Contacts of the helix formed by residues 128 - 148 (chain A) in PDB entry 1O8A
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 128 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A ALA 3.8 4.0 - - - +
127A LEU* 1.3 86.1 - - + +
129A ALA* 1.3 67.2 + - - +
130A GLN* 3.1 3.6 - - + +
131A GLU* 2.9 26.7 + - + +
132A LEU 2.9 18.5 + - - -
206A GLN* 3.7 21.1 - - - +
210A LEU* 4.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A MET* 4.0 11.2 - - + +
127A LEU 3.4 2.1 + - - -
128A PRO* 1.3 70.6 - - - +
130A GLN* 1.3 61.7 + - - +
132A LEU* 3.3 9.8 + - - +
133A GLU* 3.1 24.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
128A PRO* 3.0 3.4 + - + +
129A ALA* 1.3 79.4 - - - +
131A GLU* 1.3 79.2 + - - +
133A GLU* 3.4 18.5 - - + +
134A GLU* 3.2 24.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 4.1 8.9 - - + +
128A PRO* 2.9 35.3 + - + +
130A GLN* 1.3 99.4 + - - +
132A LEU* 1.3 58.2 + - - +
134A GLU* 3.3 11.8 + - - +
135A TYR* 2.8 30.8 + - - +
203A LEU* 3.8 26.6 - - + +
206A GLN* 3.9 18.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A MET* 3.4 24.5 - - + -
89A ALA* 3.6 27.1 - - + -
124A ARG* 3.6 43.3 - - + +
125A ALA* 4.7 4.3 - - - +
127A LEU* 4.1 20.8 - - + +
128A PRO 2.9 11.9 + - - +
129A ALA* 3.6 10.8 - - - +
130A GLN 3.2 0.2 - - - -
131A GLU* 1.3 77.8 - - - +
133A GLU* 1.3 57.2 + - - +
135A TYR* 3.2 1.9 + - + +
136A ASN* 2.8 50.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 5.6 0.2 - - - +
86A MET* 4.2 17.0 - - + +
129A ALA 3.1 14.5 + - - +
130A GLN* 3.4 18.3 - - + +
132A LEU* 1.3 77.1 - - - +
134A GLU* 1.3 64.8 + - + +
136A ASN* 3.4 6.2 + - - +
137A LYS* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLN* 3.2 15.9 + - + +
131A GLU* 3.7 11.5 - - - +
133A GLU* 1.3 84.9 - - + +
135A TYR* 1.3 55.8 + - - +
137A LYS* 3.4 6.3 + - - +
138A ILE* 2.9 41.8 + - + +
199A LYS* 3.1 37.9 - - - +
203A LEU* 3.9 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 3.8 41.4 + - + -
127A LEU* 4.0 12.8 - - + -
131A GLU 2.8 18.8 + - - +
132A LEU* 3.2 4.5 + - + +
134A GLU* 1.3 76.8 - - - +
136A ASN* 1.3 62.9 + - - +
138A ILE* 3.3 4.3 + - + +
139A LEU* 3.1 54.2 + - + +
200A TYR* 3.9 31.1 - + - -
203A LEU* 3.6 28.7 - - + +
204A ILE* 3.4 43.4 - - + +
207A ALA* 5.7 1.3 - - + -
517A SER* 4.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.8 17.7 - - + +
85A ASN* 3.6 28.9 + - + +
86A MET* 3.9 9.7 - - - -
124A ARG* 2.9 35.9 + - - +
132A LEU* 2.8 43.3 + - - +
133A GLU* 3.9 4.7 - - - +
135A TYR* 1.3 77.6 - - - +
137A LYS* 1.3 62.8 + - - +
139A LEU* 3.4 7.0 + - - +
140A LEU* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 4.2 23.4 - - + +
133A GLU 3.0 17.7 + - - +
134A GLU* 3.8 6.3 - - - +
135A TYR 3.3 0.2 - - - -
136A ASN* 1.3 74.4 - - - +
138A ILE* 1.3 61.2 + - + +
140A LEU* 3.3 3.1 + - + +
141A ASP* 2.8 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A GLU* 2.9 28.6 + - + +
135A TYR* 3.3 6.7 + - + +
137A LYS* 1.3 77.7 - - + +
139A LEU* 1.3 62.2 + - + +
141A ASP* 3.3 7.0 + - - +
142A MET* 2.9 31.8 + - + +
196A PHE* 4.1 23.7 - - + +
199A LYS* 3.4 41.1 - - + -
200A TYR* 3.9 26.9 - - + -
203A LEU* 3.9 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ARG* 3.4 39.9 - - - +
135A TYR* 3.1 41.3 + - + +
136A ASN* 3.7 4.3 - - - +
137A LYS 3.3 0.2 - - - -
138A ILE* 1.3 75.6 - - + +
140A LEU* 1.3 64.4 + - - +
142A MET* 3.3 12.0 + - + +
143A GLU* 3.0 24.3 + - - +
200A TYR* 3.9 33.9 - - + -
515A PRO 4.4 4.0 - - - +
516A SER 5.5 1.6 - - - +
517A SER* 4.1 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 3.3 43.2 + - + -
78A SER* 3.8 26.5 - - - +
81A LEU* 3.8 17.0 - - + -
82A LEU* 3.5 35.9 - - + -
136A ASN 3.1 17.2 + - - +
137A LYS* 3.7 4.9 - - + +
139A LEU* 1.3 78.4 - - - +
141A ASP* 1.3 60.1 + - - +
143A GLU* 4.5 2.5 - - + -
144A THR* 2.9 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LYS* 2.8 56.8 + - - +
138A ILE* 3.8 3.7 - - - +
140A LEU* 1.3 79.1 - - - +
142A MET* 1.3 56.3 + - - +
144A THR* 3.9 5.5 + - - -
145A THR* 2.7 38.3 + - - +
196A PHE* 3.7 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ILE* 2.9 20.4 + - + +
139A LEU* 3.8 13.0 - - + +
141A ASP* 1.3 75.8 - - - +
143A GLU* 1.3 64.6 + - - +
145A THR* 3.4 0.6 + - - -
146A TYR* 3.1 25.1 + - - +
193A ILE* 3.6 31.1 - - + +
196A PHE* 3.5 33.9 - - + -
197A TYR* 4.1 12.8 - - - -
200A TYR* 3.7 38.8 - - + -
515A PRO* 3.3 37.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 3.6 23.6 - - + +
70A ASN* 5.5 1.8 - - - +
139A LEU 3.0 17.3 + - - +
140A LEU* 3.7 5.8 - - + +
142A MET* 1.3 78.9 - - - +
144A THR* 1.3 61.8 + - - +
146A TYR* 3.4 4.4 + - - +
147A SER* 2.9 42.3 + - - -
351A VAL* 3.8 12.4 - - + +
512A PHE* 3.6 16.0 - - - -
515A PRO 4.4 4.8 + - - +
516A SER* 2.4 36.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A TYR* 2.7 29.5 + - - -
73A ILE* 4.1 22.1 - - + +
78A SER* 4.9 1.6 + - - +
140A LEU* 2.9 20.6 + - - +
141A ASP* 3.9 5.4 - - - -
143A GLU* 1.3 77.4 - - - +
145A THR* 1.3 64.3 + - - +
146A TYR 3.3 0.2 + - - -
147A SER* 3.3 5.0 + - - -
148A VAL* 3.1 40.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ASP* 2.7 24.6 + - - +
142A MET 3.7 4.0 - - - -
144A THR* 1.3 77.6 - - - +
146A TYR* 1.3 63.0 + - - +
148A VAL* 3.7 6.7 + - - +
149A ALA* 3.4 23.0 + - + +
188A LYS 5.1 1.1 - - - +
189A ALA* 4.9 1.8 - - - +
192A ALA* 3.6 34.5 - - + +
193A ILE* 3.9 15.0 - - + -
196A PHE* 3.9 12.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A MET 3.1 17.8 + - - +
143A GLU* 3.7 6.1 - - - +
145A THR* 1.3 79.8 - - - +
147A SER* 1.3 69.0 + - - +
148A VAL 3.3 1.0 + - - -
149A ALA* 3.5 8.5 + - - -
161A LEU* 3.4 25.7 - - + +
185A TRP* 3.6 31.5 - + - -
189A ALA* 4.4 6.7 - - + -
193A ILE* 4.6 3.6 - - + -
279A TRP* 3.6 13.3 - - - -
353A HIS* 5.8 1.8 - - + -
509A GLY 3.6 15.9 - - - -
510A ALA 3.5 22.2 - - - -
511A LYS 3.9 0.2 - - - -
512A PHE* 3.1 54.5 + + + +
515A PRO* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 4.2 7.2 - - - -
143A GLU* 2.9 32.1 + - - -
144A THR 4.1 2.5 - - - -
146A TYR* 1.3 82.4 - - - +
148A VAL* 1.3 60.1 + - - +
149A ALA 3.6 0.8 - - - +
160A GLN* 5.3 2.8 + - - -
349A GLU* 4.1 4.7 - - - +
350A VAL 3.9 23.8 - - - +
351A VAL* 3.6 22.7 - - - +
352A CYS 4.9 1.6 + - - -
512A PHE* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 4.3 13.2 - - + -
144A THR* 3.1 31.1 + - + +
145A THR* 4.1 6.3 - - - +
147A SER* 1.3 79.3 - - - +
149A ALA* 1.3 68.1 + - - +
150A THR* 3.6 11.0 + - - +
160A GLN* 5.7 1.8 - - - +
349A GLU* 3.3 45.0 - - + +
----------------------------------------------------------
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