Contacts of the helix formed by residues 155 - 162 (chain A) in PDB entry 1IPA
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 SER 155 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 3.6 9.9 - - - +
127A PRO* 3.8 4.3 - - - +
152A ASP* 3.5 25.1 + - - -
153A LEU 3.6 1.8 - - - -
154A TYR* 1.3 80.2 - - - +
156A PRO* 1.3 71.0 - - - +
157A GLN* 3.5 18.3 + - - +
158A VAL* 2.8 34.5 + - - +
159A ILE* 3.1 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 4.7 2.2 - - - +
18A LEU* 4.0 27.8 - - + +
23A ARG* 3.5 21.3 - - - +
30A LEU* 5.2 14.4 - - + +
87A LEU 6.0 0.4 - - - +
89A VAL* 4.1 27.1 - - + +
154A TYR 4.0 3.1 - - - +
155A SER* 1.3 82.5 - - - +
157A GLN* 1.3 71.1 + - - +
159A ILE* 3.5 9.5 + - + +
160A ARG* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU 5.0 4.9 + - - -
23A ARG* 5.1 1.0 - - - +
89A VAL* 3.7 24.1 - - + +
127A PRO* 3.2 35.2 - - + +
128A GLY* 4.1 11.7 - - - +
155A SER* 3.5 9.7 - - - +
156A PRO* 1.3 93.9 - - - +
158A VAL* 1.3 64.8 + - - +
160A ARG* 4.4 4.0 - - - +
161A ASN* 3.0 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PRO* 3.5 32.1 - - + +
130A LEU* 3.8 27.1 - - + -
131A GLY* 3.7 4.1 - - - -
134A LEU* 4.3 0.2 - - + -
152A ASP* 3.4 20.9 - - + +
153A LEU* 4.8 4.7 - - + +
155A SER* 2.8 26.5 + - - +
157A GLN* 1.3 76.1 - - - +
159A ILE* 1.3 59.5 + - - +
162A SER* 2.9 32.1 + - - -
166A VAL* 3.3 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 3.8 22.4 - - + -
30A LEU 3.9 10.5 - - - +
31A ILE* 4.8 7.9 - - + -
32A GLU 5.1 4.3 - - - +
36A GLU* 4.0 22.0 - - + +
153A LEU 4.3 4.0 - - - +
154A TYR* 3.6 17.9 - - - +
155A SER 3.1 18.7 + - - +
156A PRO* 3.7 5.6 - - + +
158A VAL* 1.3 78.6 - - - +
160A ARG* 1.3 61.7 + - - +
162A SER* 3.3 4.2 + - - -
163A THR* 3.2 1.9 + - - -
164A GLY 3.0 27.8 + - - +
166A VAL* 4.0 11.4 - - + -
167A PHE* 3.8 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU 6.0 0.4 - - - +
36A GLU* 4.8 6.5 - - - +
89A VAL* 4.5 15.6 + - + -
90A ARG* 3.8 67.0 - - - +
91A ASP* 4.8 6.9 + - - +
92A ASN 5.5 0.4 + - - -
135A ARG* 5.4 0.2 + - - -
156A PRO 3.0 18.1 + - - +
157A GLN* 4.2 1.8 - - - +
159A ILE* 1.3 79.5 - - - +
161A ASN* 1.3 69.7 + - - +
163A THR* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 161 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLY* 2.9 40.6 + - - +
129A ASN* 5.8 0.2 - - - +
131A GLY* 3.2 12.0 - - - +
132A ALA* 3.5 18.5 + - + +
135A ARG* 3.6 18.4 + - - +
157A GLN* 3.0 20.3 + - - +
160A ARG* 1.3 88.3 + - - +
162A SER* 1.3 57.1 + - - +
163A THR* 3.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 162 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLY* 3.1 17.0 - - - -
134A LEU* 4.3 6.5 - - - -
135A ARG* 4.1 6.9 - - - +
158A VAL 2.9 23.2 + - - -
159A ILE 3.3 1.4 + - - -
160A ARG 3.1 0.4 - - - -
161A ASN* 1.3 76.3 - - - +
163A THR* 1.3 74.0 + - - +
164A GLY 3.2 12.1 + - - -
165A VAL* 3.0 23.3 + - - +
166A VAL* 3.4 27.6 + - - +
----------------------------------------------------------
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