Contacts of the strand formed by residues 133 - 140 (chain A) in PDB entry 4GUN
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 GLY 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ILE* 4.1 9.7 - - - +
131A GLY 4.0 2.0 + - - -
132A SER* 1.3 76.4 - - - +
134A TRP* 1.3 69.7 + - - -
152A THR 3.1 13.0 - - - -
154A ASN 3.7 9.4 - - - -
171A ALA* 2.9 30.0 + - - +
172A TRP* 3.5 10.9 + - - +
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Residues in contact with TRP 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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79A ASN* 3.4 55.0 - - + -
80A HIS* 3.7 18.2 - + - -
83A PHE* 3.8 18.6 - + + -
129A ILE* 3.5 7.8 - - - +
133A GLY* 1.3 73.7 - - - -
135A ALA* 1.3 59.3 + - - +
136A PHE* 3.5 20.4 - + + -
151A THR* 3.1 8.7 - - - -
152A THR* 2.9 33.7 + - - +
154A ASN 3.2 21.6 + - - -
155A GLN* 3.0 15.6 + - - -
168A ALA* 4.1 10.8 - - + -
169A ILE 3.3 15.7 - - - -
170A ASP* 3.4 56.1 - - + -
172A TRP* 3.7 6.9 - - - +
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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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122A THR* 4.3 15.5 - - + +
126A LEU* 3.4 35.6 - - + +
134A TRP* 1.3 73.8 - - - +
136A PHE* 1.3 65.4 + - - +
149A VAL* 4.9 4.0 - - + -
150A VAL 3.3 9.2 - - - +
151A THR* 4.3 10.8 - - + +
167A ILE 3.8 0.3 - - - +
168A ALA* 3.7 0.2 - - - -
169A ILE* 3.0 33.8 + - + +
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Residues in contact with PHE 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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79A ASN* 3.2 29.2 - - - -
82A LEU* 4.2 10.3 - - + -
122A THR* 5.8 0.7 - - - -
134A TRP* 3.5 26.7 - + + -
135A ALA* 1.3 75.4 - - - +
137A ILE* 1.3 62.7 + - - +
138A VAL* 3.7 18.0 + - + -
148A ASP 3.7 0.5 - - - +
149A VAL* 3.3 7.0 - - - +
150A VAL* 2.8 40.8 + - + +
152A THR* 3.6 25.8 - - + -
156A ASP 4.3 0.2 - - - -
157A THR* 4.1 7.9 - - - -
158A ILE* 3.6 24.7 - - + -
165A PRO* 4.1 9.0 - - + -
167A ILE* 3.2 8.1 - - - +
168A ALA* 3.7 30.1 - - + -
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Residues in contact with ILE 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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104A LEU* 5.5 1.6 - - + -
118A LEU* 4.0 27.6 - - + -
122A THR* 3.8 25.4 - - + +
136A PHE* 1.3 72.6 - - - +
138A VAL* 1.4 57.6 + - - +
147A LEU* 4.3 19.5 - - + -
148A ASP 3.5 6.7 - - - +
149A VAL* 4.4 2.5 - - + -
165A PRO* 4.0 0.2 - - - +
166A ILE* 2.8 46.5 + - + +
167A ILE* 3.1 28.2 + - + +
192A TRP* 4.1 11.2 - - + -
197A TRP* 3.7 29.8 - - + -
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Residues in contact with VAL 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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136A PHE* 3.7 11.9 - - + -
137A ILE* 1.4 78.2 - - - +
139A LYS* 1.3 61.2 + - - +
140A ASN* 5.9 0.4 - - + -
146A ALA 3.7 0.3 - - - +
147A LEU* 3.1 8.8 - - - +
148A ASP* 2.8 53.9 + - + +
150A VAL* 3.6 31.0 - - + -
158A ILE* 3.8 19.1 - - + -
163A LEU* 4.2 23.3 - - + -
164A VAL 3.3 11.9 - - - +
165A PRO* 4.5 0.4 - - + -
166A ILE* 4.0 4.3 - - - -
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Residues in contact with LYS 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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138A VAL* 1.3 72.4 - - - +
140A ASN* 1.3 64.6 + - - +
141A LYS* 3.8 12.1 + - + +
145A GLY* 3.8 18.8 - - - +
146A ALA 3.6 3.1 - - - -
147A LEU* 4.3 1.6 - - + -
162A HIS 3.8 0.2 - - - +
163A LEU* 3.5 7.3 - - - +
164A VAL* 3.0 46.8 + - + +
166A ILE* 3.8 16.1 - - + +
204A TYR* 2.7 73.7 + - + +
205A SER* 5.1 0.6 - - - +
206A ALA 5.3 3.0 + - - -
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Residues in contact with ASN 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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138A VAL* 5.9 0.7 - - + -
139A LYS* 1.3 72.0 - - - +
141A LYS* 1.3 58.1 + - - +
142A GLN* 3.1 21.3 + - - +
143A ASN* 3.1 27.9 - - - +
145A GLY* 3.0 27.8 + - - -
146A ALA 2.9 14.3 + - - +
148A ASP* 6.6 0.2 - - + -
162A HIS* 3.2 32.5 + - - -
163A LEU* 3.8 12.4 - - + +
148D ASP* 2.9 31.9 + - - -
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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