Contacts of the strand formed by residues 137 - 147 (chain I) in PDB entry 1W72
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 137 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I SER* 3.4 9.2 + - - -
133I THR* 4.0 13.5 + - - +
135I GLY* 3.2 12.5 + - - +
136I GLY* 1.3 83.2 - - - +
138I ALA* 1.3 60.2 + - - +
192I THR* 3.9 22.2 - - + +
193I VAL 3.2 14.4 - - - +
194I PRO* 4.8 1.6 - - + -
195I SER* 3.3 9.7 + - - -
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Residues in contact with ALA 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I PRO* 4.4 12.3 - - + -
130I SER* 4.1 13.0 - - - +
137I THR* 1.3 74.9 - - - +
139I ALA* 1.3 60.2 + - - +
140I LEU* 4.0 1.3 - - + -
192I THR* 3.4 5.0 - - - -
193I VAL* 2.8 45.7 + - + +
195I SER* 4.2 2.9 - - - +
198I LEU* 3.9 29.6 - - + -
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Residues in contact with ALA 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I PRO* 3.5 18.4 - - - +
138I ALA* 1.3 71.2 - - - +
140I LEU* 1.3 60.6 + - - +
190I VAL* 3.7 20.0 - - + -
191I VAL 3.6 4.7 - - - -
192I THR* 4.4 8.1 - - + +
116M THR* 3.8 27.6 - - + +
118M PHE* 3.2 16.6 - - + -
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Residues in contact with LEU 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU 3.6 3.8 - - - -
126I PRO* 3.3 33.7 - - + -
138I ALA* 4.6 2.9 - - + -
139I ALA* 1.3 75.2 - - - +
141I GLY* 1.3 59.1 + - - +
157I TRP* 4.4 2.9 - - + -
190I VAL* 3.3 5.0 - - - +
191I VAL* 2.7 41.8 + - + +
193I VAL* 4.1 13.9 - - + -
198I LEU* 4.5 16.4 - - + -
206I TYR* 3.2 48.9 - - + -
225I VAL* 4.1 22.9 - - + +
227I PRO* 5.9 5.6 - - + -
118M PHE* 4.1 3.4 - - - -
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Residues in contact with GLY 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I LEU* 2.6 51.0 + - - +
140I LEU* 1.3 77.9 - - - +
142I CYS* 1.3 60.0 + - - -
157I TRP* 3.6 7.5 - - - -
189I SER 3.1 13.0 - - - -
190I VAL* 4.1 1.3 - - - -
225I VAL* 3.4 11.6 - - - +
118M PHE* 4.7 1.6 - - - -
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Residues in contact with CYS 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121I VAL* 4.1 7.2 - - + -
122I PHE 3.3 4.0 - - - +
124I LEU* 4.1 4.2 - - - +
141I GLY* 1.3 78.6 - - - -
143I LEU* 1.3 60.9 + - - +
144I VAL* 3.9 4.8 + - + +
154I VAL* 5.3 0.2 - - + -
157I TRP* 3.8 2.4 - - + -
188I SER* 3.3 6.8 - - - -
189I SER* 3.0 31.7 + - - +
208I CYS* 2.0 52.5 - - + -
210I VAL* 5.0 3.4 - - + -
221I LYS* 4.0 11.0 - - - -
225I VAL* 3.6 17.5 - - - -
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Residues in contact with LEU 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I SER 3.4 2.8 - - - +
121I VAL* 3.3 5.9 - - - -
122I PHE* 2.8 48.5 + - + +
124I LEU* 3.9 19.4 - - + +
142I CYS* 1.3 70.1 - - - +
144I VAL* 1.3 67.0 + - - +
145I LYS* 4.5 9.4 - - + -
186I SER* 5.0 1.3 - - - -
187I LEU 3.8 3.8 - - - +
188I SER* 3.7 17.9 - - - +
1229I GOL 4.8 7.6 - - - -
124M GLU* 4.1 15.0 - - - +
131M THR* 3.8 32.3 - - + +
133M VAL* 4.2 7.6 - - + -
178M TYR* 3.7 21.1 - - + -
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Residues in contact with VAL 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I PRO* 3.3 33.2 - - + -
120I SER 3.7 2.5 - - - +
121I VAL* 4.7 4.7 - - + +
142I CYS* 4.5 7.0 - - + +
143I LEU* 1.3 74.0 - - - +
145I LYS* 1.3 58.4 - - - +
147I TYR* 3.8 12.3 - - + -
152I VAL* 4.1 5.2 - - + -
154I VAL* 4.2 5.4 - - + -
186I SER* 3.2 5.6 - - - -
187I LEU* 2.7 65.3 + - + +
189I SER* 6.0 0.2 - - - -
210I VAL* 3.9 35.2 - - + -
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Residues in contact with LYS 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I PRO* 3.1 4.6 - - - +
120I SER* 2.8 42.5 + - - +
122I PHE* 3.7 21.0 - - + -
143I LEU* 4.5 9.9 - - + -
144I VAL* 1.3 74.4 - - - +
146I ASP* 1.3 86.6 + - - +
147I TYR 3.5 1.8 - - - -
186I SER* 3.4 3.4 - - - -
1229I GOL 3.3 28.3 - - - +
124M GLU* 2.5 33.0 + - - +
129M LYS* 3.5 30.5 - - - +
131M THR* 3.8 9.6 + - - -
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Residues in contact with ASP 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I LYS* 2.6 43.5 + - - +
118I GLY 3.7 4.7 - - - +
120I SER* 5.4 4.5 + - - +
145I LYS* 1.3 94.2 - - + +
147I TYR* 1.3 57.6 + - - +
179I GLN* 3.0 30.6 + - - +
184I LEU* 3.9 19.5 - - + +
185I TYR 3.1 13.3 + - - -
186I SER* 3.1 2.0 + - - -
1229I GOL 3.7 2.8 + - - -
129M LYS* 4.7 10.9 + - - -
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Residues in contact with TYR 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117I LYS 3.2 13.2 - - - +
119I PRO* 3.7 20.2 - - + -
144I VAL* 3.8 30.1 - - + -
146I ASP* 1.3 76.7 - - - +
148I PHE* 1.3 63.6 + - - +
149I PRO 3.5 21.3 - - - -
150I GLU* 3.6 15.6 + - - -
152I VAL* 3.5 32.0 + - + +
176I ALA* 3.2 27.4 - - - +
184I LEU* 3.6 3.4 - - - -
185I TYR* 2.9 57.9 + + + -
186I SER* 3.9 4.5 - - - -
187I LEU* 3.5 16.4 - - + +
212I HIS* 3.7 3.1 - - - +
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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