Contacts of the helix formed by residues 139 - 160 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I ARG* 3.9 11.1 + - - +
138I PHE* 1.3 75.7 - - - +
140I GLU* 1.3 60.1 + - - +
141I PRO* 3.4 12.8 - - - +
142I HIS* 3.0 23.4 + - - +
143I ALA* 2.7 27.4 + - - +
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Residues in contact with GLU 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137I ARG* 4.7 5.3 - - - +
139I SER* 1.3 71.1 - - - +
141I PRO* 1.3 66.4 - - + +
143I ALA* 3.6 5.6 - - - +
144I ARG* 2.8 39.6 + - - +
232I ALA* 4.6 5.8 - - + -
260I HIS* 3.6 12.3 + - - +
261I PHE* 3.7 4.3 - - + -
262I SER* 2.7 49.9 + - - -
265I LEU* 3.5 24.2 - - + -
296I TRP* 3.0 22.3 + - + +
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Residues in contact with PRO 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I SER* 3.4 14.1 - - - +
140I GLU* 1.3 95.0 - - + +
142I HIS* 1.3 59.9 + - - +
144I ARG* 3.7 23.8 - - - +
145I PHE* 3.1 24.1 + - - +
313I PRO* 5.7 0.7 - - - -
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Residues in contact with HIS 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I ILE* 4.9 5.0 - - + +
138I PHE* 3.6 32.5 - + + +
139I SER* 3.0 24.1 + - - +
141I PRO* 1.3 75.4 - - - +
143I ALA* 1.3 66.3 + - - +
144I ARG 3.3 0.7 + - - -
145I PHE* 3.3 11.3 + - - +
146I TYR* 2.9 57.8 + + - -
313I PRO* 3.2 35.5 + - + +
314I PHE* 4.0 20.1 - + + +
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Residues in contact with ALA 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I PHE* 4.1 3.4 - - + +
139I SER 2.7 20.4 + - - +
140I GLU* 3.6 8.1 - - - +
142I HIS* 1.3 73.4 - - - +
144I ARG* 1.3 55.2 + - - +
146I TYR* 3.3 2.3 + - - -
147I ALA* 3.0 24.3 + - - +
228I ILE 4.7 2.0 - - - +
231I MET* 3.4 44.1 - - + +
232I ALA* 4.2 15.3 - - + +
296I TRP* 4.2 9.4 - - + -
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Residues in contact with ARG 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I GLU* 2.8 28.7 + - - +
141I PRO* 3.7 30.0 - - - +
142I HIS 3.2 0.2 - - - -
143I ALA* 1.3 71.2 - - - +
145I PHE* 1.3 61.2 + - - +
147I ALA* 3.6 0.8 - - - +
148I ALA* 2.9 31.7 + - - +
296I TRP* 2.7 69.5 + - + +
297I PHE* 3.9 12.3 - - + -
299I THR* 4.0 20.9 + - - +
300I THR* 3.6 23.6 - - - +
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Residues in contact with PHE 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I PRO 3.1 13.6 + - - +
142I HIS 3.4 8.3 - - - +
144I ARG* 1.3 76.8 - - - +
146I TYR* 1.3 71.5 + + - +
148I ALA* 3.8 6.2 + - - +
149I GLN* 3.1 46.9 + - - +
178I GLY 3.4 18.6 - - - -
179I TYR* 3.7 44.0 - + - -
305I ILE* 5.0 9.3 - - + +
310I VAL* 4.1 25.4 - - + -
311I GLU 4.7 0.9 - - - -
312I ALA* 3.9 11.9 - - + -
313I PRO* 3.4 28.3 - - + -
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Residues in contact with TYR 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I MET* 3.4 22.0 - - + -
138I PHE* 3.5 18.0 - + - -
142I HIS* 2.9 46.4 + + - -
143I ALA 3.3 5.8 + - - +
144I ARG 3.2 0.4 - - - -
145I PHE* 1.3 93.4 - + - +
147I ALA* 1.3 65.6 + - - +
149I GLN* 3.2 10.3 + - - +
150I ILE* 3.2 25.8 + - + +
174I ILE* 3.9 18.9 - - + +
178I GLY 3.7 18.3 + - - -
180I ILE* 3.7 18.2 - - + +
231I MET* 3.8 19.5 - - + -
313I PRO* 4.6 1.5 - - + +
314I PHE* 3.7 22.3 + - - +
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Residues in contact with ALA 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I ALA 3.0 17.7 + - - +
144I ARG* 3.2 7.8 + - - +
146I TYR* 1.3 74.3 - - - +
148I ALA* 1.3 60.6 + - - +
150I ILE* 3.0 10.0 + - - +
151I VAL* 2.8 34.1 + - - +
224I LEU* 4.4 3.4 - - + +
228I ILE* 3.7 34.8 - - + -
231I MET* 4.2 4.7 - - + +
296I TRP* 4.3 1.6 - - + -
297I PHE* 3.9 11.0 - - + -
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Residues in contact with ALA 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144I ARG 2.9 17.0 + - - +
145I PHE* 3.8 3.4 - - - +
147I ALA* 1.3 75.9 - - - +
149I GLN* 1.3 62.7 + - - +
152I LEU* 3.2 23.9 + - - +
297I PHE* 3.9 3.7 - - + -
300I THR* 3.9 7.0 - - + -
302I TRP* 3.5 30.5 - - + -
305I ILE* 3.2 34.5 - - + -
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Residues in contact with GLN 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102I PHE* 3.6 27.5 - - + -
145I PHE* 3.1 50.6 + - - +
146I TYR* 3.2 18.1 + - - +
147I ALA 3.1 0.8 - - - -
148I ALA* 1.3 77.7 - - - +
150I ILE* 1.3 52.9 + - - +
152I LEU* 3.5 1.0 + - - +
153I THR* 2.7 36.6 + - - -
179I TYR* 3.2 17.6 - - - +
180I ILE* 2.7 38.2 + - + +
305I ILE* 3.8 18.4 - - + -
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Residues in contact with ILE 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146I TYR 3.4 13.9 - - - +
147I ALA* 3.0 6.1 + - - +
149I GLN* 1.3 75.3 - - - +
151I VAL* 1.3 60.5 + - - +
153I THR* 3.2 4.1 + - + +
154I PHE* 2.8 63.5 + - + +
167I LEU* 3.9 9.0 - - + -
172I LEU* 3.9 30.7 - - + -
180I ILE* 4.2 17.3 - - + -
182I VAL* 4.3 9.9 - - + -
224I LEU* 3.8 17.9 - - + -
227I LEU* 4.0 19.7 - - + -
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Residues in contact with VAL 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147I ALA 2.8 23.4 + - - +
148I ALA 3.7 5.2 - - - +
150I ILE* 1.3 76.4 - - - +
152I LEU* 1.3 57.3 + - - +
155I GLU* 2.9 27.0 + - - +
221I TRP* 3.8 11.7 - - + -
224I LEU* 3.7 23.8 - - + -
288I VAL* 3.8 22.7 - - + -
291I ILE* 3.8 17.3 - - + -
292I LYS* 3.9 11.0 - - + -
297I PHE* 4.2 10.5 - - + -
302I TRP* 3.8 20.9 - - + -
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Residues in contact with LEU 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100I PHE* 3.5 23.5 - - + -
102I PHE* 4.3 5.2 - - + -
148I ALA 3.2 16.6 + - - +
149I GLN 3.8 4.0 - - - +
151I VAL* 1.3 78.8 - - - +
153I THR* 1.3 59.1 + - - +
155I GLU* 3.4 23.1 + - - +
156I TYR 3.0 22.7 + - - -
292I LYS* 3.6 23.8 - - - +
302I TRP* 3.6 37.0 - - + +
305I ILE* 4.1 16.8 - - + -
306I TYR* 4.1 16.6 - - + +
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Residues in contact with THR 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I PHE* 3.6 10.8 - - + -
102I PHE* 3.5 22.5 - - - +
103I LEU* 3.5 35.0 - - + -
149I GLN 2.7 22.5 + - - -
150I ILE* 3.2 8.6 + - - +
152I LEU* 1.3 77.0 - - - +
154I PHE* 1.3 62.9 + - + +
156I TYR* 3.3 3.3 + - - +
157I LEU* 2.9 38.6 + - + +
182I VAL* 4.4 12.9 - - + +
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Residues in contact with PHE 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I ILE* 2.8 39.0 + - + +
153I THR* 1.3 78.0 - - + +
155I GLU* 1.3 60.1 + - - +
157I LEU* 4.3 13.7 - - + -
158I HIS* 2.8 43.9 + - + -
164I TYR* 4.0 25.6 - + + -
167I LEU* 3.9 30.1 - - + -
182I VAL* 6.2 1.8 - - + -
220I ASP* 3.3 49.8 - - + -
221I TRP* 3.5 33.9 - + + -
224I LEU* 4.6 2.0 - - + -
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Residues in contact with GLU 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15I VAL* 3.4 27.1 - - - +
19I LEU* 4.3 13.5 - - + +
151I VAL 2.9 17.6 + - - +
152I LEU* 3.5 15.4 - - - +
154I PHE* 1.3 76.8 - - - +
156I TYR* 1.3 61.2 + - - +
158I HIS* 4.1 2.3 - - - +
159I SER* 3.1 24.9 + - - -
221I TRP* 4.3 5.1 - - - -
288I VAL* 3.7 30.1 - - + +
289I ASN* 5.3 1.0 - - - +
292I LYS* 3.1 31.2 + - - +
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Residues in contact with TYR 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I PHE* 4.5 6.7 - + - -
19I LEU* 4.2 8.7 - - + -
22I ALA* 3.7 33.6 + - + -
26I PHE* 5.2 0.7 - - - +
97I ALA 4.7 0.9 + - - -
98I VAL* 3.4 20.3 - - + -
99I ASN* 2.8 40.1 + - - +
100I PHE* 3.6 41.5 - + + -
103I LEU* 4.3 2.2 - - + -
152I LEU 3.0 13.2 + - - +
153I THR 3.6 7.6 - - - +
155I GLU* 1.3 75.3 - - - +
157I LEU* 1.3 81.1 + - + +
159I SER* 2.6 24.3 + - - -
160I LEU* 3.4 31.3 + - + +
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Residues in contact with LEU 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I VAL* 4.5 1.8 - - + -
103I LEU* 4.2 7.6 - - + -
153I THR* 2.9 36.0 + - + +
154I PHE* 4.0 10.3 - - + +
156I TYR* 1.3 90.2 - - + +
158I HIS* 1.3 61.0 + - + +
160I LEU* 3.0 13.5 + - - +
162I LEU* 3.0 59.1 + - + +
163I ILE 5.3 0.4 - - - -
164I TYR* 4.1 28.7 - - + +
182I VAL* 6.3 0.7 - - + -
185I PHE* 4.2 29.2 - - + -
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Residues in contact with HIS 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I PHE* 2.8 31.8 + + + +
155I GLU* 4.3 2.2 - - - +
157I LEU* 1.3 72.1 - - + +
159I SER* 1.3 65.8 + - - +
160I LEU 3.1 1.8 - - - -
161I ASP* 3.0 14.5 + - - +
162I LEU 3.1 21.1 - - - -
163I ILE* 4.7 0.2 - - - -
217I LYS* 3.5 56.9 + - + +
220I ASP* 2.8 32.0 + - + +
221I TRP* 3.4 38.8 + + + -
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Residues in contact with SER 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LEU* 3.6 37.0 + - - +
22I ALA* 5.5 0.5 - - - +
23I LYS* 4.6 12.9 - - - +
155I GLU 3.1 16.7 + - - -
156I TYR* 2.6 20.6 + - - -
158I HIS* 1.3 76.9 - - - +
160I LEU* 1.3 67.6 + - - +
161I ASP* 3.2 7.8 + - - +
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Residues in contact with LEU 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I ALA* 4.1 2.5 - - + +
23I LYS* 3.6 40.8 - - + +
26I PHE* 3.8 36.1 - - + -
98I VAL* 4.2 6.1 - - + -
156I TYR* 3.5 48.9 - - + +
157I LEU 3.0 8.7 + - - +
159I SER* 1.3 82.5 - - - +
161I ASP* 1.3 65.0 + - - +
162I LEU* 3.2 13.0 + - + +
190I ARG* 2.8 31.5 + - - +
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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