Contacts of the strand formed by residues 139 - 148 (chain H) in PDB entry 1UB6
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 VAL 139 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129H PRO* 4.3 16.2 - - + -
134H THR 5.3 2.2 - - - +
135H THR* 4.2 32.1 - - + +
136H GLY 4.0 7.6 + - - +
138H SER* 1.3 74.5 - - - +
140H THR* 1.3 74.1 + - - +
141H LEU* 3.8 7.0 + - + +
185H THR* 3.1 25.1 - - - -
186H VAL* 2.7 25.8 + - + +
188H SER* 5.1 1.3 - - - +
191H TRP* 3.5 34.1 - - + -
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Residues in contact with THR 140 (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* 4.6 0.7 - - - +
139H VAL* 1.3 83.7 - - - +
141H LEU* 1.3 63.1 + - - +
183H SER* 4.2 7.4 - - - -
184H VAL 3.4 9.9 - - - +
185H THR* 3.5 15.4 - - + +
119L THR* 4.6 11.5 + - - +
121L SER* 2.8 37.6 + - - +
123L PHE* 2.8 25.2 - - + -
140L PHE* 3.7 23.6 - - + -
142L ASN* 4.3 6.7 + - - +
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Residues in contact with LEU 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H ALA 3.7 1.6 - - - -
128H ALA* 3.9 4.0 - - + -
129H PRO* 3.4 24.0 - - + -
139H VAL* 3.8 7.8 + - + +
140H THR* 1.3 76.3 - - - +
142H GLY* 1.3 56.8 + - - +
157H TRP* 4.7 0.2 - - + -
183H SER* 3.2 3.6 - - - -
184H VAL* 2.6 53.4 + - + +
186H VAL* 5.0 4.3 - - + -
191H TRP* 3.2 42.0 - - + -
196H VAL* 3.7 38.1 - - + -
213H LEU* 3.3 22.4 - - + -
123L PHE* 4.6 3.4 - - - -
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Residues in contact with GLY 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H ALA* 2.6 50.6 + - - +
141H LEU* 1.3 77.4 - - - +
143H CYS* 1.3 61.6 + - - -
157H TRP* 3.4 10.5 - - - -
182H SER 3.0 13.2 - - - -
183H SER* 4.0 2.0 - - - -
213H LEU* 3.6 4.1 - - - +
140L PHE* 4.5 4.5 - - - -
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Residues in contact with CYS 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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124H VAL* 4.3 10.5 - - + -
125H TYR 3.4 5.4 - - - +
126H PRO* 4.5 8.7 - - - -
127H ALA* 5.2 0.9 - - - -
142H GLY* 1.3 80.6 - - - -
144H LEU* 1.3 60.6 + - - +
145H VAL* 3.9 7.5 + - + +
155H VAL* 5.3 3.8 - - + -
157H TRP* 3.7 6.5 - - + -
181H SER* 3.6 3.5 - - - -
182H SER* 2.9 31.9 + - - +
198H CYS* 2.0 52.3 - - + -
200H VAL* 5.2 1.8 - - + -
211H LYS* 4.5 2.0 - - - -
213H LEU* 4.1 10.5 - - - -
140L PHE* 5.4 1.3 - - - -
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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
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123H SER 3.4 1.7 - - - +
124H VAL* 3.4 3.5 - - - -
125H TYR* 2.7 60.0 + - + +
127H ALA* 5.0 5.7 - - + +
142H GLY 4.4 0.2 - - - -
143H CYS* 1.3 72.7 - - - +
145H VAL* 1.3 63.6 + - - +
146H LYS* 4.2 17.7 - - + -
179H THR* 3.9 19.1 - - + -
180H MET 3.8 11.4 - - - +
181H SER* 4.1 13.7 - - - +
129L GLN* 4.9 1.3 - - - +
136L SER* 3.4 26.5 - - - +
138L VAL* 4.1 22.0 - - + -
183L THR* 4.8 7.6 - - + +
185L THR* 6.2 0.2 - - + -
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Residues in contact with VAL 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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122H PRO* 3.4 32.1 - - + -
123H SER 3.4 4.3 - - - +
124H VAL* 4.4 4.9 - - + -
143H CYS* 4.3 8.3 - - + +
144H LEU* 1.3 76.5 - - - +
146H LYS* 1.3 59.1 + - - +
148H TYR* 3.5 13.3 - - + -
153H VAL* 4.7 4.5 - - + -
155H VAL* 4.4 4.0 - - + -
179H THR* 3.3 2.9 - - - +
180H MET* 2.9 58.0 + - - +
200H VAL* 3.7 38.4 - - + -
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Residues in contact with LYS 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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122H PRO 3.8 0.2 - - - -
123H SER* 2.8 39.2 + - - -
125H TYR* 3.6 34.5 - - + -
144H LEU* 4.1 11.0 - - + -
145H VAL* 1.3 74.1 - - - +
147H GLY* 1.3 61.3 + - - +
148H TYR* 3.5 3.4 - - - -
174H GLN* 4.5 12.1 - - - +
178H TYR 3.6 5.8 - - - -
179H THR* 3.2 28.9 + - + +
129L GLN* 3.9 18.6 - - - +
136L SER* 4.9 0.2 - - - +
185L THR* 4.6 13.3 - - - +
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Residues in contact with GLY 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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120H THR* 2.7 23.2 + - - -
121H PRO 3.1 10.8 - - - +
123H SER* 5.0 3.7 + - - -
146H LYS* 1.3 80.9 - - - +
148H TYR* 1.3 53.6 + - - +
177H LEU* 3.6 30.3 - - - +
178H TYR 3.2 6.1 + - - -
179H THR* 4.1 1.6 + - - -
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Residues in contact with TYR 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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120H THR* 3.3 17.5 - - - +
122H PRO* 3.7 19.7 - - + -
145H VAL* 3.5 36.8 - - + -
146H LYS 4.1 1.8 - - - -
147H GLY* 1.3 80.2 - - - +
149H PHE* 1.3 58.2 + - - +
150H PRO 3.8 4.0 - - - -
151H GLU* 3.3 23.6 - - - -
153H VAL* 3.2 16.6 - - + +
171H ALA* 3.3 16.6 - - - +
177H LEU* 3.6 4.4 - - - -
178H TYR* 2.7 72.9 + - + +
179H THR 4.0 0.2 - - - -
180H MET* 3.1 22.2 - - - +
202H HIS* 3.6 22.2 - + - +
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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