Contacts of the helix formed by residues 145 - 161 (chain C) in PDB entry 1W88
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 GLY 145 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ILE 3.0 1.0 + - - -
144C ILE* 1.3 77.4 - - - +
146C ALA* 1.3 64.6 + - - +
147C GLN* 3.0 16.5 + - - +
148C TYR* 3.1 24.3 + - - +
149C ILE 4.0 0.5 + - - -
171C THR* 4.8 3.1 + - - -
175C GLY 5.2 3.4 - - - -
178C GLN* 4.7 8.3 - - - -
180C ASN* 3.5 23.2 - - - +
181C PHE* 4.9 4.5 - - - -
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Residues in contact with ALA 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C GLN* 3.8 7.2 - - - +
143C ILE* 3.0 17.4 + - + +
144C ILE 3.5 0.8 - - - -
145C GLY* 1.3 76.8 - - - +
147C GLN* 1.3 62.4 + - - +
148C TYR 3.2 0.7 + - - -
149C ILE* 3.3 18.2 - - + +
150C GLN* 3.2 22.4 - - - +
180C ASN* 4.7 6.8 - - - +
91D ASP* 4.0 12.1 - - - +
96D GLN* 3.7 31.4 - - + +
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Residues in contact with GLN 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 3.8 18.4 - - + +
100C PRO 4.4 2.2 - - - +
101C GLY* 4.0 12.1 - - - -
138C LEU* 6.4 0.4 - - + -
141C GLN* 3.7 22.7 + - + +
143C ILE 3.5 5.9 - - - +
144C ILE* 4.3 3.9 - - - +
145C GLY* 3.0 24.1 + - - +
146C ALA* 1.3 75.3 + - - +
148C TYR* 1.3 63.9 + - + +
150C GLN* 4.5 10.8 - - - +
151C ALA* 3.0 31.0 + - - +
169C THR* 3.0 26.6 + - - +
170C TYR 2.8 24.2 + - - +
171C THR* 3.8 16.4 + - - +
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Residues in contact with TYR 148 (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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145C GLY* 3.1 14.3 + - - +
146C ALA 3.1 1.4 - - - -
147C GLN* 1.3 90.7 - - + +
149C ILE* 1.3 61.0 + - - +
151C ALA 3.6 0.2 + - - -
152C ALA 3.3 15.6 + - - -
169C THR* 3.6 20.6 - - + -
170C TYR 4.1 1.1 - - - -
171C THR* 3.6 34.3 - - + +
180C ASN 3.6 10.5 - - - +
181C PHE* 3.2 45.1 - + + -
184C GLY* 3.5 10.9 - - - -
185C ILE* 4.0 2.7 - - + -
197C PHE* 3.4 41.2 - + + +
198C VAL 3.0 26.4 + - - -
199C VAL* 3.4 15.4 - - - +
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Residues in contact with ILE 149 (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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146C ALA* 3.3 20.0 - - + +
148C TYR* 1.3 72.6 - - - +
150C GLN* 1.3 67.0 + - + +
152C ALA* 3.4 7.1 + - - +
153C GLY 3.3 15.1 + - - -
180C ASN* 3.5 50.5 - - + +
183C GLN* 3.8 14.8 - - + -
184C GLY* 3.5 16.6 - - - +
187C PHE* 6.1 0.7 - - + -
60D SER* 3.8 19.7 - - - +
61D GLY* 4.2 13.0 - - - +
64D GLY* 3.7 24.2 - - - +
65D LEU 4.0 1.2 + - - -
91D ASP* 6.1 0.2 - - - +
92D SER* 5.0 9.0 - - - -
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Residues in contact with GLN 150 (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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99C LEU* 3.7 13.8 - - + +
138C LEU* 3.5 24.7 - - + +
141C GLN* 3.8 9.3 + - - +
146C ALA* 3.2 20.7 + - - +
147C GLN* 3.9 3.2 - - - +
148C TYR 3.4 0.2 - - - -
149C ILE* 1.3 80.0 - - + +
151C ALA* 1.3 56.5 + - - +
153C GLY 3.1 3.1 + - - -
154C VAL* 2.8 28.6 + - - +
64D GLY 3.6 9.0 - - - +
67D ILE* 3.8 32.5 - - + +
68D GLY* 3.4 5.6 - - - +
71D LEU* 5.3 0.4 - - + -
96D GLN* 2.8 46.3 + - - +
100D ILE* 5.0 3.0 - - - +
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Residues in contact with ALA 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LEU* 3.5 26.6 - - + +
147C GLN 3.0 18.6 + - - +
148C TYR 3.7 5.6 - - - +
150C GLN* 1.3 73.0 - - - +
152C ALA* 1.3 56.6 + - - +
154C VAL* 3.1 2.3 + - - +
155C ALA* 2.8 36.1 + - - +
167C ALA* 3.8 8.0 - - + +
168C ILE 5.2 0.2 - - - -
169C THR* 3.8 20.6 - - + +
195C ALA* 5.0 3.4 - - + -
196C ILE 5.9 0.2 - - - +
197C PHE* 4.5 4.9 - - + -
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148C TYR 3.3 7.3 + - - +
149C ILE* 3.5 10.5 - - - +
151C ALA* 1.3 75.7 - - - +
153C GLY* 1.3 57.9 + - - +
155C ALA* 3.8 3.5 - - - +
156C LEU* 3.0 28.1 + - - +
184C GLY* 3.6 25.6 - - - +
187C PHE* 4.1 12.1 - - + -
188C ALA* 4.1 21.9 - - + +
193C ALA* 4.3 3.5 - - - +
197C PHE* 4.7 2.5 - - - -
65D LEU* 4.0 7.6 - - + +
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Residues in contact with GLY 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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149C ILE 3.3 4.8 + - - -
150C GLN 3.1 8.2 + - - -
152C ALA* 1.3 76.5 - - - +
154C VAL* 1.3 58.5 + - - +
156C LEU* 3.4 2.3 + - - +
157C GLY 2.8 23.6 + - - -
65D LEU* 3.6 36.4 - - - +
68D GLY* 3.6 13.7 - - - -
69D LEU* 3.6 4.1 + - - +
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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
----------------------------------------------------------
97C PHE* 3.9 25.6 - - + -
99C LEU* 4.2 12.8 - - + -
150C GLN 2.8 21.1 + - - +
151C ALA* 3.1 6.5 + - - +
153C GLY* 1.3 71.4 - - - +
155C ALA* 1.3 59.2 + - - +
157C GLY* 2.9 4.0 + - - -
158C LEU* 2.8 31.3 + - + +
167C ALA* 3.8 17.5 - - + -
68D GLY* 3.7 20.2 - - - +
71D LEU* 3.8 21.8 - - + -
72D GLN* 3.6 18.1 - - - +
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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
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151C ALA 2.8 20.4 + - - +
152C ALA 3.8 1.6 - - - +
154C VAL* 1.3 72.1 - - - +
156C LEU* 1.3 57.4 + - - +
158C LEU* 3.2 4.9 + - - -
159C LYS 2.9 24.8 + - - -
167C ALA* 3.8 6.7 - - + +
193C ALA* 3.8 9.6 - - + -
194C PRO* 3.3 49.3 - - - +
195C ALA* 3.8 11.9 - - + -
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Residues in contact with LEU 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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152C ALA 3.0 18.8 + - - +
153C GLY* 3.8 4.7 - - - +
155C ALA* 1.3 74.4 - - - +
157C GLY* 1.3 62.4 + - - +
159C LYS* 3.3 17.7 + - + +
160C MET* 2.9 48.0 + - + +
191C PHE* 4.2 33.0 - - + -
193C ALA* 3.9 8.8 - - + +
53D PHE* 4.4 15.7 - - + -
65D LEU* 4.0 31.2 - - + -
69D LEU* 4.2 14.4 - - + -
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Residues in contact with GLY 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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153C GLY 2.8 17.8 + - - -
154C VAL 2.9 4.7 + - - -
156C LEU* 1.3 72.7 - - - +
158C LEU* 1.3 60.9 + - - +
160C MET* 3.3 1.9 + - - +
161C ARG* 3.1 28.6 + - - +
69D LEU* 3.7 14.0 - - - +
72D GLN* 3.8 23.6 - - - -
74D PHE* 4.0 4.9 - - - -
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Residues in contact with LEU 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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95C GLU 4.6 6.3 - - - +
97C PHE* 5.0 3.1 - - + -
154C VAL* 2.8 28.4 + - + +
155C ALA* 3.2 8.9 + - - +
157C GLY* 1.3 71.2 - - - +
159C LYS* 1.3 61.8 + - - +
161C ARG* 3.4 3.6 + - - +
162C GLY 3.1 3.6 + - - -
163C LYS* 2.9 44.9 + - + +
165C ALA* 3.9 23.3 - - + +
166C VAL* 3.5 43.5 - - - +
167C ALA 3.7 3.8 - - - +
194C PRO* 4.5 1.6 - - + +
72D GLN* 3.5 27.7 - - - +
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Residues in contact with LYS 159 (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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155C ALA 2.9 16.1 + - - +
156C LEU* 3.7 19.3 - - + +
158C LEU* 1.3 75.6 - - - +
160C MET* 1.3 60.3 + - + +
162C GLY* 3.0 19.4 + - - +
163C LYS 5.2 1.3 - - - -
191C PHE* 2.7 29.6 + - - +
192C LYS* 3.9 24.4 + - - +
193C ALA* 4.6 0.9 - - - -
194C PRO* 3.7 16.5 - - + +
255C GLY* 6.0 2.2 - - - -
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Residues in contact with MET 160 (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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156C LEU* 2.9 47.0 + - + +
157C GLY 3.7 4.3 - - - +
159C LYS* 1.3 78.3 - - + +
161C ARG* 1.3 60.3 + - - +
162C GLY 3.3 0.7 + - - -
24D LEU* 3.8 21.1 - - + -
50D ASP* 3.4 31.9 - - + +
53D PHE* 4.8 8.3 - - + -
69D LEU* 4.1 15.5 - - - -
74D PHE* 3.9 19.2 - - + -
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Residues in contact with ARG 161 (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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157C GLY 3.1 17.5 + - - +
158C LEU* 3.4 6.0 + - - +
159C LYS 3.2 0.2 - - - -
160C MET* 1.3 76.7 - - - +
162C GLY* 1.3 61.4 - - - +
163C LYS* 3.4 6.7 + - + +
22D ASN* 3.4 16.8 + - - -
72D GLN* 2.7 36.5 + - - +
73D GLY* 3.0 27.5 + - - -
74D PHE* 3.5 26.8 - - + +
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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