Contacts of the strand formed by residues 139 - 149 (chain E) in PDB entry 6IAP
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 139 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D PHE* 5.0 3.5 - - - -
135E THR* 3.3 5.6 - - - +
136E SER 2.9 34.8 + - - +
138E GLY* 1.4 80.0 + - - +
140E ALA* 1.3 62.4 + - - +
187E THR* 3.9 20.6 - - + -
188E VAL 3.5 29.6 - - - +
189E PRO* 4.1 3.7 - - + +
190E SER* 4.2 0.4 - - - -
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Residues in contact with ALA 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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116D PHE* 5.6 0.2 - - - -
130E PRO* 4.4 11.7 - - + -
134E SER 3.3 5.8 - - - +
135E THR* 3.8 23.6 - - + +
139E THR* 1.3 75.8 - - - +
141E ALA* 1.3 65.6 + - - +
142E LEU* 4.6 4.7 - - + +
186E VAL 3.6 0.9 - - - +
187E THR* 3.6 5.1 - - - -
188E VAL* 2.8 34.5 + - - +
190E SER* 4.0 13.9 - - - +
193E LEU* 4.5 7.4 - - + -
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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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116D PHE* 4.1 8.0 - - + -
118D PHE* 3.7 17.7 - - + -
135D LEU* 4.0 19.7 - - + -
130E PRO* 3.2 15.8 - - - +
134E SER* 2.6 32.5 + - - +
140E ALA* 1.3 73.6 - - - +
142E LEU* 1.3 61.1 + - - +
185E VAL* 5.3 0.7 - - + -
186E VAL 3.1 10.8 - - - +
187E THR* 4.0 13.4 - - + +
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Residues in contact with LEU 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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118D PHE* 4.1 2.9 - - - -
128E LEU 3.4 13.2 - - - +
130E PRO* 3.7 27.8 - - + -
140E ALA* 4.6 8.3 - - + +
141E ALA* 1.3 77.3 - - - +
143E GLY* 1.3 55.2 + - - +
158E TRP* 3.6 29.6 - - + -
185E VAL* 3.1 8.2 - - - +
186E VAL* 2.7 48.0 + - + +
188E VAL* 5.2 4.3 - - + -
193E LEU* 5.2 4.7 - - + -
198E TYR* 3.7 38.4 - - + -
215E VAL* 4.1 12.3 - - + +
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Residues in contact with GLY 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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128E LEU* 2.7 44.6 + - - +
142E LEU* 1.3 79.1 - - - +
144E CYS* 1.3 60.0 + - - -
158E TRP* 3.5 11.7 - - - -
184E SER 2.9 14.4 - - - -
185E VAL* 3.9 2.0 - - - -
215E VAL* 3.6 10.0 - - - +
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Residues in contact with CYS 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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125E VAL* 4.0 13.7 - - + -
126E PHE 3.3 8.7 - - - +
127E PRO* 4.7 0.7 - - - -
128E LEU* 3.6 4.0 - - - +
143E GLY* 1.3 72.0 - - - -
145E LEU* 1.3 63.3 + - - +
146E VAL* 3.8 4.1 + - + +
158E TRP* 3.9 0.6 - - + -
183E SER* 3.2 8.1 - - - -
184E SER* 2.8 30.6 + - - +
200E CYS* 2.0 51.4 - - + -
202E VAL* 5.0 4.0 - - + -
213E LYS* 4.5 4.5 - - - -
215E VAL* 3.7 21.8 - - - -
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Residues in contact with LEU 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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124D GLN* 4.0 3.6 - - - +
131D SER* 3.2 27.8 - - - +
133D VAL* 4.0 18.4 - - + -
178D THR* 4.6 9.0 - - + +
124E SER 2.9 18.7 - - - +
125E VAL* 3.5 1.0 - - - -
126E PHE* 2.7 48.3 + - + +
128E LEU* 4.0 11.0 - - + +
144E CYS* 1.3 72.7 - - - +
146E VAL* 1.3 60.3 + - - +
147E LYS* 3.2 28.2 + - + -
181E SER* 4.4 11.0 - - - +
182E LEU 3.9 1.3 - - - +
183E SER* 3.4 22.0 - - - +
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Residues in contact with VAL 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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123E PRO* 3.5 29.6 - - + -
124E SER 4.0 2.5 - - - -
125E VAL* 4.8 4.0 - - + +
144E CYS* 4.8 7.6 - - + +
145E LEU* 1.3 70.1 - - - +
147E LYS* 1.4 56.5 + - - +
149E TYR* 3.6 18.6 - - + -
154E VAL* 3.8 11.7 - - + -
156E VAL* 3.8 15.7 - - + -
181E SER* 2.9 19.0 + - - -
182E LEU* 2.9 35.6 + - + +
184E SER* 5.6 1.3 - - - -
202E VAL* 3.7 33.9 - - + -
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Residues in contact with LYS 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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124D GLN* 3.5 28.3 - - - +
129D THR* 3.5 22.7 + - + +
131D SER* 4.4 7.4 - - - -
180D THR* 5.2 8.2 + - - -
123E PRO* 3.3 5.5 - - - +
124E SER* 2.7 47.6 + - - +
126E PHE* 4.2 9.0 - - + -
145E LEU* 3.7 19.7 - - + -
146E VAL* 1.4 74.9 - - - +
148E ASP* 1.4 92.0 + - - +
149E TYR 3.6 2.5 - - - -
175E GLN* 3.5 14.9 + - - +
180E TYR 4.0 0.9 - - - -
181E SER* 3.7 13.9 - - - +
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Residues in contact with ASP 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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129D THR* 5.1 3.3 - - - +
121E LYS* 3.4 19.7 - - - +
122E GLY 3.3 12.7 - - - +
124E SER* 4.7 7.0 + - - +
147E LYS* 1.4 103.0 + - - +
149E TYR* 1.3 60.9 + - - +
175E GLN* 3.1 20.6 + - - +
177E SER* 4.0 3.9 + - - -
179E LEU* 3.8 26.5 - - + +
180E TYR 3.1 12.4 + - - -
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Residues in contact with TYR 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 LYS 3.4 14.6 - - - +
122E GLY 3.9 0.2 - - - -
123E PRO* 3.6 23.1 - - + -
146E VAL* 3.6 34.1 - - + -
148E ASP* 1.3 78.9 - - - +
150E PHE* 1.3 63.0 + - - +
151E PRO 3.4 23.6 - - - -
152E GLU* 3.6 13.8 - - + +
154E VAL* 3.7 17.8 - - + +
172E ALA* 3.4 14.4 - - - +
179E LEU* 3.7 2.4 - - - -
180E TYR* 3.0 56.3 + - + -
181E SER* 4.1 6.5 - - - -
182E LEU* 3.4 24.6 - - + +
204E HIS* 3.5 10.3 - + - +
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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