Contacts of the helix formed by residues 149 - 164 (chain C) in PDB entry 1UMD
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 HIS 149 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C PHE* 3.2 35.2 + - + -
93C PRO 3.4 15.8 + - - +
94C TYR* 4.1 15.3 - - + -
140C PHE* 5.0 5.6 - - + -
143C ALA* 5.6 8.2 + - + +
145C PRO 4.9 1.4 + - - -
147C ALA* 3.8 23.4 + - - -
148C SER* 1.3 79.7 + - - +
150C VAL* 1.3 66.2 + - + +
152C PRO* 3.4 8.3 - - - +
153C ALA* 3.1 23.4 + - - +
171C CYS* 3.8 10.3 - - - -
172C THR 2.8 26.8 + - - -
173C PHE* 4.3 9.2 - - + -
97D GLN* 3.7 14.8 - - - +
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Residues in contact with VAL 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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147C ALA* 3.0 22.0 + - + +
149C HIS* 1.3 78.5 - - + +
151C PRO* 1.3 74.5 - - + +
153C ALA* 3.2 3.8 + - - +
154C ALA* 3.1 20.3 + - - +
171C CYS* 3.9 19.1 - - - -
173C PHE* 4.4 6.3 - - + -
182C ASP 4.1 0.2 - - - +
183C TRP* 3.6 47.1 - - + +
187C ILE* 3.8 23.3 - - + +
199C PHE* 3.9 10.3 - - + -
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Residues in contact with PRO 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 ALA 3.6 9.4 - - - +
150C VAL* 1.3 93.5 - - + +
152C PRO* 1.3 71.3 - - + +
154C ALA* 3.1 5.7 + - + +
155C GLY 2.9 17.8 + - - -
182C ASP* 3.5 24.5 - - + +
186C GLY* 4.0 17.9 - - - +
61D ALA 3.7 24.0 - - - +
62D ALA* 4.5 2.5 - - - -
65D GLY* 3.7 11.0 - - - -
66D ALA* 3.5 8.7 - - + +
93D GLN* 3.6 18.2 - - + +
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Residues in contact with PRO 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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92C PHE* 3.9 14.1 - - + -
140C PHE* 4.2 4.9 - - + -
148C SER 3.1 24.9 - - - +
149C HIS* 3.4 9.2 - - - +
151C PRO* 1.3 95.2 - - + +
153C ALA* 1.3 61.9 + - - +
155C GLY 3.1 1.0 + - - -
156C ALA* 2.9 22.2 + - - +
65D GLY 3.2 16.4 - - - +
68D LEU* 4.0 18.6 - - + -
69D GLY* 3.2 9.2 - - - +
93D GLN* 3.4 11.4 - - - +
97D GLN* 4.0 14.8 - - + -
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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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92C PHE* 3.6 30.0 - - + -
149C HIS 3.1 18.0 + - - +
150C VAL 3.2 6.0 + - - +
152C PRO* 1.3 75.3 - - - +
154C ALA* 1.3 63.1 + - - +
156C ALA* 3.4 2.4 + - - +
157C ALA* 3.1 22.9 + - - +
169C ALA* 4.0 7.3 - - + +
171C CYS* 3.7 24.7 - - + -
197C ALA* 4.6 3.3 - - + +
199C PHE* 4.4 4.3 - - + -
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Residues in contact with ALA 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 VAL 3.1 11.2 + - - +
151C PRO* 3.1 10.7 + - + +
153C ALA* 1.3 76.0 - - - +
155C GLY* 1.3 58.7 + - - +
157C ALA* 3.3 6.2 + - - +
158C ILE* 2.9 36.4 + - + +
186C GLY* 3.4 26.5 - - - +
189C PHE* 5.2 2.9 - - + -
190C ALA* 3.7 21.5 - - + +
195C ALA* 4.4 0.9 - - - +
199C PHE* 4.5 5.5 - - + -
66D ALA* 5.3 2.5 - - + -
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Residues in contact with GLY 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 PRO 2.9 10.5 + - - -
152C PRO 3.1 3.1 + - - -
154C ALA* 1.3 75.3 - - - +
156C ALA* 1.3 64.7 + - - +
158C ILE* 3.1 4.5 + - - +
159C SER* 2.9 19.1 + - - -
66D ALA* 3.3 32.5 - - - +
70D MET* 3.3 18.9 - - - +
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Residues in contact with ALA 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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90C TRP* 4.7 3.1 - - + -
92C PHE* 3.5 37.7 - - + -
152C PRO 2.9 7.3 + - - +
153C ALA 3.8 0.4 - - - +
155C GLY* 1.3 75.0 - - - +
157C ALA* 1.3 58.3 + - - +
159C SER* 3.1 4.7 + - - -
160C MET* 2.9 40.5 + - + +
169C ALA* 4.8 0.2 - - + -
69D GLY 3.6 16.9 - - - +
73D HIS* 4.1 15.1 - - + -
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Residues in contact with ALA 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 ALA 3.1 13.5 + - - +
154C ALA 3.5 9.0 - - - +
155C GLY 3.2 0.2 - - - -
156C ALA* 1.3 77.4 - - - +
158C ILE* 1.3 61.9 + - - +
160C MET* 3.2 13.4 + - - +
161C LYS 3.0 18.7 + - - -
169C ALA* 4.2 3.3 - - + +
195C ALA* 3.7 10.8 - - + -
196C PRO* 3.3 25.1 - - - +
197C ALA* 3.6 26.2 - - + -
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Residues in contact with ILE 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 ALA* 2.9 25.9 + - + +
155C GLY* 3.1 7.4 + - - +
157C ALA* 1.3 75.7 - - - +
159C SER* 1.3 56.7 + - - +
161C LYS* 3.2 7.3 + - + +
162C LEU* 2.9 45.5 + - + +
189C PHE* 3.5 45.5 - - + +
190C ALA* 5.2 0.2 - - - -
193C GLN* 4.0 20.2 - - + +
195C ALA* 3.9 16.8 - - + -
54D MET* 4.2 9.0 - - + -
70D MET* 3.4 23.3 - - + -
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Residues in contact with SER 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 GLY 2.9 12.2 + - - -
156C ALA 3.3 6.3 - - - -
158C ILE* 1.3 75.3 - - - +
160C MET* 1.3 60.3 + - - +
162C LEU 4.5 0.2 - - - +
163C LEU* 2.8 37.2 + - - +
70D MET* 4.0 5.8 - - - -
73D HIS* 2.8 33.7 + - - -
74D GLY 3.8 3.6 + - - -
75D LEU* 3.3 36.5 - - - +
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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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90C TRP* 3.5 46.7 - - + -
156C ALA* 2.9 20.6 + - + +
157C ALA* 3.2 13.2 + - - +
159C SER* 1.3 75.8 - - - +
161C LYS* 1.3 58.1 + - - +
164C ARG* 2.9 23.7 + - - -
165C THR* 3.1 24.1 + - - +
166C GLY 4.5 1.2 + - - -
167C GLN* 3.7 25.8 - - + +
168C VAL* 3.6 30.7 - - - +
169C ALA* 3.7 9.0 - - + -
196C PRO* 4.1 3.4 - - + +
73D HIS* 3.5 20.2 - - + +
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Residues in contact with LYS 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 ALA 3.0 12.4 + - - +
158C ILE* 3.5 11.9 - - + +
159C SER 3.2 0.2 - - - -
160C MET* 1.3 75.3 - - - +
162C LEU* 1.3 75.0 + - + +
164C ARG* 3.1 31.6 + - - +
193C GLN* 2.7 44.4 + - + +
194C GLY* 4.2 11.4 - - - +
195C ALA* 4.6 2.5 - - + -
196C PRO* 3.8 14.1 - - + +
51D ASP* 5.7 3.6 + - - -
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Residues in contact with LEU 162 (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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158C ILE* 2.9 26.7 + - + +
159C SER* 3.9 4.3 - - - +
161C LYS* 1.3 86.3 - - + +
163C LEU* 1.3 63.7 + - + +
164C ARG* 3.2 19.1 + - - +
193C GLN* 5.7 3.8 - - - +
25D VAL* 4.8 4.3 - - + -
51D ASP* 3.6 51.5 - - + +
54D MET* 3.5 30.7 - - + -
70D MET* 5.4 0.4 - - + -
75D LEU* 3.9 27.4 - - + -
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Residues in contact with LEU 163 (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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159C SER* 2.8 34.8 + - - +
162C LEU* 1.3 77.0 - - - +
164C ARG* 1.3 72.2 + - - +
165C THR* 3.3 15.7 + - + +
22D PRO 6.1 0.7 - - - +
23D ARG* 5.4 7.4 - - + -
73D HIS* 4.2 11.2 - - + +
74D GLY* 3.9 22.7 - - - +
75D LEU* 3.9 20.9 - - + -
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Residues in contact with ARG 164 (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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160C MET 2.9 11.3 + - - -
161C LYS* 3.1 22.9 + - - +
162C LEU* 3.2 11.8 + - - +
163C LEU* 1.3 83.5 - - - +
165C THR* 1.3 59.7 + - - +
166C GLY* 3.3 3.4 + - - +
51D ASP* 3.1 26.5 + - - +
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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