Contacts of the helix formed by residues 139 - 158 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C PHE* 6.2 0.2 - - + -
129C TYR* 4.0 19.7 - - + +
130C ALA* 5.3 0.2 - - - -
131C CYS* 3.5 23.1 - - - -
133C GLU* 3.6 7.6 - - - +
137C LEU 4.6 1.1 - - - +
138C MET* 1.3 97.2 - - + +
140C LEU* 1.3 65.4 + - - +
141C PRO* 3.5 7.9 - - + -
142C ILE* 3.3 18.4 - - + +
143C HIS* 3.3 17.8 + - - +
176C TYR* 5.2 0.4 - - - +
255C TYR* 4.1 5.4 - - + +
258C ALA* 3.6 32.8 - - + -
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Residues in contact with LEU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C GLU* 2.9 23.8 + - + +
134C THR* 3.8 23.6 - - + -
138C MET 3.4 1.8 + - - -
139C PRO* 1.3 68.4 - - - +
141C PRO* 1.3 75.0 - - + +
143C HIS* 3.0 1.9 + - - +
144C LEU* 2.9 60.0 + - + +
174C VAL* 4.2 15.7 - - + -
176C TYR* 4.4 0.9 - - - +
181C PRO* 3.7 19.7 - - + -
184C ILE* 5.4 0.4 - - + -
216C PRO* 4.5 11.0 - - + -
219C LEU* 3.5 29.2 - - + -
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Residues in contact with PRO 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C PHE* 3.8 22.4 - - + +
9C SER* 3.4 28.5 - - - +
133C GLU* 3.9 0.2 - - - +
139C PRO* 3.5 9.2 - - + -
140C LEU* 1.3 92.5 - - + +
142C ILE* 1.3 60.8 + - - +
145C SER* 2.7 28.6 + - - -
172C VAL* 4.0 15.1 - - + +
174C VAL* 3.9 20.4 - - + -
176C TYR* 3.3 24.0 - - + +
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Residues in contact with ILE 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C SER* 3.5 7.8 + - - +
10C GLU 3.3 28.9 - - - +
138C MET* 3.8 22.4 - - + -
139C PRO* 3.3 19.1 - - + +
141C PRO* 1.3 77.2 - - - +
143C HIS* 1.3 68.4 + - - +
145C SER* 4.2 0.4 - - - -
146C HIS* 3.1 53.5 + - + +
252C VAL* 4.0 5.8 - - - +
254C THR 4.1 6.1 - - - +
255C TYR 3.7 20.6 - - - +
256C GLY* 4.1 19.5 - - - +
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Residues in contact with HIS 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C THR* 4.0 19.7 - - + +
135C PRO* 5.7 0.7 - - + -
136C GLU* 3.2 38.5 + - + +
138C MET* 4.3 16.6 - - + -
139C PRO 3.3 11.6 + - - +
140C LEU 3.0 9.3 + - - +
142C ILE* 1.3 85.2 - - - +
144C LEU* 1.3 68.5 + - + +
146C HIS* 3.4 2.4 + - - -
147C ARG* 3.0 71.3 + - + +
365C GLY* 4.2 11.3 + - - -
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C LEU* 2.9 47.5 + - + +
141C PRO 4.2 2.0 - - - +
143C HIS* 1.3 84.7 - - + +
145C SER* 1.3 65.6 + - - +
147C ARG* 3.2 5.5 + - + +
148C LEU* 2.9 30.3 + - + +
172C VAL* 4.2 19.7 - - + -
174C VAL* 5.5 0.2 - - + -
184C ILE* 3.8 28.5 - - + -
214C THR* 3.7 28.0 - - + +
215C LEU* 4.4 5.2 - - + -
216C PRO* 4.0 12.1 - - + -
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Residues in contact with SER 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C SER 3.4 20.8 + - - -
10C GLU* 3.5 21.9 - - - -
11C SER* 3.5 4.5 - - - -
141C PRO 2.7 22.9 + - - -
142C ILE* 3.6 6.3 - - - -
144C LEU* 1.3 78.7 - - - +
146C HIS* 1.3 62.1 + - - +
148C LEU 3.4 5.7 + - - -
149C VAL* 3.5 4.3 + - - +
170C SER* 2.5 30.3 + - - -
172C VAL* 3.5 15.0 + - - +
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Residues in contact with HIS 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C SER* 2.6 30.1 + - - -
138C MET* 5.7 1.3 - - + -
142C ILE* 3.1 39.4 + - + +
143C HIS* 3.7 2.7 - - - +
145C SER* 1.3 75.2 - - - +
147C ARG* 1.3 90.5 + - - +
148C LEU 3.3 0.3 + - - -
149C VAL* 3.3 5.1 - - - +
150C GLU* 3.0 24.8 + - - +
252C VAL* 3.0 35.8 + - + -
254C THR 4.7 2.8 + - - -
361C TYR* 3.4 21.3 - - - +
362C GLY* 3.5 21.2 - - - -
364C PHE 4.9 7.6 + - - -
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Residues in contact with ARG 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C GLU* 5.7 0.4 - - - -
143C HIS* 3.0 64.5 + - + +
144C LEU* 3.2 5.4 + - + +
146C HIS* 1.3 94.8 - - - +
148C LEU* 1.3 57.1 + - - +
150C GLU* 2.9 30.6 + - + +
151C ARG* 2.9 29.6 + - - +
214C THR* 3.5 23.5 + - + -
361C TYR* 3.7 14.1 + - - +
364C PHE 5.6 0.8 + - - -
365C GLY 4.4 4.0 + - - -
366C ARG* 3.6 29.1 - - - +
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Residues in contact with LEU 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C LEU* 2.9 22.3 + - + +
145C SER 3.7 4.3 - - - +
146C HIS 3.2 0.4 - - - -
147C ARG* 1.3 76.6 - - - +
149C VAL* 1.3 59.4 + - - +
151C ARG* 3.1 7.7 + - - +
152C GLN* 3.0 22.2 + - - +
170C SER* 3.9 16.2 - - - -
172C VAL* 3.7 19.1 - - + -
187C VAL* 3.5 28.5 - - + -
189C LEU* 4.0 7.9 - - + -
210C VAL* 3.5 34.9 - - + +
211C ILE* 3.6 24.2 - - + +
214C THR* 3.7 14.8 - - + -
215C LEU* 5.2 3.4 - - + -
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Residues in contact with VAL 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C SER* 3.7 10.8 - - - +
12C VAL 3.7 20.0 - - - +
13C SER* 3.9 13.0 - - - +
145C SER 3.5 8.0 + - - +
146C HIS 3.3 10.1 - - - +
148C LEU* 1.3 73.2 - - - +
150C GLU* 1.3 63.8 + - - +
152C GLN* 3.3 10.7 - - + +
153C ALA* 3.1 26.2 + - - +
168C ALA* 4.0 17.9 - - + +
169C LYS 4.0 5.6 - - - -
170C SER* 3.6 34.5 - - - +
189C LEU* 5.3 2.9 - - + -
361C TYR* 3.7 12.3 + - + -
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Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C HIS 3.0 16.7 + - - +
147C ARG* 2.9 38.4 + - - +
149C VAL* 1.3 75.1 - - - +
151C ARG* 1.3 66.8 + - - +
153C ALA* 3.3 3.0 + - + +
154C ASN* 3.0 33.3 + - - +
361C TYR* 3.7 35.6 - - + +
366C ARG* 5.0 7.7 + - - +
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Residues in contact with ARG 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ARG 2.9 20.1 + - - +
148C LEU* 3.1 7.6 + - - +
150C GLU* 1.3 78.4 - - - +
152C GLN* 1.3 57.4 + - - +
154C ASN* 3.1 9.9 + - - +
155C LEU* 2.9 51.8 + - + +
209C GLU* 2.8 28.8 + - - +
210C VAL* 3.7 24.2 + - - +
213C PRO* 4.3 19.2 - - - +
214C THR* 4.0 13.7 - - - +
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Residues in contact with GLN 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C SER* 4.7 0.9 - - - -
148C LEU 3.0 11.7 + - - +
149C VAL* 3.3 17.2 - - + +
150C GLU 3.3 0.4 - - - -
151C ARG* 1.3 76.9 - - - +
153C ALA* 1.3 70.4 + - - +
155C LEU* 4.5 0.7 - - - +
156C ARG* 2.9 32.3 + - - +
164C LEU* 3.6 16.9 - - + +
165C ARG 3.4 17.8 + - - +
166C PRO 3.9 10.4 - - - +
168C ALA* 3.4 26.4 - - + +
189C LEU* 5.1 7.4 - - + -
191C THR* 2.9 28.4 + - - -
210C VAL* 4.3 23.3 - - + -
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Residues in contact with ALA 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C SER* 5.6 0.7 - - - -
14C GLU* 3.5 13.0 - - + +
149C VAL 3.1 7.7 + - - +
150C GLU* 3.6 8.5 - - + +
152C GLN* 1.3 87.2 + - - +
154C ASN* 1.3 60.2 + - - +
156C ARG* 3.4 11.0 + - - +
157C ARG* 3.0 42.7 + - - +
361C TYR* 3.2 28.3 - - + +
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Residues in contact with ASN 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C GLU* 3.0 24.8 + - - +
151C ARG* 3.4 13.5 - - - +
153C ALA* 1.3 76.9 - - - +
155C LEU* 1.3 65.5 + - + +
157C ARG* 3.4 7.7 + - - +
158C ASP* 2.8 36.1 + - - +
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Residues in contact with LEU 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ARG* 2.9 42.3 + - - +
154C ASN* 1.3 73.4 - - + +
156C ARG* 1.3 62.6 + - - +
158C ASP* 3.8 8.3 - - - +
159C GLY* 3.1 18.0 + - - -
160C ARG* 3.1 41.0 + - + -
161C LEU* 3.8 8.0 + - + +
164C LEU* 4.0 14.6 - - + -
209C GLU* 3.4 36.1 - - + +
210C VAL* 3.5 23.8 - - + -
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Residues in contact with ARG 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 4.1 10.9 - - - +
77C ILE 3.0 28.2 + - - -
78C GLY* 3.9 12.7 - - - -
152C GLN* 2.9 23.0 + - - +
153C ALA* 3.5 10.1 + - - +
155C LEU* 1.3 77.9 - - - +
157C ARG* 1.3 92.5 + - - +
159C GLY* 3.4 11.4 + - - -
161C LEU 4.5 3.8 - - - +
162C PRO* 5.7 1.4 - - - +
164C LEU* 3.4 40.5 - - + +
165C ARG* 3.4 19.4 + - - +
166C PRO* 3.5 22.2 + - - +
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Residues in contact with ARG 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU* 2.5 43.9 + - - -
76C ARG* 3.0 32.6 + - - +
77C ILE 3.9 1.6 + - - -
153C ALA* 3.0 31.8 + - - +
154C ASN* 3.9 7.2 + - - +
155C LEU 3.3 0.2 - - - -
156C ARG* 1.3 94.4 - - - +
158C ASP* 1.3 60.3 + - - +
159C GLY* 3.1 6.0 + - - -
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Residues in contact with ASP 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ASN* 2.8 26.1 + - - +
155C LEU* 3.3 9.0 - - - +
157C ARG* 1.3 77.6 - - + +
159C GLY* 1.3 59.0 + - - +
160C ARG* 3.0 28.3 + - - +
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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