Contacts of the strand formed by residues 131 - 140 (chain A) in PDB entry 5H8H
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 VAL 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PHE* 4.2 6.7 - - + -
61A PHE* 3.2 37.9 - - + -
129A PRO* 4.3 0.3 - - - +
130A PHE* 1.4 93.1 - - + +
132A GLU* 1.3 73.7 + - - +
216A ALA* 4.2 16.8 - - + -
243A GLY* 3.0 5.7 - - - -
244A TYR* 2.8 42.7 + - + +
275A GLU* 5.7 3.8 - - - +
279A LEU* 4.6 11.4 - - + -
303B 5YC 3.5 8.1 + - - -
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131A VAL* 1.3 86.9 - - - +
133A THR* 1.3 65.5 + - - +
216A ALA* 3.9 7.6 + - - +
238A ILE* 3.8 21.6 - - + +
241A THR* 3.0 23.7 + - - +
242A THR 3.7 8.5 - - - +
144B TYR* 3.6 35.8 - - + +
248B ARG* 5.3 4.6 + - - +
303B 5YC 3.5 29.0 - - - +
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Residues in contact with THR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 3.8 9.6 - - + +
131A VAL 3.7 0.2 + - - -
132A GLU* 1.3 76.3 - - - +
134A GLY* 1.3 60.1 + - - +
214A ASP* 2.6 28.8 + - - +
215A ALA* 3.6 5.6 + - - -
216A ALA* 3.2 18.1 + - - +
238A ILE* 3.4 7.4 - - - +
241A THR* 3.4 11.3 + - - -
242A THR* 2.8 38.1 + - + +
243A GLY* 3.8 17.9 - - - +
244A TYR* 3.7 27.1 - - + -
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Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A THR* 5.8 0.4 - - - -
133A THR* 1.3 81.0 + - - +
135A ILE* 1.3 65.2 + - - +
173A THR* 4.7 0.7 + - - -
214A ASP* 3.4 10.0 - - - +
215A ALA* 2.8 22.0 + - - +
238A ILE* 3.4 9.3 - - - +
239A PHE 3.6 5.2 - - - -
240A ALA 3.7 10.8 - - - -
242A THR* 4.0 7.4 - - - -
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Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A GLY* 1.3 77.2 - - - +
136A SER* 1.3 63.7 + - - +
137A VAL* 5.7 0.3 - - - +
148A LEU* 3.8 18.3 - - + +
172A SER 5.8 0.2 - - - -
173A THR* 4.1 26.2 - - + +
176A ASN* 3.4 42.0 - - + +
177A ILE* 4.9 2.7 - - + -
212A ILE* 3.5 31.0 - - + -
213A TYR 3.6 3.1 - - - +
215A ALA* 4.3 0.2 - - - -
237A TYR 4.0 0.5 - - - +
238A ILE* 3.6 3.2 - - - +
239A PHE* 2.8 54.0 + - + +
240A ALA* 4.2 4.7 - - + +
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Residues in contact with SER 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE* 1.3 71.4 - - - +
137A VAL* 1.3 66.3 + - - +
212A ILE* 3.7 4.5 - - - +
213A TYR 3.0 29.5 + - - +
215A ALA* 3.1 30.9 - - - +
218A LEU* 3.4 11.0 - - - +
219A ASN* 4.3 5.5 + - - -
232A THR* 4.3 16.6 - - - -
233A ILE* 6.1 0.4 - - - -
237A TYR 2.7 25.1 + - - -
238A ILE* 4.0 1.2 - - - +
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Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ILE* 5.4 0.4 - - + +
136A SER* 1.3 80.2 - - - +
138A MET* 1.3 60.8 - - - +
139A VAL* 4.0 18.4 - - + -
145A VAL* 4.8 0.2 - - + -
148A LEU* 4.0 35.0 - - + +
153A PHE* 3.8 30.5 - - + -
210A ALA* 4.0 7.2 - - + -
211A PHE 3.6 4.0 - - - +
212A ILE* 4.0 9.0 - - + -
218A LEU* 4.3 0.9 - - - -
232A THR* 3.2 4.3 - - - -
233A ILE* 2.9 54.0 + - + +
237A TYR 5.1 0.6 + - - -
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Residues in contact with MET 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 1.3 72.2 - - - +
139A VAL* 1.3 61.9 + - - +
200A LEU* 3.5 30.7 - - - -
203A LEU* 3.7 16.9 - - + +
210A ALA* 3.4 5.5 - - - -
211A PHE* 2.8 45.1 + - + +
218A LEU* 3.3 46.3 - - + +
221A LYS* 4.3 3.1 - - + -
222A ALA* 3.6 27.6 - - + +
230A LEU* 3.9 22.2 - - + +
231A VAL 3.3 7.9 - - - +
232A THR* 4.2 7.2 - - + +
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Residues in contact with VAL 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A VAL* 4.0 12.1 - - + -
138A MET* 1.3 79.7 - - - +
140A SER* 1.3 70.4 + - - +
141A ARG* 3.6 0.4 + - - -
142A GLY 5.4 0.2 - - - +
143A THR* 3.7 30.3 - - + +
145A VAL* 4.0 9.2 - - + -
203A LEU* 4.5 2.2 - - - -
209A ASP 3.8 16.4 - - - +
210A ALA* 3.9 12.6 - - + -
230A LEU* 3.5 8.1 - - - -
231A VAL* 2.8 46.0 + - + +
233A ILE* 3.8 20.0 - - + -
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A VAL* 1.3 77.2 - - - +
141A ARG* 1.3 70.0 + - - +
143A THR* 2.9 29.8 + - - -
203A LEU* 4.5 13.5 + - - +
204A LYS* 5.5 1.2 - - - -
209A ASP 4.6 2.6 + - - -
229A LYS* 3.7 8.4 - - - +
230A LEU* 3.9 16.9 - - - +
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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