Contacts of the strand formed by residues 149 - 160 (chain A) in PDB entry 5W30
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 GLU 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A PRO* 3.9 29.4 - - - +
141A VAL* 4.1 6.6 - - - +
142A ALA 3.2 21.2 - - - +
143A LYS* 3.8 30.3 + - + +
147A GLY 4.2 0.8 + - - +
148A LYS* 1.3 76.9 - - - +
150A LYS* 1.3 66.7 + - - +
151A ILE* 5.5 0.5 - - - +
188A ASN* 3.5 6.1 - - - +
189A GLU* 3.0 54.6 + - + +
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Residues in contact with LYS 150 (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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140A GLY 4.8 0.2 - - - -
141A VAL* 4.1 0.2 - - - -
142A ALA* 3.0 49.4 + - + +
143A LYS 4.6 1.1 - - - -
144A GLY* 3.8 26.2 - - - +
145A LYS* 3.4 25.0 - - + +
149A GLU* 1.3 80.8 - - - +
151A ILE* 1.3 70.9 + - - +
187A ALA 3.3 12.6 - - - +
188A ASN* 3.8 14.8 - - - +
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Residues in contact with ILE 151 (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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56A ILE* 4.5 9.4 - - + -
58A PHE* 3.7 48.9 - - + -
60A PRO* 5.6 1.1 - - + -
65A PHE* 4.8 0.4 - - + -
138A ILE* 6.2 0.7 - - + -
140A GLY 3.6 8.3 - - - +
141A VAL* 3.9 16.6 - - + -
149A GLU* 5.5 1.1 - - - +
150A LYS* 1.3 80.3 - - - +
152A GLY* 1.3 61.0 + - - +
153A PHE* 3.8 29.8 - - + -
186A GLU* 3.7 2.6 - - - +
187A ALA* 3.0 47.8 + - + +
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Residues in contact with GLY 152 (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 ILE* 3.8 3.3 - - - +
139A GLY* 2.8 25.5 + - - -
140A GLY 3.2 17.6 + - - -
151A ILE* 1.3 75.4 - - - +
153A PHE* 1.3 62.4 + - - +
185A VAL 3.2 11.7 - - - -
186A GLU* 4.4 3.8 - - - -
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Residues in contact with PHE 153 (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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56A ILE* 4.3 14.6 - - + -
65A PHE* 3.6 44.4 - + + -
68A LEU* 4.7 7.4 - - + -
136A ALA* 6.0 0.4 - - + -
137A GLU 3.4 13.2 - - - +
138A ILE* 4.1 10.3 - - + -
139A GLY* 3.8 2.5 - - - +
151A ILE* 3.8 26.0 - - + -
152A GLY* 1.3 75.3 - - - +
154A SER* 1.3 69.0 + - - +
155A LEU* 4.0 28.5 - - + -
184A GLU* 3.8 6.1 + - - +
185A VAL* 2.9 72.2 + - + +
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Residues in contact with SER 154 (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 ASP 3.3 2.3 - - - +
136A ALA* 3.3 4.0 - - - -
137A GLU* 2.8 47.9 + - - +
153A PHE* 1.3 76.1 - - - +
155A LEU* 1.3 66.8 + - - +
156A ASN* 3.3 18.8 + - - -
182A ASN* 5.1 2.0 - - - -
183A ILE 3.2 9.4 - - - -
184A GLU* 3.4 24.0 - - - -
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Residues in contact with LEU 155 (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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65A PHE* 5.5 0.2 - - + -
68A LEU* 3.6 29.6 - - + -
104A PHE* 5.4 1.8 - - + -
119A MET* 4.2 16.6 - - + -
134A LEU* 4.1 28.5 - - + -
135A ASP 3.4 2.7 - - - +
136A ALA* 3.8 23.6 - - + +
153A PHE* 4.0 20.0 - - + -
154A SER* 1.3 82.6 - - - +
156A ASN* 1.3 63.5 + - - +
181A LEU 3.6 2.5 - - - +
183A ILE* 2.8 58.3 + - + +
185A VAL* 6.0 0.2 - - + -
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Residues in contact with ASN 156 (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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133A VAL 4.4 0.2 - - - +
134A LEU* 3.4 6.4 - - - +
135A ASP* 2.6 54.0 + - + +
137A GLU* 5.4 4.0 + - - +
154A SER* 3.3 27.7 + - - -
155A LEU* 1.3 75.4 - - - +
157A GLY* 1.3 58.4 + - - +
181A LEU 3.2 10.6 - - - +
182A ASN* 2.9 26.3 + - - +
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Residues in contact with GLY 157 (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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133A VAL 4.2 8.1 - - - -
134A LEU* 4.0 13.4 - - - +
135A ASP* 5.4 2.0 - - - -
156A ASN* 1.3 75.5 - - - +
158A LYS* 1.3 60.4 + - - -
159A ILE* 5.4 0.2 - - - -
180A ASN* 3.7 4.2 - - - +
181A LEU* 2.8 39.9 + - - +
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Residues in contact with LYS 158 (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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132A ILE* 5.9 0.3 - - - +
133A VAL 5.2 2.3 + - - +
157A GLY* 1.3 73.4 - - - -
159A ILE* 1.3 64.7 + - - +
178A ASP* 4.9 14.4 - - + +
179A ILE 3.3 6.5 - - - +
180A ASN* 3.5 17.9 - - - +
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Residues in contact with ILE 159 (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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123A LEU* 3.8 22.9 - - + -
125A ILE* 4.1 16.2 - - + -
132A ILE* 3.9 32.5 - - + -
134A LEU* 5.8 0.4 - - + -
157A GLY 4.2 0.4 - - - -
158A LYS* 1.3 78.2 - - - +
160A LYS* 1.3 64.1 + - - +
164A PHE* 4.2 11.7 - - + -
178A ASP* 3.6 3.5 - - - -
179A ILE* 2.8 60.9 + - + +
181A LEU* 3.9 31.9 - - + -
301A UNL 4.6 4.0 - - + -
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Residues in contact with LYS 160 (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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158A LYS 6.0 0.2 - - - -
159A ILE* 1.3 77.9 - - - +
161A ARG* 1.3 55.8 + - - +
162A SER* 3.0 6.3 - - - +
163A ASP* 2.7 64.0 + - - +
164A PHE* 3.6 8.5 - - - -
177A ASP* 3.4 25.4 - - + +
178A ASP* 3.9 18.8 - - - +
179A ILE* 5.6 0.2 - - - -
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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