Contacts of the helix formed by residues 139 - 160 (chain P) in PDB entry 3E8E
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 139 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137P ARG* 5.0 7.2 - - - +
138P PHE* 1.3 77.1 - - - +
140P GLU* 1.3 55.3 + - - +
141P PRO* 3.6 10.8 - - - +
142P HIS* 3.1 25.6 + - - +
143P ALA* 2.7 32.6 + - - +
232P ALA* 5.7 0.2 - - - -
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Residues in contact with GLU 140 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139P SER* 1.3 73.2 - - - +
141P PRO* 1.3 62.1 - - + +
143P ALA* 4.3 4.5 - - - -
144P ARG* 2.8 44.8 + - - +
232P ALA* 4.7 7.4 - - + -
260P HIS* 3.8 10.1 - - + +
261P PHE* 3.8 1.6 - - - -
262P SER* 2.7 50.5 + - - -
265P LEU* 3.4 25.8 - - + +
296P TRP* 3.1 21.9 + - + +
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Residues in contact with PRO 141 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139P SER* 3.5 13.5 - - - +
140P GLU* 1.3 96.1 - - + +
142P HIS* 1.3 59.2 + - - +
144P ARG* 3.5 24.4 - - - +
145P PHE* 3.2 21.5 + - - +
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Residues in contact with HIS 142 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135P ILE* 5.2 5.8 - - + +
138P PHE* 3.9 26.6 - + + +
139P SER* 3.1 26.9 + - - +
141P PRO* 1.3 75.1 - - - +
143P ALA* 1.3 66.6 + - - +
145P PHE* 3.1 16.6 + - - +
146P TYR* 2.9 51.8 + + - -
313P PRO* 3.2 41.4 + - + +
314P PHE* 3.8 18.8 - + + -
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Residues in contact with ALA 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138P PHE* 4.0 6.8 - - + +
139P SER 2.7 20.2 + - - +
140P GLU* 3.8 7.4 - - - +
142P HIS* 1.3 73.5 - - - +
144P ARG* 1.3 56.4 + - - +
146P TYR 3.3 1.7 + - - -
147P ALA* 3.0 24.8 + - - +
228P ILE 4.9 1.3 - - - +
231P MET* 3.2 45.2 - - + +
232P ALA* 4.5 11.9 - - + +
296P TRP* 4.1 9.6 - - + -
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Residues in contact with ARG 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140P GLU* 2.8 29.4 + - - +
141P PRO* 3.5 35.8 - - - +
143P ALA* 1.3 70.5 - - - +
145P PHE* 1.3 67.7 + - - +
147P ALA* 3.7 0.9 - - - +
148P ALA* 3.0 23.6 + - - +
296P TRP* 2.7 71.9 + - + +
297P PHE* 4.1 10.4 - - + -
299P THR* 4.1 18.8 + - - -
300P THR* 3.3 26.2 - - - +
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Residues in contact with PHE 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141P PRO 3.2 12.4 + - - +
142P HIS* 3.1 12.0 + - - +
144P ARG* 1.3 80.5 - - - +
146P TYR* 1.3 69.9 + + - +
148P ALA* 3.7 14.0 + - - +
149P GLN* 3.1 37.6 + - - +
178P GLY 3.5 20.4 - - - -
179P TYR* 3.7 36.3 - + - -
305P ILE* 4.8 11.1 - - + +
310P VAL* 4.0 26.5 - - + -
311P GLU 4.3 4.5 - - - -
312P ALA* 3.8 11.7 - - + -
313P PRO* 3.4 26.2 - - + -
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Residues in contact with TYR 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128P MET* 3.5 28.9 - - + -
138P PHE* 3.7 23.4 - + - -
142P HIS* 2.9 47.8 + + - -
143P ALA 3.3 5.0 + - - +
144P ARG 3.3 0.4 - - - -
145P PHE* 1.3 87.6 - + - +
147P ALA* 1.3 65.5 + - - +
148P ALA 3.2 0.2 - - - -
149P GLN* 3.1 19.3 + - - +
150P ILE* 3.3 18.1 + - + +
174P ILE* 4.3 12.6 - - + +
178P GLY 3.6 23.0 + - - -
180P ILE* 3.7 24.6 - - + +
227P LEU* 6.2 0.2 - - + -
231P MET* 4.0 8.5 - - - -
313P PRO* 4.2 3.4 - - + +
314P PHE* 4.2 17.0 + - - +
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Residues in contact with ALA 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143P ALA 3.0 17.1 + - - +
144P ARG 3.7 4.5 - - - +
146P TYR* 1.3 76.6 - - - +
148P ALA* 1.3 62.4 - - - +
150P ILE* 3.4 9.2 + - - +
151P VAL* 3.0 30.3 + - - +
224P LEU* 4.4 4.6 - - + +
227P LEU* 5.6 0.2 - - - -
228P ILE* 3.7 35.0 - - + -
231P MET* 4.2 4.2 - - + +
296P TRP* 4.1 10.1 - - + -
297P PHE* 4.2 4.3 - - + -
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Residues in contact with ALA 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144P ARG 3.0 16.6 + - - +
145P PHE* 3.7 3.6 - - - +
146P TYR 3.2 0.2 - - - -
147P ALA* 1.3 77.6 - - - +
149P GLN* 1.3 56.5 + - - +
151P VAL 3.3 0.7 + - - -
152P LEU* 3.0 27.3 + - - +
297P PHE* 4.0 3.3 - - + -
300P THR* 3.9 7.0 - - + -
302P TRP* 3.3 30.8 - - + -
305P ILE* 3.2 34.5 - - + -
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Residues in contact with GLN 149 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P PHE* 3.8 28.0 - - + -
145P PHE* 3.1 53.0 + - - +
146P TYR* 3.1 14.7 + - - +
148P ALA* 1.3 76.8 - - - +
150P ILE* 1.3 58.3 + - + +
152P LEU* 3.4 3.8 + - - +
153P THR* 2.8 34.4 + - - -
179P TYR* 3.4 15.9 - - - +
180P ILE* 2.7 39.4 + - + +
305P ILE* 3.9 18.2 - - + -
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Residues in contact with ILE 150 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P PHE* 6.3 0.2 - - + -
146P TYR* 3.3 15.7 + - + +
147P ALA* 3.8 6.1 - - - +
148P ALA 3.3 0.2 - - - -
149P GLN* 1.3 75.4 - - - +
151P VAL* 1.3 56.6 + - - +
153P THR* 3.6 4.3 - - - +
154P PHE* 2.8 68.0 + - + +
167P LEU* 3.8 7.6 - - + -
172P LEU* 4.0 28.5 - - + -
180P ILE* 4.1 17.7 - - + -
182P VAL* 4.1 11.7 - - + -
224P LEU* 3.8 16.4 - - + -
227P LEU* 4.0 18.4 - - + -
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Residues in contact with VAL 151 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147P ALA 3.0 24.5 + - - +
148P ALA 3.7 4.3 - - - +
150P ILE* 1.3 71.9 - - - +
152P LEU* 1.3 62.6 + - - +
155P GLU* 3.0 26.7 + - - +
221P TRP* 3.9 11.6 - - + -
224P LEU* 3.5 26.5 - - + -
288P VAL* 3.7 24.9 - - + -
291P ILE* 3.9 21.3 - - + -
292P LYS* 4.3 5.8 - - + -
297P PHE* 4.3 9.2 - - + -
302P TRP* 4.1 17.9 - - + -
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Residues in contact with LEU 152 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100P PHE* 3.6 19.7 - - + -
102P PHE* 4.5 4.5 - - + -
148P ALA 3.0 17.9 + - - +
149P GLN* 3.7 5.2 - - - +
151P VAL* 1.3 76.8 - - - +
153P THR* 1.3 58.3 + - - +
155P GLU* 3.4 13.1 + - - +
156P TYR 3.1 21.5 + - - -
292P LYS* 3.6 34.5 - - - +
302P TRP* 3.7 35.2 - - + +
305P ILE* 4.2 10.5 - - + -
306P TYR* 3.7 30.3 - - + +
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Residues in contact with THR 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100P PHE* 3.7 13.3 - - + -
102P PHE* 3.6 22.2 + - - +
103P LEU* 3.5 34.5 - - + -
149P GLN 2.8 24.2 + - - -
150P ILE* 3.7 8.0 - - - +
152P LEU* 1.3 74.8 - - - +
154P PHE* 1.3 63.9 + - + +
156P TYR* 3.3 3.5 + - - +
157P LEU* 2.9 37.7 + - + +
182P VAL* 4.3 13.3 - - + +
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Residues in contact with PHE 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150P ILE* 2.8 43.0 + - + +
153P THR* 1.3 76.9 - - + +
155P GLU* 1.3 59.5 + - - +
157P LEU* 4.3 11.2 - - + -
158P HIS* 2.9 45.7 + - - +
164P TYR* 3.9 27.8 - + + -
167P LEU* 3.8 28.5 - - + -
182P VAL* 6.2 2.9 - - + -
220P ASP* 3.3 47.3 - - + -
221P TRP* 3.7 30.3 - + + -
224P LEU* 4.5 2.2 - - + -
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Residues in contact with GLU 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P VAL* 3.8 21.8 - - - +
19P LEU* 4.2 16.6 - - + +
151P VAL 3.0 19.1 + - - +
152P LEU* 3.4 15.1 - - - +
153P THR 3.3 0.2 - - - -
154P PHE* 1.3 77.3 - - - +
156P TYR* 1.3 60.5 + - - +
158P HIS* 4.2 2.9 - - - +
159P SER* 3.3 23.6 + - - -
221P TRP* 4.4 5.3 - - - -
288P VAL* 3.1 35.2 - - + +
289P ASN* 5.1 1.0 - - - +
292P LYS* 3.2 30.0 + - - +
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Residues in contact with TYR 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P PHE* 4.3 11.7 - + - -
19P LEU* 4.2 8.3 - - + +
22P ALA* 3.9 28.1 + - + -
26P PHE* 5.1 0.7 - - - +
97P ALA 4.7 1.7 + - - -
98P VAL* 3.5 19.6 - - + -
99P ASN* 2.8 39.1 + - - +
100P PHE* 3.5 40.8 - + + -
103P LEU* 4.2 2.5 - - + -
152P LEU 3.1 11.1 + - - +
153P THR 3.5 6.5 - - - +
154P PHE 3.3 0.2 - - - -
155P GLU* 1.3 78.1 - - - +
157P LEU* 1.3 80.8 + - + +
159P SER* 2.6 23.5 + - - -
160P LEU* 3.5 32.2 - - + +
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Residues in contact with LEU 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98P VAL* 4.5 2.5 - - + -
103P LEU* 4.3 7.6 - - + -
153P THR* 2.9 33.8 + - + +
154P PHE* 4.1 9.4 - - + +
156P TYR* 1.3 93.2 - - + +
158P HIS* 1.3 61.4 + - + +
160P LEU* 3.0 18.2 + - - +
161P ASP 3.3 0.2 + - - -
162P LEU* 3.0 57.0 + - + +
163P ILE 5.5 0.2 - - - -
164P TYR* 4.1 28.3 - - + -
182P VAL* 6.2 0.4 - - + -
185P PHE* 4.3 28.3 - - + -
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Residues in contact with HIS 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154P PHE* 2.9 30.2 + + + +
155P GLU* 4.3 2.9 - - - +
157P LEU* 1.3 79.3 - - + +
159P SER* 1.3 56.0 + - - +
160P LEU 3.2 0.2 - - - -
161P ASP* 3.1 13.0 + - - +
162P LEU 3.3 20.4 - - - +
163P ILE* 4.8 0.2 - - - -
217P LYS* 3.4 65.8 + - + +
220P ASP* 2.8 31.3 + - + +
221P TRP* 3.5 33.2 + + + -
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Residues in contact with SER 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P LEU* 3.5 34.8 + - - +
23P LYS* 4.2 17.0 - - - +
155P GLU 3.3 15.1 + - - -
156P TYR* 2.6 20.3 + - - -
158P HIS* 1.3 76.5 - - - +
160P LEU* 1.3 68.4 + - - +
161P ASP* 3.2 5.5 + - - +
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Residues in contact with LEU 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P LEU 4.9 0.2 - - - +
22P ALA* 4.1 4.7 - - + +
23P LYS* 3.5 45.1 - - + +
26P PHE* 3.7 33.2 - - + -
98P VAL* 4.7 0.4 - - + -
156P TYR* 3.5 48.5 - - + +
157P LEU 3.0 6.6 + - - +
159P SER* 1.3 83.8 - - - +
161P ASP* 1.3 65.7 + - - +
162P LEU* 3.3 18.6 + - + +
190P ARG* 2.8 28.4 + - - +
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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) + - + + + + + -
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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