Contacts of the helix formed by residues 139 - 158 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B TYR* 4.0 17.9 - - + +
130B ALA* 5.7 0.2 - - - -
131B CYS* 3.5 15.7 - - - -
133B GLU* 3.6 12.3 - - - +
137B LEU 4.8 0.4 - - - +
138B MET* 1.3 100.8 - - + +
140B LEU* 1.3 66.3 + - - +
141B PRO* 3.5 7.6 - - + -
142B ILE* 3.5 14.9 - - + +
143B HIS* 3.5 16.1 + - - +
176B TYR* 5.2 0.7 - - - +
255B TYR* 4.0 5.4 - - + +
258B ALA* 3.6 32.5 - - + -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLU* 2.9 24.9 + - + +
134B THR* 3.6 25.4 - - + -
138B MET 3.6 1.6 + - - -
139B PRO* 1.3 70.8 - - - +
141B PRO* 1.3 72.0 - - + +
143B HIS* 3.0 6.7 + - - +
144B LEU* 3.0 47.7 + - + +
174B VAL* 4.3 11.0 - - + -
176B TYR* 4.3 2.0 - - - +
181B PRO* 3.7 24.5 - - + -
216B PRO* 5.1 5.6 - - + -
219B LEU* 3.3 32.5 - - + -
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Residues in contact with PRO 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PHE* 3.9 21.1 - - + +
9B SER* 3.6 28.0 - - - +
133B GLU* 4.1 0.2 - - - +
139B PRO* 3.6 8.1 - - + -
140B LEU* 1.3 91.7 - - + +
142B ILE* 1.3 60.8 + - - +
144B LEU* 3.5 5.1 + - + +
145B SER* 2.8 27.9 + - - -
172B VAL* 4.1 10.7 - - + +
174B VAL* 4.0 24.2 - - + -
176B TYR* 3.3 22.9 - - + +
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Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER* 3.5 7.1 + - - +
10B GLU 3.1 30.7 - - - +
138B MET* 3.9 19.7 - - + -
139B PRO* 3.5 17.9 - - + +
141B PRO* 1.3 78.1 - - - +
143B HIS* 1.3 65.6 + - - +
145B SER* 3.2 2.2 + - - -
146B HIS* 2.9 49.8 + - + +
252B VAL* 4.1 8.3 - - - +
254B THR 4.4 3.1 - - - +
255B TYR 3.5 24.7 - - - +
256B GLY* 3.7 26.7 - - - +
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Residues in contact with HIS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 3.8 20.8 - - + +
135B PRO* 5.7 0.4 - - + -
136B GLU* 3.2 36.8 + - - -
138B MET* 4.5 17.5 - - + -
139B PRO 3.6 10.8 - - - +
140B LEU* 3.0 12.7 + - - +
142B ILE* 1.3 83.4 - - - +
144B LEU* 1.3 66.6 + - - +
146B HIS* 3.5 3.0 + - - -
147B ARG* 3.1 69.9 + - + +
364B PHE 5.9 0.2 - - - -
365B GLY* 4.0 12.3 + - - -
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Residues in contact with LEU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.0 43.1 + - + +
141B PRO 3.8 3.6 - - - +
143B HIS* 1.3 78.3 - - + +
145B SER* 1.3 59.8 + - - +
147B ARG* 3.3 6.2 + - + +
148B LEU* 2.9 34.5 + - - +
172B VAL* 4.2 21.1 - - + -
174B VAL* 4.7 1.8 - - + -
184B ILE* 3.5 32.3 - - + -
214B THR* 3.6 27.3 - - + +
215B LEU* 4.3 7.4 - - + -
216B PRO* 4.0 16.6 - - + -
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Residues in contact with SER 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B SER 3.5 17.2 + - - -
10B GLU* 3.8 5.4 - - - -
11B SER* 3.6 18.8 - - - -
141B PRO 2.8 22.3 + - - -
142B ILE* 3.2 6.5 + - - -
144B LEU* 1.3 75.3 - - - +
146B HIS* 1.3 62.4 + - - +
148B LEU 3.4 1.2 + - - -
149B VAL* 3.3 15.1 + - - +
170B SER* 2.7 30.3 + - - -
172B VAL* 3.4 18.8 + - - +
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Residues in contact with HIS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER* 2.8 29.1 + - - -
138B MET* 5.8 1.3 - - + -
142B ILE* 2.9 39.5 + - + +
143B HIS* 3.7 3.1 - + - +
145B SER* 1.3 75.6 - - - +
147B ARG* 1.3 78.2 + - - +
149B VAL* 3.3 5.4 - - - +
150B GLU* 2.9 29.3 + - - +
252B VAL* 3.0 34.9 + - + -
254B THR 4.8 3.2 + - - -
361B TYR* 3.1 28.6 - - - +
362B GLY* 3.3 23.6 - - - -
364B PHE 4.8 8.5 + - - -
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B HIS* 3.1 60.6 + - + +
144B LEU* 3.3 9.2 + - + +
146B HIS* 1.3 97.1 - - - +
148B LEU* 1.3 61.8 + - - +
150B GLU* 2.7 30.3 + - + +
151B ARG* 2.9 31.5 + - - +
214B THR* 3.6 19.3 + - + -
361B TYR* 3.6 21.4 + - - +
364B PHE 5.5 0.6 + - - -
365B GLY* 4.3 3.2 + - - -
366B ARG* 3.6 23.4 - - - +
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU 2.9 15.1 + - - +
145B SER 3.8 4.3 - - - +
146B HIS 3.3 0.2 - - - -
147B ARG* 1.3 77.0 - - - +
149B VAL* 1.3 62.7 + - - +
151B ARG* 3.4 5.0 + - - +
152B GLN* 3.2 16.8 + - - +
170B SER* 4.0 15.0 - - - -
172B VAL* 3.4 24.5 - - + -
187B VAL* 3.3 28.0 - - + -
189B LEU* 4.2 9.5 - - + +
210B VAL* 3.6 19.6 - - - +
211B ILE* 3.6 39.7 - - + +
214B THR* 3.9 15.3 - - + -
215B LEU* 4.8 7.4 - - + -
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B SER* 3.6 11.2 - - - +
12B VAL* 3.5 20.9 - - - +
13B SER* 3.9 23.4 - - - +
145B SER 3.3 8.5 + - - +
146B HIS 3.3 13.5 - - - +
148B LEU* 1.3 74.8 - - - +
150B GLU* 1.3 65.1 + - - +
152B GLN* 3.2 9.8 + - + +
153B ALA* 3.1 21.5 + - - +
168B ALA* 4.0 13.7 - - + +
169B LYS 4.1 2.9 - - - +
170B SER* 3.8 31.4 - - - +
189B LEU* 5.6 2.5 - - + -
361B TYR* 3.7 11.1 + - + -
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B HIS 2.9 17.4 + - - +
147B ARG* 2.7 42.3 + - + +
149B VAL* 1.3 76.6 - - - +
151B ARG* 1.3 58.4 + - - +
153B ALA* 3.2 4.4 + - + +
154B ASN* 2.9 47.6 + - - +
157B ARG* 6.0 1.6 - - - +
361B TYR* 3.8 34.4 - - + -
366B ARG* 4.9 10.1 + - - +
368B GLU* 5.5 2.9 - - - +
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Residues in contact with ARG 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ARG 2.9 18.9 + - - +
148B LEU 3.4 5.8 - - - +
150B GLU* 1.3 76.5 - - - +
152B GLN* 1.3 57.7 + - - +
154B ASN* 3.2 15.9 + - - +
155B LEU* 3.0 46.0 + - + +
160B ARG* 4.1 25.7 - - - +
209B GLU* 2.9 27.1 + - - +
210B VAL* 3.6 26.0 - - + +
213B PRO* 3.9 23.0 - - - +
214B THR* 3.6 12.6 - - - +
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Residues in contact with GLN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER* 4.3 2.1 - - - -
148B LEU 3.2 5.5 + - - +
149B VAL* 3.2 14.5 + - + +
151B ARG* 1.3 78.8 - - - +
153B ALA* 1.3 79.3 + - - +
155B LEU* 4.7 2.0 - - - -
156B ARG* 3.0 27.4 + - - +
164B LEU* 3.3 29.8 - - + +
165B ARG 3.7 11.7 + - - -
166B PRO 4.0 12.5 - - - +
168B ALA* 3.7 25.4 - - + +
189B LEU* 5.2 6.7 - - + -
191B THR* 3.0 27.3 + - - +
210B VAL* 3.9 22.2 - - + +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B SER* 5.6 0.2 - - - -
14B GLU* 3.8 1.1 - - + +
149B VAL 3.1 5.6 + - - +
150B GLU* 3.2 8.3 + - + +
152B GLN* 1.3 87.7 + - - +
154B ASN* 1.3 58.9 + - - +
156B ARG* 3.2 14.2 + - - +
157B ARG* 2.9 54.9 + - - +
361B TYR* 3.3 28.0 - - + +
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Residues in contact with ASN 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B GLU* 2.9 34.0 + - - +
151B ARG* 3.2 16.4 + - - +
153B ALA* 1.3 75.7 - - - +
155B LEU* 1.3 59.4 + - + +
157B ARG* 3.2 23.6 + - - +
158B ASP* 3.0 37.7 + - - +
160B ARG* 5.2 5.6 - - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ARG* 3.0 33.3 + - - +
152B GLN 4.0 3.4 - - - +
154B ASN* 1.3 72.9 - - + +
156B ARG* 1.3 64.0 + - - +
158B ASP* 3.4 3.1 - - - +
160B ARG* 3.2 60.1 + - + +
161B LEU* 3.1 48.5 + - + +
164B LEU* 4.2 9.2 - - + -
209B GLU* 3.5 35.4 - - + +
210B VAL* 4.1 8.3 - - + -
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 4.2 12.9 - - - +
76B ARG 5.4 0.6 + - - -
77B ILE 3.2 27.4 + - - -
78B GLY* 4.4 5.5 - - - -
152B GLN* 3.0 20.2 + - - +
153B ALA* 3.2 12.6 + - - +
155B LEU* 1.3 76.7 - - - +
157B ARG* 1.3 96.0 + - - +
159B GLY* 3.2 14.4 + - - -
161B LEU 3.9 10.5 - - - +
162B PRO* 4.9 3.8 - - + +
164B LEU* 3.7 19.0 - - + +
165B ARG* 3.4 33.5 + - - +
166B PRO* 3.6 24.9 + - - +
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B GLU* 2.7 37.0 + - - -
76B ARG* 5.1 10.5 - - - -
150B GLU* 6.0 1.8 - - - +
153B ALA* 2.9 27.4 + - - +
154B ASN* 3.2 26.8 + - - +
156B ARG* 1.3 99.5 - - - +
158B ASP* 1.3 57.8 + - - +
159B GLY 3.3 1.2 + - - -
361B TYR* 5.9 1.8 - - - -
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B ASN* 3.0 19.0 + - - +
155B LEU* 3.4 4.0 - - - +
157B ARG* 1.3 76.2 - - - +
159B GLY* 1.3 59.7 + - - +
160B ARG* 2.6 65.4 + - - +
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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