Contacts of the strand formed by residues 133 - 140 (chain A) in PDB entry 3SPY
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 ILE 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ILE* 4.4 6.5 - - + -
116A GLU 3.7 6.5 - - - +
117A VAL* 4.2 2.7 - - + -
131A HIS 3.6 0.2 + - - -
132A PRO* 1.3 69.9 - - - +
134A ASP* 1.3 60.2 - - - +
135A ALA 3.9 8.1 - - - +
136A ILE* 3.7 32.1 - - + -
151A LEU* 3.5 16.2 - - - +
194A GLU* 3.0 16.3 + - - +
197A LEU* 4.4 7.2 - - + +
198A LEU* 4.2 19.3 - - + -
225A TYR* 3.7 28.0 - - + -
226A VAL* 3.9 24.9 - - + -
229A ARG* 3.7 27.4 - - + -
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Residues in contact with ASP 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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116A GLU 3.0 17.3 + - - +
117A VAL* 4.3 0.2 - - - -
118A THR* 2.6 36.5 + - - -
132A PRO* 4.3 5.9 - - + +
133A ILE* 1.3 74.0 - - - +
135A ALA* 1.3 60.9 + - - +
150A ASP* 3.9 4.3 - - - +
151A LEU* 2.9 42.3 + - + +
154A SER* 5.4 3.1 + - - -
197A LEU* 4.7 1.1 - - - -
313A ARG* 3.3 28.2 + - - +
317A HIS* 5.9 0.2 - - - -
320A TYR* 2.6 27.7 + - - -
321A ILE* 4.6 0.9 - - - +
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Residues in contact with ALA 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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115A ILE* 3.3 5.2 - - - +
116A GLU* 2.8 47.8 + - + +
133A ILE* 3.7 1.9 - - - +
134A ASP* 1.3 84.5 + - - +
136A ILE* 1.3 65.6 + - - +
137A THR 4.3 0.2 - - - -
148A VAL* 6.2 0.9 - - + -
149A PHE 3.2 8.3 - - - +
197A LEU* 5.0 0.9 - - - +
320A TYR* 4.5 1.8 - - + -
321A ILE* 3.6 26.0 - - + -
324A ASN* 4.1 9.2 - - - +
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Residues in contact with ILE 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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113A PHE* 4.2 3.8 - - + -
114A ASP 3.6 5.2 - - - +
115A ILE* 3.9 20.4 - - + -
133A ILE* 3.7 18.8 - - + -
135A ALA* 1.3 80.0 - - - +
137A THR* 1.3 71.3 + - - +
138A HIS* 4.1 0.4 - - + -
147A TYR 3.5 1.0 - - - +
148A VAL* 3.4 2.9 - - - +
149A PHE* 2.8 46.1 + - + +
197A LEU* 4.0 23.3 - - + -
198A LEU* 4.6 6.3 - - + -
201A TYR* 3.8 52.7 - - + +
226A VAL* 4.9 4.9 - - + -
324A ASN* 3.6 1.1 - - - -
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Residues in contact with THR 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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113A PHE* 3.2 5.4 - - - +
114A ASP 3.0 32.6 + - - +
136A ILE* 1.3 73.2 + - - +
138A HIS* 1.3 63.7 + - - +
139A TYR 4.1 0.2 - - - -
146A PHE* 4.2 18.8 - - + -
147A TYR 3.3 6.5 - - - +
148A VAL* 3.8 16.4 - - + +
324A ASN* 2.4 26.6 + - - -
325A ILE* 3.7 25.8 - - + +
328A VAL* 3.5 25.0 - - + +
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Residues in contact with HIS 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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111A ALA* 3.6 28.4 - - + +
112A ASN 3.6 2.9 - - - -
113A PHE* 3.9 10.5 - - + +
136A ILE* 4.6 0.7 - - + -
137A THR* 1.3 74.2 - - - +
139A TYR* 1.3 68.2 + - - +
140A ASP* 4.4 7.1 + - + -
146A PHE* 4.4 0.4 - - - -
147A TYR* 2.8 45.4 + - - +
149A PHE* 4.4 2.2 - - + -
201A TYR* 2.9 37.5 + - + -
204A PHE* 3.3 36.2 - + + -
205A TRP* 4.0 17.9 - + - -
208A LYS 4.7 5.0 + - - -
210A PRO* 4.1 5.2 - - + +
213A LEU* 5.0 0.7 - - + -
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Residues in contact with TYR 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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110A VAL 4.7 1.8 - - - -
111A ALA* 3.4 5.4 - - - -
112A ASN* 2.8 39.6 + - + +
137A THR 4.1 1.0 - - - -
138A HIS* 1.3 75.8 - - - +
140A ASP* 1.3 63.6 + - - +
141A SER* 3.6 26.8 + - - -
144A ASP* 2.6 45.6 + - - +
145A ARG 3.3 19.5 - - - -
146A PHE* 3.8 28.0 - + + +
328A VAL* 3.7 23.8 - - + +
332A LEU* 3.6 34.5 - - + -
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Residues in contact with ASP 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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109A ARG* 2.9 43.3 + - - +
110A VAL 4.0 2.5 - - - -
111A ALA* 4.9 1.9 - - - +
138A HIS* 3.8 9.9 + - + -
139A TYR* 1.3 77.6 - - - +
141A SER* 1.3 54.3 + - - +
142A ILE 3.0 6.3 + - - -
143A ASP* 2.8 34.4 + - + -
144A ASP* 2.8 33.4 + - - -
145A ARG 3.1 8.2 + - - +
147A TYR* 4.1 21.8 - - + -
208A LYS* 3.7 11.2 - - + +
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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