Contacts of the helix formed by residues 139 - 158 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR* 4.3 15.5 - - + -
131A CYS* 3.4 23.1 - - - -
133A GLU* 3.7 6.3 - - - +
137A LEU 4.8 0.4 - - - +
138A MET* 1.3 100.0 - - + +
140A LEU* 1.3 66.2 + - - +
141A PRO* 3.5 7.2 - - + -
142A ILE* 3.4 26.4 - - + +
143A HIS* 3.4 6.4 + - - +
176A TYR* 5.2 0.7 - - - +
255A TYR* 4.0 5.2 - - + +
258A ALA* 3.6 32.8 - - + -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLU* 3.0 28.4 + - + +
134A THR* 3.8 22.0 - - + -
138A MET 3.5 1.6 + - - -
139A PRO* 1.3 72.7 - - - +
141A PRO* 1.3 63.9 - - + +
143A HIS* 3.1 3.7 + - + +
144A LEU* 2.8 53.8 + - + +
174A VAL* 4.2 15.3 - - + -
176A TYR* 4.2 1.6 - - - +
181A PRO* 3.8 20.0 - - + -
216A PRO* 4.7 9.2 - - + -
219A LEU* 3.5 29.6 - - + -
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Residues in contact with PRO 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 4.1 20.4 - - + +
9A SER* 3.7 22.4 - - - +
139A PRO* 3.6 9.4 - - + -
140A LEU* 1.3 89.7 - - + +
142A ILE* 1.3 58.2 + - - +
144A LEU* 3.5 2.5 + - + +
145A SER* 2.9 31.9 + - - -
172A VAL* 3.9 20.9 - - + +
174A VAL* 3.8 23.8 - - + -
176A TYR* 3.3 21.5 - - - +
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A SER* 3.5 4.9 + - - -
10A GLU 3.4 26.7 - - - +
138A MET* 3.8 17.7 - - + -
139A PRO* 3.4 31.2 - - + +
141A PRO* 1.3 76.3 - - - +
143A HIS* 1.3 69.1 + - - +
145A SER* 3.3 1.3 + - - -
146A HIS* 3.0 64.2 + - + +
252A VAL* 4.0 6.5 - - - +
254A THR 4.1 5.2 - - - +
255A TYR 3.8 14.1 - - - +
256A GLY* 3.6 23.6 - - - +
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Residues in contact with HIS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 3.8 24.8 + - + +
135A PRO* 5.5 1.4 - - - +
136A GLU* 3.1 36.3 + - + +
138A MET* 4.7 10.5 - - + +
139A PRO 3.4 10.7 + - - +
140A LEU* 3.1 9.4 + - + +
142A ILE* 1.3 84.4 - - - +
144A LEU* 1.3 78.4 + - + +
146A HIS* 3.3 2.2 + - - -
147A ARG* 3.1 67.9 + - + +
365A GLY* 4.7 3.8 + - - -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 2.8 44.4 + - + +
141A PRO 4.0 2.9 - - - +
143A HIS* 1.3 84.8 - - + +
145A SER* 1.3 57.5 + - - +
147A ARG* 3.8 4.6 - - + +
148A LEU* 2.9 34.2 + - + +
172A VAL* 4.1 18.4 - - + -
184A ILE* 3.7 29.8 - - + -
214A THR* 4.1 16.7 - - + +
215A LEU* 3.9 17.9 - - + -
216A PRO* 3.9 23.1 - - + -
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Residues in contact with SER 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A SER 3.3 21.1 + - - -
10A GLU* 3.6 6.3 - - - -
11A SER* 3.6 23.3 - - - -
141A PRO 2.9 20.8 + - - -
142A ILE* 3.5 6.5 - - - -
143A HIS 3.2 0.2 - - - -
144A LEU* 1.3 73.8 - - - +
146A HIS* 1.3 66.4 + - - +
148A LEU* 3.3 1.9 + - - +
149A VAL* 3.3 13.5 + - - +
170A SER* 2.7 23.7 + - - -
172A VAL* 3.5 16.2 + - - +
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Residues in contact with HIS 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A SER* 2.9 28.2 + - - -
138A MET* 5.5 2.0 - - + -
142A ILE* 3.0 43.5 + - + +
143A HIS* 3.6 5.6 - - - +
145A SER* 1.3 76.3 - - - +
147A ARG* 1.3 81.3 + - - +
149A VAL* 3.0 7.8 - - - +
150A GLU* 2.8 28.6 + - - +
252A VAL* 2.9 32.5 + - + -
254A THR 4.7 3.2 + - - -
361A TYR* 3.3 19.6 - - - +
362A GLY* 3.4 23.5 - - - -
364A PHE 4.8 8.2 + - - -
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Residues in contact with ARG 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A HIS* 3.1 67.1 + - + +
144A LEU* 3.9 2.9 - - + +
146A HIS* 1.3 100.8 - - - +
148A LEU* 1.3 55.9 + - - +
150A GLU* 2.7 34.6 + - - +
151A ARG* 2.9 31.9 + - - +
214A THR* 3.7 21.8 - - + +
361A TYR 3.6 3.6 + - - -
365A GLY* 4.4 9.0 + - - -
366A ARG* 3.4 27.0 - - - +
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU 2.9 15.5 + - - +
145A SER 3.5 4.7 - - - +
146A HIS 3.2 0.4 - - - -
147A ARG* 1.3 77.3 - - - +
149A VAL* 1.3 61.7 + - - +
151A ARG* 3.5 4.5 + - - +
152A GLN* 3.2 18.0 + - - +
170A SER* 3.9 15.0 - - - -
172A VAL* 3.6 24.9 - - + -
187A VAL* 3.5 29.6 - - + -
189A LEU* 4.2 9.6 - - + +
210A VAL* 3.5 19.6 - - - +
211A ILE* 3.5 39.7 - - + +
214A THR* 4.0 12.8 - - + -
215A LEU* 5.1 6.1 - - + -
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Residues in contact with VAL 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 3.5 20.0 - - - +
12A VAL 3.7 10.8 - - - +
13A SER* 3.9 25.5 - - - +
145A SER 3.3 8.3 + - - +
146A HIS* 3.0 16.6 - - - +
148A LEU* 1.3 77.1 - - - +
150A GLU* 1.3 65.3 + - - +
152A GLN* 3.4 9.2 + - + +
153A ALA* 3.2 21.1 + - - +
168A ALA* 4.2 8.5 - - + +
169A LYS 4.0 4.9 - - - -
170A SER* 3.5 33.9 - - - +
189A LEU* 5.6 2.5 - - + -
361A TYR* 3.9 10.7 + - + -
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Residues in contact with GLU 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A HIS 2.8 14.2 + - - +
147A ARG* 2.7 44.2 + - - +
149A VAL* 1.3 72.0 - - - +
151A ARG* 1.3 60.6 + - - +
153A ALA* 3.1 4.4 + - - +
154A ASN* 2.9 44.1 + - - +
361A TYR* 3.4 45.0 - - + -
366A ARG* 3.8 10.9 + - - +
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Residues in contact with ARG 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ARG 2.9 18.7 + - - +
148A LEU 3.5 5.8 - - - +
150A GLU* 1.3 77.1 - - - +
152A GLN* 1.3 61.8 + - - +
154A ASN* 3.2 13.7 + - - +
155A LEU* 3.0 48.6 + - + +
160A ARG* 4.4 17.6 - - - +
209A GLU* 2.9 28.7 + - - +
210A VAL* 3.5 27.9 + - + +
213A PRO* 4.0 19.3 - - - +
214A THR* 3.8 12.3 - - - +
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Residues in contact with GLN 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER* 4.4 3.1 - - - -
148A LEU 3.2 10.3 + - - +
149A VAL* 3.6 14.7 - - - +
150A GLU 3.3 0.4 - - - -
151A ARG* 1.3 78.7 - - - +
153A ALA* 1.3 83.7 + - - +
155A LEU 4.7 0.2 - - - +
156A ARG* 3.1 25.7 + - - +
164A LEU* 3.4 26.1 - - + +
165A ARG 3.5 15.3 + - - -
166A PRO 3.9 11.1 - - - +
168A ALA* 3.8 23.6 - - + +
189A LEU* 5.1 8.3 - - + -
191A THR* 3.0 26.6 + - - +
210A VAL* 4.0 18.4 - - + +
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER* 5.7 0.9 - - - -
14A GLU* 3.6 13.0 - - + +
149A VAL 3.2 5.3 + - - +
150A GLU* 3.1 9.5 + - - +
152A GLN* 1.3 89.4 + - - +
154A ASN* 1.3 58.0 + - - +
156A ARG* 3.2 12.7 + - - +
157A ARG* 2.9 41.0 + - - +
361A TYR* 3.3 27.6 - - + +
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Residues in contact with ASN 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A GLU* 2.9 32.8 + - - +
151A ARG* 3.6 14.4 - - - +
153A ALA* 1.3 77.0 - - - +
155A LEU* 1.3 65.6 + - + +
157A ARG* 3.3 9.2 + - - +
158A ASP* 3.0 38.0 + - - +
160A ARG* 5.0 2.5 - - - +
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ARG* 3.0 39.9 + - - +
152A GLN 4.1 3.1 - - - +
154A ASN* 1.3 74.6 - - + +
156A ARG* 1.3 65.3 + - - +
158A ASP* 3.7 4.9 - - - -
159A GLY 3.5 0.5 + - - -
160A ARG* 3.3 49.2 + - + +
161A LEU* 3.0 57.8 + - + +
164A LEU* 4.2 2.0 - - + -
209A GLU* 3.7 31.9 - - + +
210A VAL* 4.0 9.6 - - + -
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 4.2 11.3 + - - +
77A ILE 3.1 27.2 + - - -
78A GLY* 4.1 10.5 - - - -
152A GLN* 3.1 20.2 + - - +
153A ALA* 3.4 12.2 - - - +
155A LEU* 1.3 76.2 - - - +
157A ARG* 1.3 96.0 + - - +
159A GLY* 3.2 14.2 + - - -
161A LEU 3.7 11.9 - - - +
162A PRO* 4.7 4.0 - - + +
164A LEU* 3.5 25.7 - - + +
165A ARG* 3.4 26.8 + - - +
166A PRO* 3.5 23.5 + - - +
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Residues in contact with ARG 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 2.7 45.8 + - - -
76A ARG* 3.4 31.0 + - - +
77A ILE 4.1 0.4 + - - -
153A ALA* 2.9 29.5 + - - +
154A ASN* 3.3 9.1 + - - +
156A ARG* 1.3 101.0 - - - +
158A ASP* 1.3 58.8 + - - +
159A GLY* 3.2 1.3 + - - -
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Residues in contact with ASP 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASN* 3.0 23.7 + - - +
155A LEU* 3.6 1.6 - - - +
157A ARG* 1.3 75.9 - - - +
159A GLY* 1.3 58.8 + - - +
160A ARG* 2.8 59.9 + - - +
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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
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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