Contacts of the strand formed by residues 141 - 151 (chain H) in PDB entry 3HMX
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 141 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H LYS* 4.8 7.3 + - - +
140H GLY* 1.3 76.6 + - - -
142H ALA* 1.3 61.5 + - - +
189H THR* 4.9 13.5 - - + -
190H VAL 3.2 25.4 - - - +
191H PRO* 4.6 0.9 - - + -
192H SER* 3.3 4.6 + - - +
116L PHE* 4.3 13.4 - - + -
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Residues in contact with ALA 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H PRO* 4.4 10.8 - - + -
133H SER 5.9 0.7 - - - +
135H LYS* 4.8 9.2 - - + -
141H THR* 1.3 75.2 - - - +
143H ALA* 1.3 60.8 + - - +
144H LEU* 4.8 0.2 - - - -
189H THR* 3.8 3.7 - - - +
190H VAL* 2.7 43.1 + - + +
192H SER* 3.6 16.6 + - - +
195H LEU* 4.3 21.3 - - + -
116L PHE* 4.4 4.3 - - - -
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Residues in contact with ALA 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H PRO* 3.5 22.7 - - - +
142H ALA* 1.3 73.9 - - - +
144H LEU* 1.3 67.9 + - - +
188H VAL 3.4 10.1 - - - +
189H THR* 4.5 5.2 - - + +
116L PHE* 3.3 45.0 - - + -
118L PHE* 3.6 15.5 - - + -
135L LEU* 4.5 8.5 - - + -
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Residues in contact with LEU 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H LEU 3.3 15.7 - - - +
132H PRO* 3.7 18.8 - - + -
142H ALA 4.3 0.2 - - - +
143H ALA* 1.3 82.9 - - - +
145H GLY* 1.3 58.8 + - - +
160H TRP* 4.4 2.9 - - + -
187H VAL* 3.0 9.6 - - - +
188H VAL* 2.8 50.5 + - + +
190H VAL* 3.5 31.4 - - + -
195H LEU* 5.1 1.1 - - + -
200H TYR* 4.0 32.3 - - + -
217H VAL* 3.9 22.7 - - + +
118L PHE* 3.8 7.5 - - - -
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Residues in contact with GLY 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H PRO* 3.5 1.2 - - - +
130H LEU* 2.6 45.8 + - - +
144H LEU* 1.3 81.2 - - - +
146H CYS* 1.3 58.2 + - - -
160H TRP* 3.3 17.7 - - - -
186H SER 3.1 13.2 - - - -
187H VAL* 3.9 2.7 - - - -
217H VAL* 4.0 3.5 - - - +
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Residues in contact with CYS 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H VAL* 3.8 15.9 - - + -
128H PHE 3.3 5.6 - - - +
129H PRO* 5.0 0.2 - - - -
130H LEU* 4.5 2.7 - - - -
145H GLY* 1.3 73.6 - - - -
147H LEU* 1.3 61.7 + - - +
148H VAL* 3.6 8.4 + - + +
158H VAL* 6.1 0.4 - - + -
160H TRP* 3.7 1.4 - - + -
185H SER* 3.7 0.7 + - - -
186H SER* 2.9 32.8 + - - +
202H CYS* 2.0 53.2 - - + -
204H VAL* 5.0 0.2 - - + -
215H LYS* 4.0 9.6 - - - -
217H VAL* 3.9 20.6 - - - -
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Residues in contact with LEU 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H SER 3.3 6.1 - - - +
127H VAL* 3.6 1.0 - - - -
128H PHE* 2.7 47.2 + - + +
130H LEU* 4.3 23.7 - - + +
145H GLY 4.1 0.8 + - - -
146H CYS* 1.3 70.3 - - - +
148H VAL* 1.3 59.6 + - - +
149H LYS* 3.9 22.8 - - + +
183H SER* 4.0 8.3 - - - +
184H LEU 3.4 17.3 - - - +
185H SER* 4.6 7.0 - - - +
124L GLN* 4.3 9.9 - - - +
131L SER* 3.6 35.4 - - - +
133L VAL* 5.0 5.2 - - + -
178L THR* 5.7 6.7 - - + -
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Residues in contact with VAL 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H PRO* 3.5 32.1 - - + -
126H SER 3.6 3.6 - - - +
127H VAL* 4.7 2.9 - - + +
146H CYS* 3.6 9.6 + - + +
147H LEU* 1.3 70.8 - - - +
149H LYS* 1.3 59.1 + - - +
151H TYR* 4.0 12.6 - - + -
156H VAL* 4.8 5.8 - - + -
158H VAL* 4.2 7.4 - - + -
183H SER* 3.3 3.2 + - - -
184H LEU* 2.8 65.2 + - + +
186H SER* 5.4 0.7 - - - +
204H VAL* 3.8 32.5 - - + -
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Residues in contact with LYS 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H SER* 2.9 37.2 + - - +
128H PHE* 5.1 10.1 - - + -
147H LEU* 3.9 20.2 - - + +
148H VAL* 1.3 76.8 - - - +
150H ASP* 1.3 99.4 + - - +
151H TYR* 3.8 2.5 - - - -
177H GLN* 3.7 21.9 - - - +
182H TYR 4.0 0.4 - - - -
183H SER* 3.8 5.4 - - - +
124L GLN* 4.1 9.4 - - - +
129L THR* 3.7 22.3 + - - +
131L SER* 3.8 24.7 - - - +
180L THR* 5.1 9.8 + - - -
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Residues in contact with ASP 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H LYS* 3.2 29.5 + - - +
124H GLY 3.2 4.5 - - - +
126H SER* 5.2 4.3 + - - +
149H LYS* 1.3 108.9 + - - +
151H TYR* 1.3 56.5 + - - +
177H GLN* 2.8 31.7 + - - -
179H SER* 4.5 0.9 + - - -
181H LEU* 4.0 24.3 - - + +
182H TYR 3.0 14.5 + - - -
183H SER* 4.1 0.4 - - - -
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Residues in contact with TYR 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H LYS* 3.4 15.9 - - - +
125H PRO* 3.5 31.6 - - + -
148H VAL* 4.0 17.5 - - + -
150H ASP* 1.3 77.6 - - - +
152H PHE* 1.3 63.1 + - - +
153H PRO 3.4 23.3 - - - -
154H GLU* 3.6 16.7 + - + +
156H VAL* 3.9 15.6 - - + +
174H ALA* 3.2 27.9 - - - +
181H LEU* 3.7 3.6 - - - +
182H TYR* 2.8 57.4 + - + +
183H SER* 3.8 9.6 - - - -
184H LEU* 3.8 10.5 - - + +
206H HIS* 3.9 8.5 - + - +
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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