Contacts of the strand formed by residues 140 - 150 (chain H) in PDB entry 4OQT
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 140 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135H SER* 5.1 3.3 - - - -
136H THR* 5.4 2.6 + - - -
139H GLY* 1.3 75.2 - - - -
141H ALA* 1.3 60.6 + - - +
188H THR* 5.0 10.8 - - - +
189H VAL 3.2 15.5 - - - +
190H PRO* 4.4 4.0 - - + -
191H SER* 4.2 1.1 - - - +
115L SER* 5.3 3.5 + - - -
117L PHE* 4.4 17.8 - - - -
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Residues in contact with ALA 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H PRO* 4.8 5.2 - - + -
132H SER 5.4 1.1 - - - +
135H SER* 4.0 12.1 - - - +
139H GLY 3.7 0.6 + - - -
140H THR* 1.3 74.5 - - - +
142H ALA* 1.3 60.6 - - - +
187H VAL 4.0 0.2 - - - +
188H THR* 3.3 5.6 - - - -
189H VAL* 2.8 35.0 + - - +
191H SER* 3.6 22.9 - - - -
194H LEU* 3.9 24.5 - - + -
117L PHE* 4.4 5.4 - - - -
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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
----------------------------------------------------------
131H PRO* 3.4 20.4 - - - +
132H SER 4.3 2.5 + - - +
141H ALA* 1.3 74.0 - - - +
143H LEU* 1.3 60.4 - - - +
187H VAL 3.5 6.1 - - - +
188H THR* 4.1 7.2 - - + -
117L PHE* 3.5 46.6 - - + -
119L PHE* 3.5 14.2 - - + -
136L LEU* 3.9 15.7 - - + -
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Residues in contact with LEU 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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129H LEU* 3.3 17.0 - - - +
131H PRO* 4.0 10.3 - - + -
142H ALA* 1.3 74.3 - - - +
144H GLY* 1.3 60.9 + - - +
159H TRP* 3.6 26.7 - - + -
186H VAL* 3.2 7.5 - - - +
187H VAL* 2.9 41.7 + - + +
189H VAL* 4.2 9.9 - - + -
194H LEU* 3.7 22.2 - - + -
199H TYR* 3.5 36.1 - - + -
216H VAL* 3.6 22.0 - - + +
119L PHE* 4.3 3.8 - - - -
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Residues in contact with GLY 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H LEU* 2.7 40.5 + - - +
143H LEU* 1.3 81.1 - - - +
145H CYS* 1.3 56.4 + - - -
159H TRP* 3.4 16.8 - - - -
185H SER 3.0 13.5 - - - -
186H VAL* 4.0 0.2 - - - -
216H VAL* 3.2 12.2 - - - +
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Residues in contact with CYS 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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126H VAL* 4.1 13.0 - - + -
127H PHE 3.4 5.4 - - - +
129H LEU* 4.3 3.6 - - - -
144H GLY* 1.3 71.7 - - - -
146H LEU* 1.3 60.9 + - - +
147H VAL* 3.8 4.8 + - + +
157H VAL* 5.5 1.1 - - + -
159H TRP* 3.7 4.0 - - + -
184H SER* 3.4 3.8 + - - -
185H SER* 2.9 33.8 + - - +
201H CYS* 2.0 53.4 - - + -
203H VAL* 4.9 3.6 - - + -
214H LYS* 4.3 6.3 - - - -
216H VAL* 3.9 19.5 - - - -
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Residues in contact with LEU 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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125H SER 3.2 8.8 - - - +
126H VAL* 3.4 1.1 - - - -
127H PHE* 2.6 46.7 + - + +
129H LEU* 4.4 11.2 - - + +
145H CYS* 1.3 71.8 - - - +
147H VAL* 1.3 59.6 + - - +
148H LYS* 3.5 14.3 + - + -
182H SER* 4.0 14.8 - - - +
183H LEU 3.5 13.2 - - - +
184H SER* 3.2 22.2 - - - +
125L GLN* 4.4 8.3 - - - +
132L SER* 3.6 33.2 - - - +
134L VAL* 5.0 9.9 - - + -
179L THR* 5.1 7.9 - - + -
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Residues in contact with VAL 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H PRO* 3.5 26.2 - - + -
125H SER 3.7 3.4 - - - -
126H VAL* 4.5 3.1 - - + -
145H CYS* 3.8 4.9 + - + +
146H LEU* 1.3 70.3 - - - +
148H LYS* 1.3 57.9 + - - +
150H TYR* 3.8 17.3 - - + -
155H VAL* 4.1 9.0 - - + -
157H VAL* 3.9 19.1 - - + -
182H SER* 3.2 4.0 + - - -
183H LEU* 2.8 50.2 + - + +
203H VAL* 3.6 39.5 - - + -
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Residues in contact with LYS 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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124H PRO* 3.6 0.7 - - - +
125H SER* 2.9 38.1 + - - +
127H PHE* 4.3 14.1 - - + -
146H LEU* 4.1 14.8 - - + +
147H VAL* 1.3 75.5 - - - +
149H ASP* 1.3 98.7 + - - +
150H TYR* 3.8 2.2 - - - -
176H GLN* 3.6 12.2 + - - +
181H TYR 3.9 0.4 - - - -
182H SER* 3.5 15.5 - - - +
125L GLN* 3.9 27.1 - - - +
130L THR* 4.4 23.0 - - - +
132L SER* 4.0 11.7 + - - +
181L THR* 5.4 5.1 - - - +
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Residues in contact with ASP 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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122H LYS* 3.0 33.0 + - - +
123H GLY 3.1 8.5 - - - +
125H SER* 5.6 3.2 - - - -
148H LYS* 1.3 112.8 + - - +
150H TYR* 1.3 56.2 + - - +
176H GLN* 3.3 15.8 + - - +
178H SER* 4.0 10.8 + - - -
180H LEU* 3.9 18.2 - - + -
181H TYR 3.0 14.1 + - - -
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Residues in contact with TYR 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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122H LYS* 3.3 15.3 - - - +
124H PRO* 3.8 19.3 - - + -
147H VAL* 3.8 25.4 - - + -
149H ASP* 1.3 78.4 - - - +
151H PHE* 1.3 65.0 + - - +
152H PRO 3.8 10.3 - - - -
153H GLU* 2.8 28.3 + - - -
155H VAL* 3.3 26.9 - - + +
173H ALA* 3.2 17.7 - - - +
180H LEU* 3.7 4.4 - - - +
181H TYR* 3.0 58.7 + + + +
182H SER* 3.9 7.2 - - - -
183H LEU* 3.8 5.3 - - - +
205H HIS* 3.8 18.6 - + - +
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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