Contacts of the strand formed by residues 142 - 152 (chain X) in PDB entry 3HI6
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 THR 142 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141X SER* 1.3 83.7 - - - +
143X ALA* 1.3 61.2 + - - +
190X THR* 4.8 13.0 - - - +
191X VAL 3.4 15.0 - - - +
192X PRO* 4.9 3.6 - - + -
193X SER* 3.5 4.3 + - - -
115Y PHE* 4.3 18.1 - - - -
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Residues in contact with ALA 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X PRO* 4.6 7.4 - - + -
142X THR* 1.3 74.1 - - - +
144X ALA* 1.3 60.3 + - - +
189X VAL 4.0 0.3 - - - +
190X THR* 3.1 7.1 - - - -
191X VAL* 2.7 37.5 + - + +
193X SER* 3.5 13.8 + - - +
196X LEU* 3.8 33.4 - - + -
115Y PHE* 4.5 3.6 - - - -
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Residues in contact with ALA 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X PRO* 3.4 20.2 - - - +
143X ALA* 1.3 74.1 - - - +
145X LEU* 1.3 64.7 + - - +
189X VAL 3.5 5.6 - - - +
190X THR* 3.9 13.5 - - + -
115Y PHE* 3.6 42.0 - - + -
117Y PHE* 3.5 12.2 - - + -
134Y LEU* 4.0 13.2 - - + -
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Residues in contact with LEU 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131X LEU 3.3 14.4 - - - +
133X PRO* 3.8 18.2 - - + -
144X ALA* 1.3 77.0 - - - +
146X GLY* 1.3 61.0 + - - +
161X TRP* 3.6 20.2 - - + -
188X VAL* 3.3 4.8 - - - +
189X VAL* 2.9 55.8 + - + +
191X VAL* 4.4 8.1 - - + -
196X LEU* 4.0 20.4 - - + -
201X TYR* 3.8 32.5 - - + -
218X VAL* 4.1 9.4 - - + +
117Y PHE* 3.9 7.9 - - - -
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Residues in contact with GLY 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X PRO* 3.6 0.2 - - - +
131X LEU* 2.7 44.9 + - - +
145X LEU* 1.3 78.4 - - - +
147X CYS* 1.3 61.1 + - - -
161X TRP* 3.6 9.9 - - - -
187X SER 3.1 13.0 - - - -
188X VAL* 4.1 0.7 - - - -
218X VAL* 3.3 15.1 - - - +
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Residues in contact with CYS 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128X VAL* 4.1 14.4 - - + -
129X PHE 3.3 7.6 - - - +
131X LEU* 3.9 4.9 - - - +
146X GLY* 1.3 79.0 - - - -
148X LEU* 1.3 60.4 + - - +
149X VAL* 3.7 8.2 + - + +
159X VAL* 5.6 0.2 - - + -
161X TRP* 4.0 1.2 - - + -
186X SER* 3.3 4.0 - - - -
187X SER* 2.9 34.8 + - - +
203X CYS* 2.0 52.3 - - + -
216X LYS* 4.2 5.2 - - - -
218X VAL* 3.7 15.9 - - - -
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Residues in contact with LEU 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127X SER 3.5 2.3 - - - +
128X VAL* 3.3 5.0 - - - -
129X PHE* 2.7 51.9 + - + +
131X LEU* 4.0 14.1 - - + +
147X CYS* 1.3 70.3 - - - +
149X VAL* 1.3 61.5 + - - +
150X LYS* 4.5 16.4 - - + -
184X SER* 5.2 3.8 - - - +
185X LEU 3.7 11.2 - - - +
186X SER* 3.3 20.9 - - - +
123Y GLN* 3.9 14.6 - - - +
130Y SER* 3.6 31.9 - - - +
132Y VAL* 4.8 9.2 - - + -
177Y THR* 5.1 9.9 - - + +
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Residues in contact with VAL 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X PRO* 3.4 32.1 - - + -
127X SER 3.6 2.9 - - - +
128X VAL* 4.6 4.7 - - + +
147X CYS* 4.4 10.1 - - + +
148X LEU* 1.3 73.8 - - - +
150X LYS* 1.3 57.5 + - - +
152X TYR* 3.8 12.9 - - + -
157X VAL* 4.3 5.8 - - + -
159X VAL* 4.3 7.0 - - + -
184X SER* 3.2 5.2 - - - -
185X LEU* 2.7 56.9 + - + +
187X SER* 5.6 0.4 - - - +
205X VAL* 3.8 34.3 - - + -
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Residues in contact with LYS 150 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X PRO* 3.2 3.3 - - - +
127X SER* 2.7 44.0 + - - +
129X PHE* 4.2 15.9 - - + -
148X LEU* 4.5 13.7 - - + -
149X VAL* 1.3 73.9 - - - +
151X ASP* 1.3 92.4 + - - +
152X TYR* 3.7 1.1 - - - -
178X GLN* 3.4 19.5 + - - -
183X TYR 3.8 0.2 - - - -
184X SER* 3.9 13.0 - - - -
123Y GLN* 3.9 21.1 - - - +
128Y THR* 4.2 23.0 - - - +
129Y ALA 6.0 0.2 - - - +
130Y SER* 4.1 14.5 + - - +
179Y THR* 4.8 13.5 - - - +
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Residues in contact with ASP 151 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124X LYS* 3.4 29.2 + - - +
125X GLY 3.4 14.0 - - - +
127X SER* 4.7 4.5 + - - +
150X LYS* 1.3 103.0 + - - +
152X TYR* 1.3 56.0 + - - +
178X GLN* 3.0 26.9 + - - +
180X SER* 4.5 2.8 + - - -
182X LEU* 3.7 21.1 - - + +
183X TYR 2.9 15.0 + - - -
184X SER* 4.1 0.2 - - - -
128Y THR* 5.8 0.9 - - - +
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Residues in contact with TYR 152 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124X LYS 3.2 13.5 - - - +
126X PRO* 3.7 33.2 - - + -
149X VAL* 3.8 24.5 - - + -
150X LYS 4.4 0.2 - - - -
151X ASP* 1.3 75.3 - - - +
153X PHE* 1.3 62.9 + - - +
154X PRO 3.6 21.1 - - - -
155X GLU* 4.3 11.6 - - - +
157X VAL* 4.0 20.6 + - + +
175X ALA* 3.1 26.5 - - - +
182X LEU* 3.7 3.8 - - - -
183X TYR* 2.8 70.8 + + + +
184X SER* 3.9 2.9 - - - -
185X LEU* 3.4 13.7 - - - +
207X HIS* 3.8 10.8 - + + -
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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