Contacts of the strand formed by residues 159 - 164 (chain E) in PDB entry 5JLH
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 159 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152E MET* 3.4 32.0 - - + +
153E ASP 3.2 7.2 - - - +
154E SER* 3.0 18.6 - - - +
158E VAL* 1.3 79.5 - - - +
160E HIS* 1.3 71.6 + - - +
161E THR* 4.7 2.7 - - - +
176E ARG* 3.5 0.3 - - - -
177E LEU* 2.8 57.3 + - + +
179E LEU* 3.1 20.2 + - - +
180E ALA* 4.6 1.0 + - - -
260E LEU* 5.6 2.4 - - - +
273E ILE* 4.7 2.8 - - + +
276E THR* 5.7 0.4 - - - +
302E THR* 5.0 0.2 - - - +
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Residues in contact with HIS 160 (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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72E HIS 5.6 0.6 + - - -
73E GLY* 5.8 1.6 - - - -
107E ALA* 3.2 26.3 - - + +
108E PRO* 3.6 44.3 + - + -
136E GLN* 4.6 2.2 - - - -
152E MET* 3.7 2.8 - - - +
153E ASP* 2.5 61.1 + - + +
158E VAL* 2.9 51.9 + - + +
159E THR* 1.3 77.7 - - - +
161E THR* 1.3 70.3 + - - +
162E VAL* 5.3 0.9 - - + -
175E LEU 3.5 7.0 - - - +
176E ARG* 3.8 18.3 + - + -
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Residues in contact with THR 161 (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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150E ILE* 3.7 26.0 - - + -
151E VAL 3.4 7.6 - - - +
152E MET* 3.6 17.6 - - + +
159E THR* 4.7 2.3 - - - +
160E HIS* 1.3 82.8 + - - +
162E VAL* 1.3 67.9 + - - +
163E PRO* 3.8 0.7 - - - +
174E ILE* 3.3 2.8 - - - -
175E LEU* 2.8 44.0 + - - +
177E LEU* 6.1 0.7 - - - +
276E THR* 4.5 9.5 + - - -
277E THR* 4.7 11.4 - - + +
280E SER* 3.3 23.8 - - - +
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Residues in contact with VAL 162 (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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108E PRO* 3.9 27.8 - - + -
135E ILE* 5.3 4.3 - - + -
137E ALA* 3.9 21.3 - - + -
138E VAL* 5.0 6.5 - - + -
149E GLY 4.0 0.9 - - - +
150E ILE* 4.2 0.9 - - - -
151E VAL* 3.0 32.0 + - - +
161E THR* 1.3 81.4 - - - +
163E PRO* 1.3 74.3 - - - +
164E ILE* 3.7 19.1 + - + +
169E ALA* 5.3 3.8 - - + -
174E ILE* 3.7 31.0 - - + -
374E PHE* 6.0 2.5 - - + -
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Residues in contact with PRO 163 (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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149E GLY 3.7 4.9 - - - +
150E ILE* 3.9 19.3 - - + -
161E THR 3.8 6.5 - - - +
162E VAL* 1.3 93.7 - - + +
164E ILE* 1.3 60.5 + - - +
170E LEU* 3.7 24.5 + - + +
173E ALA* 3.4 42.2 - - + +
174E ILE* 4.1 2.9 - - + +
280E SER* 4.6 1.3 - - - -
284E CYS* 4.0 19.5 - - - -
292E LEU* 4.0 13.2 - - + -
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Residues in contact with ILE 164 (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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138E VAL* 3.9 26.7 - - + -
141E LEU* 3.3 34.1 - - + -
147E THR 3.7 8.5 - - - +
148E THR* 3.3 3.1 - - - +
149E GLY 2.8 39.7 + - - +
151E VAL* 5.8 1.1 - - + -
162E VAL* 4.2 11.2 - - + +
163E PRO* 1.3 75.6 - - - +
165E TYR* 1.3 61.6 + - - +
167E GLY* 3.3 9.9 - - - +
168E TYR 3.2 27.1 - - - +
169E ALA* 3.6 17.9 - - + +
170E LEU* 6.0 0.7 - - - -
288E ILE* 5.7 0.4 - - - -
292E LEU* 3.7 4.9 - - - +
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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