Contacts of the helix formed by residues 129 - 138 (chain A) in PDB entry 1IC8
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 PRO 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN 3.8 7.4 - - - +
128A ILE* 1.3 89.2 - - + +
130A GLN* 1.3 67.1 + - - +
131A ARG* 4.2 5.6 - - + +
132A GLU* 2.9 40.0 + - + +
133A VAL* 3.7 1.7 + - - +
202A ASN* 3.9 30.3 - - + +
203A ARG 4.5 11.4 - - - +
205A LYS* 6.1 3.1 - - + -
256A SER* 6.0 0.2 - - - +
257A ASN* 5.3 3.6 - - - +
310E T 5.1 9.0 - - - +
311E A 3.3 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 5.0 11.0 - - + -
128A ILE 3.1 6.7 + - - -
129A PRO* 1.3 69.4 - - - +
131A ARG* 1.3 64.2 + - - +
133A VAL* 2.9 26.5 + - - +
134A VAL* 3.5 6.5 + - + +
141A GLN* 2.9 38.7 + - - +
144A LEU* 4.2 17.9 - - + +
145A SER* 3.6 20.8 - - - +
148A LEU* 5.3 3.9 - - + +
149A ASN* 4.4 3.0 - - - +
311E A 2.9 27.3 + - - +
312E A 2.6 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PRO* 4.6 5.2 - - + -
130A GLN* 1.3 76.9 - - - +
132A GLU* 1.3 55.0 + - - +
134A VAL* 3.0 9.7 + - - +
135A ASP* 2.8 66.2 + - - +
141A GLN* 6.2 2.9 - - - +
202A ASN* 6.0 1.8 - - - +
309E A 5.1 3.2 - - - +
310E T 3.0 44.7 + - + +
311E A 2.7 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 3.6 19.0 - - + +
129A PRO* 2.9 21.4 + - + +
131A ARG* 1.3 76.7 - - - +
133A VAL* 1.3 59.2 + - - +
135A ASP* 3.8 7.6 - - - +
136A THR* 3.0 35.2 + - + +
165A TRP* 4.3 10.6 + - + +
169A LYS* 2.6 33.5 + - - +
202A ASN* 3.0 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A LEU* 4.3 18.4 - - + -
128A ILE* 4.6 0.2 - - + -
129A PRO 4.2 6.3 - - - +
130A GLN* 2.9 14.0 + - - +
132A GLU* 1.3 79.1 - - - +
134A VAL* 1.3 52.1 + - - +
136A THR* 2.9 8.1 + - - -
137A THR* 2.6 55.6 + - + +
139A LEU* 5.2 0.2 - - + -
144A LEU* 4.0 16.2 - - + -
162A LEU* 3.9 22.0 - - + -
165A TRP* 3.5 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLN* 3.9 10.3 - - + +
131A ARG* 3.5 8.3 - - + +
133A VAL* 1.3 70.4 - - - +
135A ASP* 1.3 69.4 + - - +
136A THR 2.8 6.3 + - - -
137A THR* 3.9 7.4 - - - -
138A GLY* 2.9 22.3 + - - -
139A LEU 2.8 26.7 - - - +
140A ASN* 5.0 0.2 - - - -
141A GLN* 3.9 28.7 - - + +
144A LEU* 3.7 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ARG* 2.8 60.7 + - - +
132A GLU* 3.8 10.2 - - - +
134A VAL* 1.3 81.6 - - - +
136A THR* 1.3 62.3 + - + +
138A GLY* 5.6 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A GLU* 3.0 20.3 + - + +
133A VAL 2.9 13.3 + - - -
134A VAL 2.8 1.8 - - - -
135A ASP* 1.3 89.1 - - + +
137A THR* 1.3 62.3 + - - +
138A GLY* 3.2 2.3 + - - -
165A TRP* 3.1 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 2.6 39.0 + - + +
136A THR* 1.3 74.2 + - - +
138A GLY* 1.3 59.5 + - - +
139A LEU* 3.0 41.5 + - + +
161A ALA* 3.5 37.0 - - - +
162A LEU* 4.3 0.9 - - - -
165A TRP* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 2.9 14.8 + - - -
135A ASP 5.4 0.4 - - - -
136A THR 3.2 3.1 - - - -
137A THR* 1.3 78.6 - - - +
139A LEU* 1.3 62.9 + - - +
140A ASN 4.1 0.3 + - - -
158A LYS* 5.9 1.2 - - - +
----------------------------------------------------------
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