Contacts of the strand formed by residues 137 - 147 (chain E) in PDB entry 2P5W
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 LYS 137 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D MET* 3.9 14.8 - - + -
169D MET* 3.5 32.3 - - + +
171D PHE* 3.6 52.2 - - + -
131E GLU* 3.8 5.2 - - - +
132E ILE* 3.5 20.1 + - - +
135E THR* 3.1 30.2 + - - +
136E GLN* 1.3 83.2 + - - +
138E ALA* 1.3 62.8 + - - +
192E ARG* 3.6 20.0 - - - +
193E VAL 3.5 10.8 - - - +
194E SER* 4.9 1.8 - - - -
195E ALA 3.8 2.0 - - - +
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Residues in contact with ALA 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E PRO* 3.5 25.8 - - + -
131E GLU* 3.6 3.8 - - - -
132E ILE* 4.0 8.3 - - + -
137E LYS* 1.3 75.3 - - - +
139E THR* 1.3 61.3 + - - +
140E LEU* 4.0 1.2 + - - +
191E LEU 3.7 2.1 - - - +
192E ARG* 3.4 1.7 - - - +
193E VAL* 2.7 41.8 + - + +
195E ALA* 4.5 3.6 - - - -
198E TRP* 3.6 26.2 - - + -
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Residues in contact with THR 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D LEU* 3.3 21.0 - - - +
138D LEU* 3.7 23.7 - - + +
140D THR* 5.3 1.4 + - - -
164D LEU* 5.0 2.5 - - + -
127E PRO* 3.4 14.6 - - - +
131E GLU* 2.5 36.6 + - - +
138E ALA* 1.3 71.4 - - - +
140E LEU* 1.3 71.0 + - - +
141E VAL* 4.7 0.2 - - + -
190E ARG* 3.9 23.1 - - + -
191E LEU 3.5 7.6 - - - +
192E ARG* 3.1 22.6 + - + +
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Residues in contact with LEU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E VAL* 4.2 17.7 - - + -
125E PHE 3.5 7.9 - - - +
126E GLU* 5.6 0.2 - - - -
127E PRO* 4.0 19.3 - - + -
138E ALA 4.2 8.1 - - - +
139E THR* 1.3 77.5 - - - +
141E VAL* 1.3 60.9 + - - +
156E TRP* 4.0 15.9 - - + -
190E ARG* 3.3 5.2 - - - -
191E LEU* 2.8 54.2 + - + +
193E VAL* 4.5 10.3 - - + -
198E TRP* 4.2 11.7 - - + -
205E PHE* 3.7 43.3 - - + -
236E ALA* 4.5 2.9 - - + -
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Residues in contact with VAL 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D LEU* 3.4 26.9 - - + -
136D VAL* 4.2 22.0 - - + -
138D LEU* 4.4 20.9 - - + -
177D VAL* 4.1 22.9 - - + -
124E VAL* 3.4 2.9 - - - +
125E PHE* 2.8 45.0 + - + -
139E THR* 4.7 2.2 - - + -
140E LEU* 1.3 76.6 - - - +
142E CYS* 1.3 71.0 + - - +
143E LEU* 4.8 1.8 - - + +
156E TRP* 4.2 2.9 - - - -
188E SER* 4.6 3.4 - - - -
189E SER 3.3 10.5 - - - +
190E ARG* 4.7 2.0 - - + -
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Residues in contact with CYS 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E VAL* 3.7 18.6 - - - -
123E ALA 3.5 5.2 - - - -
124E VAL* 4.5 1.3 - - - +
141E VAL* 1.3 76.0 - - - +
143E LEU* 1.3 66.0 + - - +
154E LEU* 4.2 7.9 - - + -
156E TRP* 3.4 20.7 - - + -
187E LEU 4.0 0.4 - - - +
188E SER* 3.2 6.9 - - - -
189E SER* 2.9 36.6 + - - +
207E CYS* 2.0 48.5 - - + -
209E VAL* 4.7 0.7 - - - -
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Residues in contact with LEU 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D VAL* 3.8 25.4 - - + -
177D VAL* 5.2 1.8 - - + -
179D TRP* 3.7 48.7 - - + +
121E GLU 3.6 2.1 - - - +
122E VAL* 3.5 2.8 - - - -
123E ALA* 2.9 33.1 + - + +
125E PHE* 3.9 21.5 - - + -
141E VAL* 5.0 2.5 - - + -
142E CYS* 1.3 78.0 - - - +
144E ALA* 1.3 57.9 + - - +
145E THR* 3.9 16.7 + - + +
187E LEU 3.5 8.7 - - - +
188E SER* 3.7 24.7 - - - -
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Residues in contact with ALA 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E PRO* 4.3 9.6 - - + -
121E GLU 3.4 5.8 - - - -
122E VAL* 4.3 1.6 - - + -
142E CYS* 5.0 0.6 - - - -
143E LEU* 1.3 72.1 - - - +
145E THR* 1.3 61.1 + - - +
147E PHE* 3.6 18.0 - - + -
154E LEU* 5.2 3.1 - - + -
186E ALA* 3.0 5.2 - - - +
187E LEU* 2.7 46.3 + - + +
209E VAL* 4.1 27.6 - - + -
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Residues in contact with THR 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179D TRP* 4.5 10.5 - - + +
119E PRO 4.2 0.2 - - - +
120E PRO* 3.3 2.8 - - - +
121E GLU* 3.0 47.2 + - - +
143E LEU* 3.9 26.1 + - + +
144E ALA* 1.3 79.7 - - - +
146E GLY* 1.3 64.9 + - - +
147E PHE* 3.4 2.7 - - - -
176E GLU* 3.8 6.5 - - - +
185E TYR 3.5 4.3 - - - -
186E ALA* 3.9 14.8 - - + -
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Residues in contact with GLY 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E PHE* 3.1 13.3 - - - +
119E PRO 3.6 3.9 - - - +
145E THR* 1.3 72.5 - - - +
147E PHE* 1.3 57.9 + - - -
176E GLU* 2.9 16.3 + - - -
184E ARG* 2.8 45.2 + - - -
185E TYR 2.8 11.2 + - - -
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Residues in contact with PHE 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E PHE 3.4 7.9 - - - +
119E PRO 4.0 0.4 - - - -
120E PRO* 3.6 39.5 - - + -
144E ALA* 3.6 32.1 - - + -
145E THR 3.4 0.2 - - - -
146E GLY* 1.3 78.8 - - - +
148E TYR* 1.3 60.1 + - - +
149E PRO 3.5 13.2 - - - -
150E ASP* 3.9 14.8 - - - -
152E VAL* 3.7 37.7 - - + -
173E PRO* 4.2 12.3 - - + -
184E ARG* 3.3 2.6 - - - -
185E TYR* 2.6 66.0 + - + -
186E ALA* 4.0 2.5 - - - -
187E LEU* 4.1 4.5 - - + -
211E PHE* 4.2 3.8 - - + -
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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