Contacts of the strand formed by residues 147 - 153 (chain A) in PDB entry 5CEO
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 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ARG* 3.3 7.9 - - - +
144A PHE 2.9 35.3 + - - +
145A HIS 3.3 5.7 - - - +
146A GLY* 1.3 81.6 - - - +
148A GLU* 1.3 66.9 + - - +
149A VAL* 3.6 2.9 + - + +
177A LYS* 2.8 35.3 + - - +
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Residues in contact with GLU 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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141A LEU* 4.1 29.8 - - + +
142A GLY 3.5 6.5 - - - +
143A ARG* 4.7 3.1 - - + +
147A GLU* 1.3 76.3 - - - +
149A VAL* 1.4 63.0 + - - +
177A LYS* 4.7 4.3 + - - -
191A GLU 4.7 0.2 - - - -
192A PHE* 3.9 32.3 + - + +
194A ALA* 5.8 1.2 - - - +
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Residues in contact with VAL 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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125A ILE* 5.3 1.1 - - + -
141A LEU* 3.4 7.1 - - - +
142A GLY 2.8 43.9 + - - +
143A ARG 4.3 0.4 - - - +
144A PHE* 3.8 36.8 - - + +
147A GLU* 4.2 4.7 - - + +
148A GLU* 1.4 77.8 - - - +
150A ALA* 1.3 62.5 + - - +
151A VAL* 3.7 21.1 - - + -
177A LYS* 4.3 26.5 - - + +
189A LEU* 4.4 6.3 - - + -
190A MET 3.4 15.5 - - - +
192A PHE* 4.1 5.6 - - - -
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Residues in contact with ALA 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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139A VAL* 4.5 2.9 - - + -
140A PHE 3.4 7.9 - - - +
149A VAL* 1.3 71.9 - - - +
151A VAL* 1.3 60.5 + - - +
152A LYS 4.0 0.7 - - - -
188A ILE 3.7 1.0 - - - +
189A LEU* 3.4 4.2 - - - -
190A MET* 2.7 34.8 + - + +
191A GLU 3.8 6.5 - - - +
192A PHE* 3.9 9.9 - - + +
501A 50D 3.3 50.5 - - + +
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Residues in contact with VAL 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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122A PHE* 5.9 0.9 - - + -
125A ILE* 3.9 12.8 - - + -
128A LEU* 3.8 34.3 - - + -
139A VAL* 3.7 3.0 - - - +
140A PHE* 2.8 43.4 + - + +
142A GLY 4.5 1.6 - - - +
149A VAL* 3.7 26.9 - - + +
150A ALA* 1.3 74.9 - - - +
152A LYS* 1.3 59.7 + - - +
153A LYS* 3.7 2.0 + - - +
187A CYS* 3.7 33.0 - - + -
188A ILE 3.6 4.0 - - - +
189A LEU* 4.5 6.3 - - + -
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Residues in contact with LYS 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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136A GLN* 3.9 18.8 + - - +
137A GLY* 5.2 1.3 - - - -
138A ALA 3.8 4.0 - - - +
139A VAL* 4.1 16.2 - - + -
150A ALA 4.0 1.0 - - - -
151A VAL* 1.3 70.9 - - - +
153A LYS* 1.3 71.8 + - - +
154A VAL* 3.7 25.3 + - - +
176A PHE* 6.3 0.8 - - - -
187A CYS* 3.3 4.3 - - - +
188A ILE* 2.8 50.4 + - + +
190A MET* 3.5 21.9 - - + -
254A ASP* 4.4 16.3 + - - +
501A 50D 4.1 14.8 - - - +
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Residues in contact with LYS 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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136A GLN* 5.6 0.7 - - - +
137A GLY* 4.8 4.2 - - - -
138A ALA* 2.9 39.9 + - + +
140A PHE* 4.5 11.2 - - + -
151A VAL* 3.7 2.8 + - - +
152A LYS* 1.3 79.1 - - - +
154A VAL* 1.3 89.7 + - - +
155A ARG* 4.6 4.2 + - - +
184A PRO 3.2 26.2 + - - -
185A CYS* 4.1 7.0 - - - +
186A TYR* 3.0 21.5 + - - +
187A CYS* 4.2 5.8 - - + +
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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