Contacts of the strand formed by residues 159 - 164 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D MET* 3.4 33.3 - - + +
153D ASP 3.2 7.2 - - - +
154D SER* 3.0 18.6 - - - +
158D VAL* 1.3 79.6 - - - +
160D HIS* 1.3 70.9 + - - +
161D THR* 4.7 2.0 - - - +
176D ARG* 3.5 0.3 - - - -
177D LEU* 2.8 57.0 + - + +
179D LEU* 3.1 21.2 + - - +
180D ALA* 4.7 0.9 - - - -
260D LEU* 5.6 2.1 - - - +
273D ILE* 4.7 2.6 - - + +
276D THR* 5.7 0.7 - - - +
302D THR* 5.0 0.3 - - - +
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Residues in contact with HIS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D HIS 5.5 0.6 + - - -
73D GLY* 5.8 1.1 - - - -
107D ALA* 3.3 25.9 - - + +
108D PRO* 3.6 43.8 + - + -
136D GLN* 4.6 2.7 - - - -
137D ALA* 5.9 0.4 - - + -
152D MET* 3.7 2.6 - - - +
153D ASP* 2.5 59.6 + - + +
158D VAL* 3.0 52.6 + - + +
159D THR* 1.3 76.8 - - - +
161D THR* 1.3 70.0 + - - +
162D VAL* 5.2 1.1 - - + -
175D LEU 3.5 6.5 - - - +
176D ARG* 3.8 19.3 + - + +
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Residues in contact with THR 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ILE* 3.7 25.4 - - + -
151D VAL 3.4 8.5 - - - +
152D MET* 3.6 16.7 - - + +
159D THR* 4.7 2.6 - - - +
160D HIS* 1.3 81.8 + - - +
162D VAL* 1.3 65.2 + - - +
163D PRO* 3.8 0.9 - - - +
174D ILE* 3.3 4.3 - - - -
175D LEU* 2.8 44.7 + - - +
177D LEU* 6.0 0.7 - - - +
276D THR* 4.5 10.2 + - - -
277D THR* 4.7 11.2 - - - +
280D SER* 3.3 24.0 - - - +
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Residues in contact with VAL 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D PRO* 3.9 27.6 - - + -
135D ILE* 5.3 3.8 - - + -
137D ALA* 3.9 22.2 - - + -
138D VAL* 5.0 6.3 - - + -
149D GLY 4.0 0.5 - - - +
150D ILE* 3.8 1.1 - - - -
151D VAL* 3.0 32.9 + - - +
160D HIS* 5.2 0.2 - - + -
161D THR* 1.3 80.1 - - - +
163D PRO* 1.3 74.8 - - - +
164D ILE* 3.7 19.0 + - + +
169D ALA* 5.3 4.3 - - + -
170D LEU 5.5 0.2 - - - +
174D ILE* 3.7 30.3 - - + -
374D PHE* 5.9 2.7 - - + -
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Residues in contact with PRO 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLY 3.7 5.2 - - - +
150D ILE* 3.9 17.5 - - + -
161D THR 3.8 6.5 - - - +
162D VAL* 1.3 94.0 - - + +
164D ILE* 1.3 60.9 + - - +
170D LEU* 3.8 25.0 + - + +
173D ALA* 3.4 41.5 - - + +
174D ILE* 4.1 3.8 - - + +
280D SER* 4.6 4.9 - - - -
284D CYS* 4.0 19.3 - - - -
292D LEU* 4.0 13.9 - - + -
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Residues in contact with ILE 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D VAL* 4.0 26.2 - - + -
141D LEU* 3.3 34.1 - - + -
147D THR 3.7 9.0 - - - +
148D THR* 3.3 3.1 - - - +
149D GLY 2.8 38.8 + - - +
151D VAL* 5.8 1.8 - - + -
162D VAL* 4.2 11.7 - - + +
163D PRO* 1.3 75.5 - - - +
165D TYR* 1.3 60.7 + - - +
167D GLY 3.3 9.4 - - - +
168D TYR 3.2 28.3 - - - +
169D ALA* 3.6 16.8 - - + +
170D LEU* 6.0 0.9 - - - -
288D ILE* 5.7 0.4 - - - -
292D LEU* 3.8 5.3 - - - +
42E VAL 4.6 1.8 - - - +
43E MET* 4.4 3.4 - - - -
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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