + - - +
167A ASN 5.3 0.2 - - - -
275A TRP* 3.6 39.8 - - + -
278A ASN* 3.0 33.4 + - + +
279A LEU* 4.8 8.3 - - + -
282A THR* 3.6 29.2 - - + +
286A PHE* 4.4 13.7 - - + -
299A ILE* 3.8 27.8 - - + -
303A LEU* 4.3 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A CYS* 4.0 29.6 - - + -
117A SER* 4.3 7.9 - - - +
127A VAL* 4.1 12.8 - - + -
129A VAL* 3.6 31.2 - - + -
161A VAL* 3.0 16.1 + - + +
162A ILE 4.3 1.1 - - - +
164A MET* 1.3 76.8 - - - +
166A SER* 1.3 68.0 + - - +
167A ASN 3.2 3.1 - - - -
168A LEU* 3.0 46.6 + - + +
217A ILE* 3.8 29.6 - - + -
221A LEU* 3.6 9.9 - - + +
275A TRP* 4.1 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ILE* 3.1 25.7 + - - -
163A GLN* 3.6 11.8 + - - -
164A MET 3.6 0.4 - - - -
165A LEU* 1.3 78.4 - - - +
167A ASN* 1.3 61.9 + - - +
168A LEU 3.6 0.3 + - - -
169A SER* 4.7 2.4 + - - -
170A GLN* 4.9 3.6 - - - +
217A ILE* 6.5 0.4 - - - +
220A THR* 3.6 33.0 - - - +
221A LEU* 3.7 8.2 - - - +
----------------------------------------------------------
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