Contacts of the helix formed by residues 135 - 157 (chain C) in PDB entry 3OMA
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 PHE 135 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C MET 4.2 0.2 - - - -
134C ALA* 1.3 96.6 - - + +
136C PRO* 1.3 67.0 - - - +
137C ARG* 3.1 24.9 + - - +
138C MET* 3.1 31.9 + - + -
139C ASN 3.0 17.5 + - - -
206C ILE* 4.5 10.5 - - + -
207C ASN* 2.9 32.8 + - - +
210C THR* 3.8 27.6 - - + -
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Residues in contact with PRO 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C THR* 3.4 44.4 - - - +
132C ASP* 4.3 17.5 - - + +
133C MET* 3.3 19.7 - - + +
134C ALA 3.5 4.9 - - - +
135C PHE* 1.3 82.0 - - - +
137C ARG* 1.3 71.5 + - + +
139C ASN* 3.4 9.0 - - + +
140C ASN 3.2 19.9 + - - -
207C ASN* 5.0 0.2 - - - +
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Residues in contact with ARG 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C THR* 4.4 12.1 - - + -
134C ALA 3.4 23.0 + - - -
135C PHE* 3.4 29.4 - - - +
136C PRO* 1.3 84.4 - - + +
138C MET* 1.3 71.9 + - - +
140C ASN* 3.1 7.1 + - - +
141C LEU* 3.1 21.2 + - - +
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Residues in contact with MET 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C PHE* 3.1 36.1 + - + +
137C ARG* 1.3 82.9 - - - +
139C ASN* 1.3 57.0 + - - +
141C LEU* 3.2 11.2 + - + +
142C SER* 3.0 28.5 + - - -
203C LEU* 3.7 53.7 - - + +
206C ILE* 4.1 25.4 - - + -
207C ASN* 4.6 3.6 - - - +
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Residues in contact with ASN 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C THR 4.9 2.2 + - - -
26C HIS* 4.1 9.1 - - - +
29C ILE* 3.6 25.9 - - + +
121C ASN* 3.4 37.9 + - - +
132C ASP* 4.9 0.2 + - - -
133C MET* 3.5 16.9 - - + +
135C PHE 3.0 6.7 + - - +
136C PRO* 3.4 13.0 - - + +
137C ARG 3.2 0.2 - - - -
138C MET* 1.3 76.5 - - - +
140C ASN* 1.3 60.4 + - - +
142C SER* 3.3 22.9 - - - -
143C TYR 3.6 3.6 + - - -
203C LEU 6.0 0.4 - - - -
204C GLY* 5.5 4.8 - - - -
207C ASN* 3.3 22.4 + - - +
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Residues in contact with ASN 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE 3.4 17.3 - - - +
22C MET* 4.0 6.9 + - - +
23C SER 3.4 16.0 - - - +
24C THR* 3.9 17.4 - - + +
29C ILE* 3.8 14.6 - - + +
32C LEU* 5.8 0.2 - - - +
136C PRO 3.2 12.6 + - - +
137C ARG* 3.1 10.4 + - - +
139C ASN* 1.3 72.8 - - - +
141C LEU* 1.3 67.5 + - - +
143C TYR* 3.2 13.3 + - - +
144C TRP* 3.4 30.0 + - - +
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Residues in contact with LEU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C ARG 3.1 11.3 + - - +
138C MET* 3.4 11.9 - - + +
140C ASN* 1.3 76.5 - - - +
142C SER* 1.3 66.1 + - - +
144C TRP* 2.9 13.0 + - + +
145C LEU* 2.9 44.6 + - + +
203C LEU* 3.8 21.5 - - + -
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Residues in contact with SER 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TYR* 3.1 16.2 - - - -
138C MET 3.0 10.5 + - - -
139C ASN* 3.3 20.0 - - - -
141C LEU* 1.3 75.2 - - - +
143C TYR* 1.3 62.4 + - - -
145C LEU* 3.3 3.2 + - - -
146C TYR 3.0 11.8 + - - -
200C SER* 3.0 33.6 + - - +
203C LEU* 3.3 27.0 - - - +
204C GLY* 3.3 14.8 + - - -
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Residues in contact with TYR 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE* 3.8 28.4 - + - -
29C ILE* 4.6 9.4 - - + -
32C LEU* 3.6 46.3 + - + +
33C TYR* 3.2 28.4 + + + -
36C THR* 2.6 32.9 + - - +
139C ASN 3.6 4.4 + - - +
140C ASN* 3.2 10.1 + - - +
141C LEU 3.2 1.2 - - - -
142C SER* 1.3 79.5 - - - +
144C TRP* 1.3 75.4 + + - +
146C TYR* 3.4 22.1 + + - +
147C VAL* 3.1 44.6 + - + +
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Residues in contact with TRP 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE* 3.8 54.7 + + + -
22C MET* 5.6 1.0 - - - +
140C ASN* 3.4 36.5 + - - +
141C LEU* 2.9 15.0 + - + +
143C TYR* 1.3 83.1 - + - +
145C LEU* 1.3 62.7 + - + +
147C VAL* 3.2 30.5 + - + +
148C ALA* 2.8 30.6 + - - +
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Residues in contact with LEU 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C LEU* 2.9 31.2 + - + +
142C SER 3.6 6.7 - - - +
144C TRP* 1.3 77.2 - - + +
146C TYR* 1.3 51.7 + - - +
148C ALA* 3.3 4.9 + - + +
149C GLY* 2.8 33.3 + - - -
196C LEU* 3.7 41.3 - - + +
199C ALA* 3.7 25.1 - - + -
200C SER* 3.8 7.0 - - - +
203C LEU* 3.8 27.1 - - + -
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Residues in contact with TYR 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C TYR* 3.6 30.3 - + + -
36C THR* 3.5 33.4 - - + +
37C GLY* 3.2 23.0 + - - -
40C VAL* 3.7 2.1 - - - +
108C PHE 4.7 0.7 - - - -
109C PHE* 2.9 41.6 + + - -
113C PRO* 3.6 21.0 - - + +
142C SER 3.0 13.2 + - - +
143C TYR* 3.5 19.3 - + - +
144C TRP 3.2 0.2 - - - -
145C LEU* 1.3 77.0 - - - +
147C VAL* 1.3 52.6 + - - +
149C GLY* 3.8 1.4 - - - -
150C THR* 2.7 52.2 + - - -
196C LEU 5.2 0.4 - - - -
197C SER* 5.4 2.2 - - - +
200C SER* 3.7 15.8 - - - +
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Residues in contact with VAL 147 (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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36C THR* 4.8 8.3 - - + -
143C TYR* 3.1 50.5 + - + +
144C TRP* 3.2 24.0 + - + +
146C TYR* 1.3 76.0 - - + +
148C ALA* 1.3 61.5 + - - +
150C THR* 3.4 8.1 + - - -
151C SER* 2.9 40.8 + - - +
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Residues in contact with ALA 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C TRP 2.8 20.6 + - - +
145C LEU* 3.6 9.0 - - + +
147C VAL* 1.3 71.6 - - - +
149C GLY* 1.3 65.3 + - - +
151C SER* 3.1 8.4 + - - -
152C LEU* 3.0 26.7 + - + +
196C LEU* 3.6 20.4 - - + -
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Residues in contact with GLY 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C PHE* 3.4 13.2 - - - -
145C LEU 2.8 19.7 + - - -
148C ALA* 1.3 72.2 - - - +
150C THR* 1.3 60.5 + - - +
152C LEU 3.2 2.9 + - - -
153C ALA 3.1 17.8 + - - -
193C ALA* 3.3 29.7 - - - +
196C LEU* 3.4 12.3 - - - +
197C SER 4.6 0.4 - - - -
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Residues in contact with THR 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C THR* 5.8 2.5 - - + -
40C VAL* 3.8 33.2 - - + -
105C LEU* 4.8 1.8 - - + -
109C PHE* 3.2 23.5 - - + -
146C TYR* 2.7 38.8 + - - -
147C VAL* 3.7 8.9 - - - -
148C ALA 3.3 0.2 - - - -
149C GLY* 1.3 72.0 - - - +
151C SER* 1.3 62.0 + - - +
153C ALA* 3.4 3.1 + - - +
154C VAL* 3.1 34.6 + - + +
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Residues in contact with SER 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C VAL* 2.9 29.4 + - - +
148C ALA* 3.1 8.9 + - - -
150C THR* 1.3 77.7 - - - +
152C LEU* 1.3 61.4 + - - +
154C VAL* 3.6 4.8 + - - +
155C ALA* 3.0 27.5 + - - +
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Residues in contact with LEU 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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148C ALA* 3.0 17.2 + - + +
149C GLY 3.2 1.3 + - - +
151C SER* 1.3 76.2 - - - +
153C ALA* 1.3 56.1 + - - +
155C ALA* 3.0 8.6 + - + +
156C SER* 2.8 35.5 + - - -
189C LEU* 3.6 32.4 - - + +
192C PHE* 3.5 33.7 - - + -
193C ALA* 3.8 8.7 - - + +
196C LEU* 3.7 17.7 - - + -
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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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104C ILE* 4.5 8.5 - - + -
105C LEU* 4.3 11.4 - - + -
109C PHE* 3.6 33.4 - - + -
149C GLY 3.1 6.2 + - - +
150C THR 3.6 8.5 - - - +
151C SER 3.4 0.2 - - - -
152C LEU* 1.3 74.9 - - - +
154C VAL* 1.3 60.5 + - - +
156C SER* 2.6 28.0 + - - -
157C LEU* 3.7 8.1 + - - +
190C ALA* 5.2 2.9 - - - +
193C ALA* 3.5 9.1 - - + +
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Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 5.5 15.5 - - + -
105C LEU* 4.6 16.8 - - + -
150C THR* 3.1 28.3 + - + +
151C SER* 4.0 4.7 - - - +
153C ALA* 1.3 72.4 - - - +
155C ALA* 1.3 65.1 + - - +
157C LEU* 3.3 23.2 + - + +
158C PHE* 3.2 32.6 - - + -
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Residues in contact with ALA 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C SER 3.0 19.9 + - - +
152C LEU* 3.0 14.3 + - + +
154C VAL* 1.3 71.7 - - - +
156C SER* 1.3 60.6 + - - +
157C LEU 3.0 2.2 - - - -
158C PHE* 2.8 25.8 + - - +
159C ALA* 3.0 11.8 + - - +
189C LEU* 4.3 13.0 - - + -
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Residues in contact with SER 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C LEU 2.8 11.6 + - - -
153C ALA* 2.6 22.0 + - - -
155C ALA* 1.3 75.9 - - - +
157C LEU* 1.3 65.5 + - - +
158C PHE 3.2 0.9 + - - -
159C ALA* 3.3 14.1 + - - -
167C GLY* 3.3 5.0 - - - -
168C SER* 5.2 2.7 + - - -
186C SER* 2.6 47.6 + - - -
189C LEU* 4.0 7.8 - - - +
190C ALA* 4.0 14.2 - - - +
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 6.2 0.2 - - + -
47C PHE* 3.7 31.9 - - + -
97C VAL* 3.9 34.5 - - + +
98C MET* 5.9 1.8 - - - -
101C GLY* 4.3 15.0 - - - +
105C LEU* 5.7 2.2 - - + -
153C ALA 3.8 9.4 - - - +
154C VAL* 3.3 32.3 - - + +
155C ALA 3.0 0.6 - - - -
156C SER* 1.3 84.0 + - - +
158C PHE* 1.3 74.5 + - + +
166C LEU* 3.9 8.0 - - - +
167C GLY* 3.9 16.3 + - - -
168C SER 6.0 1.1 - - - +
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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
------------------------------------------------------------
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