Contacts of the helix formed by residues 139 - 158 (chain D) in PDB entry 3IML
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 139 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 6.2 0.2 - - + -
129D TYR* 3.8 23.1 - - + +
130D ALA* 5.5 0.2 - - - -
131D CYS* 3.5 14.9 - - - -
133D GLU* 3.7 4.7 - - - +
137D LEU 4.7 0.9 - - - +
138D MET* 1.3 103.0 - - + +
140D LEU* 1.3 65.3 + - - +
141D PRO* 4.0 9.9 - - + -
142D ILE* 3.4 13.1 - - + +
143D HIS* 3.3 17.7 + - - +
176D TYR* 5.0 0.7 - - - +
255D TYR* 4.4 5.2 - - + +
258D ALA* 3.6 33.4 - - + -
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D GLU* 3.0 24.3 + - + +
134D THR* 3.9 24.5 - - + -
138D MET 3.5 1.4 + - - -
139D PRO* 1.3 71.0 - - - +
141D PRO* 1.3 72.8 - - + +
143D HIS* 3.0 2.1 + - - +
144D LEU* 2.9 57.9 + - + +
174D VAL* 4.1 17.5 - - + -
176D TYR* 4.1 1.6 - - - +
181D PRO* 3.8 20.4 - - + -
216D PRO* 4.7 7.2 - - + -
219D LEU* 3.4 32.8 - - + -
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Residues in contact with PRO 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D PHE* 3.7 21.8 - - + +
9D SER* 3.4 28.2 - - - +
139D PRO* 3.5 10.5 - - + -
140D LEU* 1.3 91.1 - - + +
142D ILE* 1.3 59.9 + - - +
144D LEU 3.9 0.2 + - - -
145D SER* 2.9 28.4 + - - -
172D VAL* 3.9 15.8 - - + +
174D VAL* 4.1 19.5 - - + -
176D TYR* 3.2 24.5 - - + +
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Residues in contact with ILE 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D SER* 3.4 5.9 + - - +
10D GLU 3.4 25.1 - - - +
138D MET* 3.7 23.1 - - + -
139D PRO* 3.4 26.9 - - + +
141D PRO* 1.3 77.7 - - - +
143D HIS* 1.3 65.0 + - - +
145D SER* 3.3 2.6 + - - -
146D HIS* 2.9 55.2 + - + +
252D VAL* 3.8 10.1 - - - +
254D THR 4.1 5.6 - - - +
255D TYR 3.9 13.9 - - - +
256D GLY* 3.7 26.0 - - - +
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Residues in contact with HIS 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D THR* 3.6 23.0 + - + +
135D PRO* 5.4 0.8 - - - +
136D GLU* 3.3 34.2 + - + +
138D MET* 4.2 19.0 - - + +
139D PRO 3.3 15.9 - - - +
140D LEU 3.0 3.5 + - - +
142D ILE* 1.3 83.2 - - - +
144D LEU* 1.3 72.5 + - + +
146D HIS* 3.3 8.9 + - - +
147D ARG* 2.9 65.1 + - + +
365D GLY* 4.2 9.7 + - - -
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D LEU* 2.9 44.1 + - + +
141D PRO 4.4 0.9 - - - +
143D HIS* 1.3 84.3 - - + +
145D SER* 1.3 65.6 + - - +
147D ARG* 3.8 4.6 - - + +
148D LEU* 3.0 30.8 + - + +
172D VAL* 4.1 25.4 - - + -
174D VAL* 5.1 0.2 - - + -
184D ILE* 4.0 26.7 - - + -
214D THR* 3.6 31.4 - - + +
215D LEU* 4.9 6.5 - - + -
216D PRO* 3.9 12.8 - - + -
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Residues in contact with SER 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D SER 3.4 16.5 + - - -
10D GLU* 3.6 20.9 - - - -
11D SER* 3.4 5.1 - - - -
141D PRO 2.9 21.4 + - - -
142D ILE* 3.5 6.3 - - - -
143D HIS 3.3 0.2 - - - -
144D LEU* 1.3 78.9 - - - +
146D HIS* 1.3 63.1 + - - +
148D LEU 3.5 5.5 + - - -
149D VAL* 3.5 5.9 + - - +
170D SER* 2.7 29.2 + - - -
172D VAL* 3.4 19.6 + - - +
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Residues in contact with HIS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D SER* 2.8 28.7 + - - -
138D MET* 5.3 1.1 - - + -
142D ILE* 2.9 39.7 + - + +
143D HIS* 3.5 7.2 - - - +
145D SER* 1.3 77.6 - - - +
147D ARG* 1.3 83.9 + - - +
149D VAL* 3.3 4.9 - - - +
150D GLU* 3.1 23.2 + - - +
252D VAL* 2.9 35.2 + - + -
254D THR 4.8 2.6 + - - -
361D TYR* 3.3 18.8 - - - +
362D GLY* 3.3 25.4 - - - -
364D PHE 4.5 9.6 - - - -
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Residues in contact with ARG 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D HIS* 2.9 53.8 + - + +
144D LEU* 3.3 4.5 + - + +
146D HIS* 1.3 105.5 - - - +
148D LEU* 1.3 56.8 - - - +
150D GLU* 2.8 34.6 + - + +
151D ARG* 2.9 30.0 + - - +
214D THR* 3.7 22.1 + - + -
361D TYR* 3.5 23.6 + - - +
364D PHE 5.5 0.2 + - - -
365D GLY* 4.2 11.3 + - - -
366D ARG* 3.6 18.7 - - - +
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Residues in contact with LEU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D LEU* 3.0 23.9 + - + +
145D SER 3.7 4.9 - - - +
146D HIS 3.2 0.4 - - - -
147D ARG* 1.3 74.5 - - - +
149D VAL* 1.3 61.7 + - - +
151D ARG* 3.3 6.6 + - - +
152D GLN* 3.0 21.1 + - - +
170D SER* 4.1 14.8 - - - -
172D VAL* 3.8 17.5 - - + -
187D VAL* 3.5 31.2 - - + -
189D LEU* 4.5 6.7 - - + -
210D VAL* 3.4 36.4 - - + +
211D ILE* 3.6 22.4 - - + +
214D THR* 3.7 14.8 - - + -
215D LEU* 4.4 6.3 - - + -
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Residues in contact with VAL 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER* 3.8 8.5 - - - +
12D VAL 3.7 19.5 - - - +
13D SER* 3.9 21.7 - - - +
145D SER 3.5 8.3 + - - +
146D HIS 3.3 11.9 - - - +
148D LEU* 1.3 72.9 - - - +
150D GLU* 1.3 67.4 + - - +
152D GLN* 3.2 10.1 + - + +
153D ALA* 3.1 22.7 + - - +
168D ALA* 4.1 8.5 - - + +
169D LYS* 3.9 7.6 - - - +
170D SER* 3.6 34.1 - - - +
189D LEU* 5.8 3.1 - - + -
361D TYR* 3.7 12.9 + - + -
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D HIS 3.1 17.3 + - - +
147D ARG* 2.8 46.5 + - + +
149D VAL* 1.3 78.3 - - - +
151D ARG* 1.3 57.1 + - - +
153D ALA* 3.3 3.8 + - - +
154D ASN* 3.0 44.3 + - - +
361D TYR* 3.6 31.4 - - + -
366D ARG* 4.2 16.0 + - - +
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Residues in contact with ARG 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ARG 2.9 19.0 + - - +
148D LEU* 3.3 7.6 - - - +
149D VAL 3.2 0.2 - - - -
150D GLU* 1.3 76.7 - - - +
152D GLN* 1.3 56.3 + - - +
154D ASN* 3.3 11.6 + - - +
155D LEU* 3.0 49.5 + - + +
209D GLU* 3.0 29.1 + - - +
210D VAL* 3.7 25.2 + - - +
213D PRO* 4.1 20.5 - - - +
214D THR* 4.1 11.0 - - - +
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Residues in contact with GLN 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D SER* 4.5 1.8 - - - -
148D LEU 3.0 12.8 + - - +
149D VAL* 3.2 14.2 + - + +
151D ARG* 1.3 74.9 - - - +
153D ALA* 1.3 82.0 + - - +
155D LEU* 4.4 2.5 - - - -
156D ARG* 2.9 27.4 + - - +
164D LEU* 3.2 29.7 - - + +
165D ARG 3.3 16.9 + - - -
166D PRO 4.1 9.4 - - - +
168D ALA* 3.7 26.3 - - + +
189D LEU* 5.4 6.7 - - + -
191D THR* 2.9 28.2 + - - +
210D VAL* 4.2 17.5 - - + +
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Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D SER* 5.5 0.4 - - - -
14D GLU* 3.5 12.6 - - + +
149D VAL 3.1 4.8 + - - +
150D GLU 3.6 7.0 - - - +
152D GLN* 1.3 87.4 + - - +
154D ASN* 1.3 61.9 + - - +
156D ARG* 3.2 14.3 + - - +
157D ARG* 2.9 42.1 + - - +
166D PRO 6.0 0.2 - - - +
361D TYR* 3.3 27.8 - - + +
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Residues in contact with ASN 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D GLU* 3.0 38.5 + - - +
151D ARG* 3.3 10.1 + - - +
153D ALA* 1.3 77.5 - - - +
155D LEU* 1.3 58.7 + - + +
157D ARG* 3.2 15.8 + - - +
158D ASP* 2.8 39.5 + - - +
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Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ARG* 3.0 42.8 + - - +
152D GLN* 3.9 4.3 - - - +
154D ASN* 1.3 76.3 - - + +
156D ARG* 1.3 65.8 + - - +
158D ASP* 4.1 8.1 - - - +
159D GLY 3.4 1.6 + - - -
160D ARG* 3.2 50.0 + - + -
161D LEU* 3.5 11.4 + - + -
164D LEU* 4.0 10.8 - - + -
209D GLU* 3.5 38.4 - - + +
210D VAL* 3.7 21.3 - - + -
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Residues in contact with ARG 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLU* 4.0 12.9 - - - +
76D ARG 5.3 0.2 + - - -
77D ILE 3.1 28.4 + - - -
78D GLY* 3.9 12.9 + - - -
152D GLN* 2.9 24.0 + - - +
153D ALA* 3.2 12.3 + - - +
155D LEU* 1.3 76.4 - - - +
157D ARG* 1.3 91.8 + - - +
159D GLY* 3.4 11.4 + - - -
161D LEU 4.4 3.6 - - - +
162D PRO* 5.6 1.3 - - - +
164D LEU* 3.6 30.7 - - + +
165D ARG* 3.4 29.3 + - - +
166D PRO* 3.5 20.5 + - - +
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Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D GLU* 2.6 44.6 + - - -
76D ARG* 3.6 25.5 + - - +
77D ILE 4.4 0.2 + - - -
153D ALA* 2.9 25.6 + - - +
154D ASN* 3.2 15.1 + - - +
156D ARG* 1.3 100.3 - - - +
158D ASP* 1.3 60.4 + - - +
159D GLY 3.2 1.1 + - - -
361D TYR* 5.0 2.4 - - - -
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Residues in contact with ASP 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ASN* 2.8 30.9 + - - +
155D LEU* 4.1 6.2 - - - +
157D ARG* 1.3 76.5 - - + +
159D GLY* 1.3 57.9 + - - +
160D ARG* 3.4 27.1 - - - +
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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
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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