Contacts of the helix formed by residues 126 - 147 (chain A) in PDB entry 4OBP
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 LYS 126 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A THR 4.3 0.4 + - - -
125A LEU* 1.3 73.2 - - - +
127A GLU* 1.3 66.9 + - - +
128A ASP* 2.8 40.1 + - - +
129A TRP* 2.9 38.0 + - + +
130A ILE* 3.2 5.2 + - - +
258A TRP* 5.4 0.2 - - - -
301A GLN* 3.2 29.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU 3.6 2.2 + - - -
126A LYS* 1.3 69.7 - - - +
128A ASP* 1.3 57.2 + - - +
130A ILE* 3.1 12.8 + - - +
131A ALA* 3.0 22.7 + - - -
258A TRP* 3.5 23.1 - - + -
259A SER* 2.5 52.1 + - - -
262A PHE* 3.6 23.4 - - + +
288A PHE* 3.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LYS* 2.8 31.8 + - - +
127A GLU* 1.3 75.6 - - - +
129A TRP* 1.3 63.7 + - - +
131A ALA* 3.6 9.3 + - + +
132A TYR* 3.2 25.8 + - - +
292A GLN* 4.3 3.0 - - + +
294A ASN* 3.6 26.4 + - + +
298A VAL* 3.4 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 4.3 7.9 - - + -
120A THR* 5.2 2.0 - - + -
125A LEU* 4.0 33.4 - - + -
126A LYS* 2.9 32.0 + - + +
128A ASP* 1.3 89.5 + - - +
130A ILE* 1.4 61.2 + - - +
132A TYR* 3.2 2.6 + - - +
133A ILE* 2.9 41.7 + - + +
298A VAL* 3.6 19.2 - - + +
301A GLN* 2.9 49.2 + - + +
302A LEU* 3.7 26.9 - - + -
305A HIS* 3.6 43.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 3.4 26.7 - - + +
126A LYS 3.6 9.0 - - - +
127A GLU* 3.1 7.4 + - - +
129A TRP* 1.4 74.8 - - - +
131A ALA* 1.4 54.3 + - - +
134A SER* 2.7 47.8 + - - +
223A ALA* 4.0 7.4 - - + +
226A MET* 3.8 30.0 - - + +
227A ALA* 3.8 31.9 - - + +
258A TRP* 4.1 6.3 - - + -
262A PHE* 3.7 35.0 - - + -
288A PHE* 4.1 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLU 3.0 9.6 + - - +
128A ASP* 3.7 12.3 - - + +
130A ILE* 1.4 76.4 - - - +
132A TYR* 1.4 60.6 + - - +
135A ARG* 3.2 15.9 + - - +
288A PHE* 3.5 47.2 - - + +
289A ILE* 3.8 3.3 - - - +
292A GLN* 2.9 27.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 5.1 2.3 + - - -
128A ASP 3.2 13.8 + - - +
129A TRP 3.2 3.1 + - - +
131A ALA* 1.4 73.8 - - - +
133A ILE* 1.3 67.4 + - + +
135A ARG* 3.4 33.2 + - - +
136A GLU* 3.2 44.7 + - + +
165A ALA 3.3 21.1 + - - -
166A GLU* 4.6 3.1 - - - -
167A VAL* 4.1 12.8 - - + -
292A GLN* 3.1 17.6 + - - +
295A GLU* 4.3 11.0 - - + -
298A VAL* 3.8 13.2 - - + -
299A ARG* 3.2 47.5 + - + -
302A LEU* 3.6 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 3.8 32.8 - - + -
116A LEU* 4.1 8.7 - - + -
125A LEU* 3.9 16.6 - - + -
129A TRP* 2.9 24.1 + - + +
132A TYR* 1.3 82.8 - - + +
134A SER* 1.4 60.3 + - - +
136A GLU* 3.2 5.0 + - - +
137A ILE* 3.0 39.7 + - + +
161A LEU* 5.3 0.2 - - + -
167A VAL* 4.3 20.8 - - + +
226A MET* 3.6 35.9 - - + -
302A LEU* 4.2 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ILE* 2.7 34.8 + - - +
131A ALA* 4.7 0.2 - - - -
133A ILE* 1.4 71.5 - - - +
135A ARG* 1.4 56.8 + - - +
137A ILE* 3.3 12.2 + - - +
138A LEU* 3.0 33.3 + - - +
219A CYS* 4.2 5.1 + - - -
223A ALA* 4.0 8.8 - - - +
226A MET* 3.5 14.6 - - - +
265A PHE* 4.0 15.4 - - - -
288A PHE* 4.8 0.2 - - - -
289A ILE* 3.6 20.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 5.5 1.2 - - - +
131A ALA 3.2 19.2 + - - +
132A TYR* 3.5 21.2 + - - +
133A ILE 3.3 0.2 - - - -
134A SER* 1.4 72.3 - - - +
136A GLU* 1.3 69.9 + - - +
138A LEU* 3.2 4.4 + - - +
139A ARG* 2.8 77.4 + - - +
284A LEU* 4.1 4.7 - - + -
289A ILE* 3.7 32.8 + - + +
290A ARG 5.7 1.4 + - - -
292A GLN* 3.6 23.3 - - - +
295A GLU* 3.1 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 3.0 20.2 + - - -
81A ASN* 2.8 39.2 + - - +
132A TYR* 3.2 36.3 + - + +
133A ILE 3.2 5.3 + - - +
135A ARG* 1.3 88.1 + - - +
137A ILE* 1.3 61.1 + - - +
139A ARG* 3.2 26.4 + - - -
140A GLY* 3.1 18.4 + - - -
166A GLU* 5.8 0.3 - - - -
167A VAL* 3.5 34.8 + - + +
169A LEU* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A ILE* 3.0 37.1 + - + +
134A SER* 3.5 12.1 - - - +
136A GLU* 1.3 74.7 - - - +
138A LEU* 1.3 57.1 + - - +
140A GLY* 3.3 3.5 + - - -
141A LEU* 2.9 40.4 + - + +
154A ILE* 4.5 10.8 - - + -
159A VAL* 3.7 28.0 - - + -
167A VAL* 4.5 1.1 - - + -
169A LEU* 3.9 20.1 - - + +
219A CYS* 4.0 20.9 - - + -
222A THR* 4.0 28.0 - - + -
226A MET* 4.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A SER 3.0 20.2 + - - +
135A ARG 3.2 4.2 + - - +
137A ILE* 1.3 73.1 - - - +
139A ARG* 1.3 53.6 + - - +
141A LEU* 3.3 6.0 + - + -
142A ALA* 2.7 32.9 + - - +
216A LEU* 3.6 31.4 - - + -
219A CYS* 3.9 18.8 - - + -
265A PHE* 4.0 15.7 - - + -
280A THR* 3.3 13.1 - - + +
283A LEU* 4.1 23.8 - - + +
284A LEU* 3.8 14.6 - - + +
289A ILE* 4.0 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 3.6 17.2 + - + +
80A ARG* 4.2 14.6 - - - +
81A ASN* 3.2 18.8 - - - +
135A ARG* 2.8 62.7 + - - +
136A GLU* 3.2 24.7 + - - +
138A LEU* 1.3 68.7 - - - +
140A GLY* 1.3 62.7 + - - +
142A ALA* 3.5 7.4 + - - +
143A HIS 3.2 17.0 + - - -
284A LEU* 3.9 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 4.2 1.3 - - - -
81A ASN* 3.6 20.7 - - - +
82A ILE* 3.5 16.1 - - - +
136A GLU 3.1 11.1 + - - -
137A ILE 3.6 3.6 - - - -
139A ARG* 1.3 76.2 - - - +
141A LEU* 1.4 61.1 + - - +
143A HIS* 3.4 6.2 + - - +
144A LEU* 3.2 18.4 + - - +
169A LEU* 3.8 15.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ILE* 2.9 35.7 + - + +
138A LEU* 3.6 10.8 - - + +
140A GLY* 1.4 72.7 - - - +
142A ALA* 1.3 54.6 + - - +
144A LEU* 3.1 6.3 + - + +
145A HIS* 2.7 52.1 + - + +
151A HIS* 3.9 8.3 - - + -
154A ILE* 3.8 23.1 - - + -
169A LEU* 4.1 7.0 - - + -
215A ASP* 3.7 51.6 - - + +
216A LEU* 4.3 11.2 - - + -
219A CYS* 4.5 1.3 - - + -
280A THR* 4.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU 2.7 20.7 + - - +
139A ARG* 3.7 6.3 - - - +
140A GLY 3.4 0.2 - - - -
141A LEU* 1.3 71.1 - - - +
143A HIS* 1.4 56.9 + - - +
145A HIS* 4.0 3.2 - - - +
146A ILE* 2.9 34.7 + - - +
280A THR* 3.6 14.3 - - + +
281A GLU* 5.7 5.4 - - + +
284A LEU* 4.0 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS 5.1 1.8 + - - -
76A TYR* 3.4 34.1 + - + -
78A HIS* 3.9 12.9 + - - +
79A HIS* 3.6 44.4 - + + +
82A ILE* 3.6 11.7 - - + -
139A ARG 3.2 5.2 + - - +
140A GLY 3.4 9.2 - - - +
141A LEU 3.2 0.6 - - - -
142A ALA* 1.4 78.1 - - - +
144A LEU* 1.3 61.3 + - + +
146A ILE* 3.4 10.0 - - - +
147A HIS* 2.7 56.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A TYR* 3.9 18.6 - - + +
82A ILE* 4.0 12.3 - - + -
140A GLY 3.2 12.7 + - - +
141A LEU* 3.1 11.2 + - + +
143A HIS* 1.3 77.9 - - - +
145A HIS* 1.3 63.6 + - + +
147A HIS* 3.1 11.4 + - - -
148A HIS 3.3 0.2 + - - -
149A VAL* 2.9 43.1 + - + +
151A HIS* 4.0 39.7 - - + +
169A LEU* 4.5 10.3 - - + -
172A PHE* 3.5 36.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 2.7 37.8 + - + +
142A ALA* 4.0 3.4 - - - +
144A LEU* 1.3 74.2 - - + +
146A ILE* 1.3 61.5 + - - +
148A HIS* 3.1 17.9 + - - +
149A VAL 3.2 20.4 - - - +
212A TYR* 3.3 50.8 + + + +
215A ASP* 2.8 29.4 + - + -
216A LEU* 4.3 4.3 - - + -
280A THR* 2.6 29.0 + - - +
281A GLU* 5.4 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA 2.9 16.7 + - - +
143A HIS* 3.4 20.4 - - - +
145A HIS* 1.3 75.7 - - - +
147A HIS* 1.3 72.9 + - + +
148A HIS* 3.3 21.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LYS* 4.2 21.6 + - - -
76A TYR* 3.7 33.4 + + + -
143A HIS* 2.7 53.6 + + - +
144A LEU* 3.1 9.4 + - - +
146A ILE* 1.3 88.3 - - + +
148A HIS* 1.4 76.9 + - - +
149A VAL* 3.3 10.4 + - + +
----------------------------------------------------------
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