Contacts of the strand formed by residues 143 - 152 (chain A) in PDB entry 5E5R
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 PHE 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A PHE* 3.2 8.0 - - - -
134A VAL* 2.8 48.3 + - + +
139A LEU* 4.0 18.4 - - + -
140A PRO* 3.8 44.4 - - + -
141A GLY 3.3 20.4 - - - -
142A ARG* 1.3 75.3 - - - +
144A LYS* 1.3 59.0 + - - +
178A PHE* 3.6 14.4 - - + -
179A TYR* 3.2 26.2 - - - -
180A ASN* 3.6 17.9 - - + -
181A PRO* 4.5 0.4 - - - -
196A ILE* 3.8 25.4 - - + -
197A ILE* 4.2 0.7 - - - -
198A GLY* 3.9 19.7 - - - -
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Residues in contact with LYS 144 (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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130A ASP 5.2 2.0 + - - -
131A ASP* 3.2 34.0 + - - +
132A TYR 3.2 12.8 - - - +
133A PHE* 3.4 25.4 - - + -
143A PHE* 1.3 73.2 - - - +
145A ALA* 1.3 75.4 + - - +
146A GLU* 5.5 2.0 + - - -
178A PHE* 3.3 2.1 - - - -
179A TYR* 2.7 60.9 + - + +
181A PRO* 3.7 25.3 - - + +
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Residues in contact with ALA 145 (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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128A LEU* 3.8 25.9 - - + +
130A ASP 4.9 5.5 - - - +
132A TYR* 2.9 31.1 + - + -
144A LYS* 1.3 85.3 + - - +
146A GLU* 1.3 61.9 + - - +
176A ILE* 4.1 8.7 - - + -
177A PHE 3.5 1.6 - - - -
178A PHE* 3.4 27.7 - - + -
179A TYR* 4.7 0.3 - - - -
238A LEU* 5.1 1.1 - - + -
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Residues in contact with GLU 146 (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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127A LEU* 4.1 13.2 - - + +
128A LEU* 3.1 30.7 + - - +
144A LYS* 3.6 2.1 + - - -
145A ALA* 1.3 76.3 - - - +
147A LYS* 1.3 71.5 + - + +
177A PHE 2.6 15.8 + - - +
179A TYR* 3.9 14.2 + - + -
187A PHE* 3.6 51.5 + - + +
188A GLN* 5.5 0.9 + - - +
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Residues in contact with LYS 147 (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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125A ALA* 5.6 3.1 - - + -
126A ILE 3.2 12.8 - - - +
127A LEU* 3.9 18.8 - - + -
128A LEU* 4.2 2.8 - - - +
146A GLU* 1.3 91.0 - - + +
148A VAL* 1.3 68.4 + - - +
149A GLU* 2.8 30.1 + - + +
175A GLN 3.9 0.2 - - - +
176A ILE* 3.5 4.3 - - - +
177A PHE* 2.9 50.1 + - + +
187A PHE* 4.1 26.9 - - + -
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Residues in contact with VAL 148 (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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124A VAL 3.7 0.9 - - - +
125A ALA* 3.2 5.5 - - - +
126A ILE* 2.7 48.1 + - + +
128A LEU* 3.8 29.2 - - + -
147A LYS* 1.3 79.2 - - - +
149A GLU* 1.3 65.6 + - - +
150A PHE* 3.9 11.4 - - + -
174A MET* 3.4 33.9 - - + -
175A GLN 3.2 12.1 - - - +
176A ILE* 3.9 15.9 - - + -
236A PHE* 6.4 0.2 - - + -
238A LEU* 4.8 6.7 - - + -
241A LEU* 5.8 1.8 - - + -
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Residues in contact with GLU 149 (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 THR* 3.9 26.4 - - + +
124A VAL 3.5 5.2 - - - -
125A ALA* 4.2 11.3 - - + +
147A LYS* 2.8 36.5 + - + +
148A VAL* 1.3 79.1 - - - +
150A PHE* 1.3 65.7 + - - +
151A HIS* 4.8 6.9 + - - +
173A GLU 4.2 0.2 - - - +
174A MET* 3.7 2.3 - - - +
175A GLN* 2.9 40.9 + - - +
177A PHE* 3.7 25.0 - - + -
258A THR* 5.7 5.2 - - - +
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Residues in contact with PHE 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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123A THR* 2.6 29.7 + - - -
124A VAL* 3.3 25.4 - - + -
126A ILE* 3.6 33.7 - - + -
148A VAL* 3.9 19.1 - - + -
149A GLU* 1.3 71.3 - - - +
151A HIS* 1.3 72.3 + - - +
152A TRP* 3.8 18.2 - - + -
172A VAL* 4.4 6.7 - - + -
173A GLU 3.6 2.9 - - - -
174A MET* 3.5 35.2 - - + -
204A PHE* 4.5 10.5 - + - -
217A ILE* 4.1 21.3 - - + -
221A LEU* 5.9 0.7 - - + -
241A LEU* 5.4 0.9 - - + -
284A PHE* 3.9 24.5 - + + -
305A ASN* 3.6 4.9 + - - -
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Residues in contact with HIS 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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62A TYR* 3.7 15.0 - - - -
123A THR* 5.3 5.4 - - - -
149A GLU* 5.0 7.1 + - - +
150A PHE* 1.3 87.4 + - - +
152A TRP* 1.3 61.0 + - - +
160A GLY 3.6 17.4 - - - +
162A GLU* 3.1 33.3 + - + -
172A VAL* 3.2 5.5 - - - -
173A GLU* 2.9 40.0 + - + +
175A GLN* 3.0 33.7 + - - -
257A THR* 4.2 4.7 + - - -
258A THR* 5.2 3.8 - - + -
305A ASN* 2.6 31.7 + - - +
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Residues in contact with TRP 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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123A THR* 4.1 2.9 - - - -
124A VAL* 4.0 24.7 - - + -
150A PHE* 3.7 20.2 - - + -
151A HIS* 1.3 80.9 - - - +
153A GLY* 1.3 72.1 + - - +
160A GLY* 3.6 7.8 + - - -
171A PRO 3.4 11.7 - - - +
172A VAL* 4.0 13.2 - - + -
284A PHE* 2.9 53.7 + + + -
285A TYR* 3.8 12.3 - + + -
287A ILE* 4.1 9.2 - - + -
302A LEU* 2.8 52.1 + - + -
303A ARG* 3.9 0.6 - - - +
304A ASN* 3.1 22.7 + - - -
305A ASN* 3.0 31.7 + - - +
306A PHE* 4.2 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