Contacts of the strand formed by residues 140 - 150 (chain E) in PDB entry 5HHM
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 140 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D MET* 4.5 15.7 - - + -
166D MET* 5.1 13.0 - - - -
168D PHE* 3.8 51.4 - - + -
134E GLU* 3.6 8.8 - - - +
135E ILE* 3.4 25.6 + - - -
138E THR* 3.2 31.8 + - - +
139E GLN* 1.3 82.6 + - - +
141E ALA* 1.3 59.7 + - - +
195E ARG* 3.5 25.4 - - - +
196E VAL 3.7 4.7 - - - +
197E SER* 5.2 1.8 - - - -
198E ALA* 4.1 2.5 - - - +
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Residues in contact with ALA 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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130E PRO* 3.8 16.8 - - + +
134E GLU* 3.7 3.1 - - - -
135E ILE* 4.1 9.6 - - + -
140E LYS* 1.3 75.2 - - - +
142E THR* 1.3 64.7 + - - +
143E LEU 3.9 0.6 + - - -
194E LEU 3.7 1.2 - - - +
195E ARG* 3.3 1.8 - - - -
196E VAL* 2.8 45.6 + - + +
198E ALA* 4.3 5.2 - - - -
201E TRP* 3.7 29.4 - - + -
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Residues in contact with THR 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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123D LEU* 3.3 21.0 - - - +
135D LEU* 3.8 25.1 - - + +
137D THR* 5.2 2.0 + - - +
161D LEU* 5.0 2.5 - - + -
172D SER* 5.6 0.9 - - - +
130E PRO* 3.4 13.5 - - - +
134E GLU* 2.6 34.9 + - - +
141E ALA* 1.3 72.1 - - - +
143E LEU* 1.3 70.9 + - - +
144E VAL* 4.4 0.9 - - + -
193E ARG* 4.0 23.1 - - + -
194E LEU 3.4 7.2 - - - +
195E ARG* 3.0 23.1 + - + +
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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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127E VAL* 3.8 23.8 - - + -
128E PHE 3.6 5.4 - - - +
129E GLU* 4.3 2.0 - - - -
130E PRO* 3.8 15.7 - - + -
141E ALA 3.9 0.6 + - - +
142E THR* 1.3 73.5 - - - +
144E VAL* 1.3 60.8 + - - +
145E CYS 4.2 0.2 - - - -
159E TRP* 3.9 15.1 - - + -
193E ARG* 3.3 5.2 - - - -
194E LEU* 2.6 52.5 + - + +
196E VAL* 5.0 7.0 - - + -
201E TRP* 3.8 25.8 - - + -
208E PHE* 3.5 44.6 - - + -
239E ALA* 4.7 2.2 - - + -
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Residues in contact with VAL 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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123D LEU* 3.8 18.8 - - + -
133D VAL* 4.0 22.9 - - + -
135D LEU* 4.1 18.2 - - + -
174D VAL* 3.8 30.7 - - + -
127E VAL* 3.7 0.7 - - - -
128E PHE* 2.8 43.6 + - + +
142E THR* 4.1 3.6 + - + -
143E LEU* 1.3 77.5 - - - +
145E CYS* 1.3 70.1 + - - +
146E LEU* 5.3 1.1 - - + -
159E TRP* 4.3 3.1 - - - -
191E SER* 4.8 0.7 - - - -
192E SER 3.6 4.7 - - - +
193E ARG* 4.1 14.8 - - + -
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Residues in contact with CYS 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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125E VAL* 4.1 14.8 - - - -
126E ALA 3.7 5.6 - - - -
127E VAL* 4.6 1.6 - - + +
144E VAL* 1.3 73.4 - - - +
146E LEU* 1.3 68.8 + - - +
147E ALA 4.2 0.7 - - - -
157E LEU* 4.1 9.0 - - - -
159E TRP* 3.3 27.9 - - + -
191E SER* 3.1 11.1 - - - -
192E SER* 2.7 37.2 + - - +
210E CYS* 2.5 40.4 - - + -
212E VAL* 5.1 0.2 - - - -
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Residues in contact with LEU 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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131D LYS* 5.9 5.6 - - + -
133D VAL* 4.4 9.2 - - + -
174D VAL* 5.5 1.3 - - + -
176D TRP* 3.6 58.1 - - + +
124E GLU 3.4 10.9 - - - +
125E VAL* 4.7 0.2 - - - -
126E ALA* 3.0 23.3 + - + +
128E PHE* 3.8 29.6 - - + -
144E VAL* 5.3 0.7 - - + -
145E CYS* 1.3 77.2 - - - +
147E ALA* 1.3 60.8 - - - +
148E THR* 3.7 19.2 + - + +
189E SER* 3.8 7.4 - - - +
190E LEU 3.6 13.9 - - - +
191E SER* 4.2 5.4 - - - -
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Residues in contact with ALA 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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123E PRO* 4.4 9.9 - - + -
124E GLU 3.5 7.6 - - - -
125E VAL* 4.4 3.1 - - + -
145E CYS* 4.2 2.8 - - - -
146E LEU* 1.3 70.7 - - - +
148E THR* 1.3 57.5 + - - +
150E PHE* 4.0 17.9 - - + -
157E LEU* 4.8 4.0 - - + -
189E SER* 3.1 4.3 + - - -
190E LEU* 2.7 48.4 + - + +
212E VAL* 4.1 27.6 - - + -
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Residues in contact with THR 148 (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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131D LYS* 6.1 1.2 - - - -
176D TRP* 4.4 7.0 - - + +
122E PRO 4.2 0.7 - - - +
123E PRO* 3.5 1.6 - - - +
124E GLU* 3.0 47.5 + - - +
146E LEU* 3.7 28.9 + - + +
147E ALA* 1.3 74.6 - - - +
149E GLY* 1.3 65.5 + - - +
150E PHE* 3.4 3.1 - - - -
179E GLU* 3.3 8.7 - - - +
188E TYR 3.4 3.4 - - - -
189E SER* 2.9 22.4 - - - +
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Residues in contact with GLY 149 (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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121E PHE* 3.3 12.0 - - - +
122E PRO 3.5 5.1 - - - +
148E THR* 1.3 72.7 - - - +
150E PHE* 1.3 56.8 + - - -
179E GLU* 2.9 26.2 + - - -
187E ARG* 3.0 37.9 + - - -
188E TYR 2.7 11.2 + - - -
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Residues in contact with PHE 150 (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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121E PHE 3.5 6.5 - - - +
122E PRO 4.2 0.2 - - - -
123E PRO* 3.7 38.1 - - + -
147E ALA* 3.8 26.2 - - + -
148E THR 4.1 4.3 - - - -
149E GLY* 1.3 78.2 - - - +
151E TYR* 1.3 61.3 + - - +
152E PRO 3.4 15.5 - - - -
153E ASP* 3.7 13.7 - - + -
155E VAL* 3.4 38.8 - - + -
176E PRO* 4.4 3.6 - - + -
187E ARG* 4.2 0.2 - - - -
188E TYR* 2.6 69.1 + - + -
189E SER 4.3 0.4 - - - -
190E LEU* 4.0 16.4 - - + -
214E PHE* 4.3 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