Contacts of the strand formed by residues 146 - 151 (chain A) in PDB entry 3EYF
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 LYS 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ALA* 1.3 78.9 - - - +
147A VAL* 1.3 73.7 + - - +
148A GLN* 3.4 38.1 + - - +
162A GLU* 5.5 0.4 - - - -
196A GLU 3.4 1.1 - - - +
197A VAL* 3.3 7.8 - - - +
198A THR* 3.0 53.1 + - + +
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Residues in contact with VAL 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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137A LEU* 4.0 21.3 - - + -
146A LYS* 1.3 84.6 - - - +
148A GLN* 1.3 67.7 + - - +
149A TRP* 4.2 13.0 - - + +
162A GLU* 4.2 16.3 + - - +
176A LEU* 3.8 29.8 - - + -
178A SER* 3.9 21.5 - - - +
195A CYS* 3.8 24.7 - - - -
196A GLU 3.5 2.9 - - - -
197A VAL* 4.5 1.6 - - + -
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Residues in contact with GLN 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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146A LYS* 3.4 36.8 + - - +
147A VAL* 1.3 76.0 - - - +
149A TRP* 1.3 64.0 + - - +
150A LYS* 3.8 10.1 + - - +
155A LEU* 3.4 30.6 - - + +
156A GLN 5.8 0.2 - - - -
194A ALA 3.5 2.3 - - - +
195A CYS* 3.6 1.0 - - - -
196A GLU* 2.8 65.1 + - + +
198A THR* 4.9 3.8 + - - -
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Residues in contact with TRP 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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118A ILE* 3.9 16.8 - - + -
133A VAL* 3.6 49.6 - - + -
134A VAL 3.8 1.6 - - - -
135A CYS* 3.5 35.9 - - + -
147A VAL* 4.2 10.2 - - + +
148A GLN* 1.3 75.0 - - - +
150A LYS* 1.3 62.2 + - - +
155A LEU* 3.5 7.4 - - - +
156A GLN* 2.9 52.1 + - + +
160A SER* 3.7 24.8 - - - -
178A SER* 3.2 28.7 + - - -
180A LEU* 3.6 25.9 - - + +
193A TYR* 5.6 1.6 - - + -
194A ALA 3.4 21.3 - - - -
195A CYS* 4.3 4.7 - - + -
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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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148A GLN* 4.9 7.3 - - + +
149A TRP* 1.3 78.5 - - - +
151A VAL* 1.3 67.2 + - - +
152A ASP 4.1 0.7 - - - -
153A ASN* 4.2 23.8 - - + +
154A ALA 3.3 8.5 - - - +
155A LEU* 4.2 21.5 - - - -
192A VAL* 3.5 2.7 - - - +
194A ALA* 2.7 53.7 + - + +
196A GLU* 3.4 38.3 + - + +
207A THR* 6.6 0.2 - - + -
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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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150A LYS* 1.3 77.6 - - - +
152A ASP* 1.3 63.4 + - - +
153A ASN 3.1 0.2 - - - -
154A ALA* 2.7 38.0 + - - +
156A GLN* 3.7 28.9 - - + +
180A LEU* 4.2 13.0 - - + -
182A LEU* 5.3 7.0 - - + -
190A HIS* 3.7 31.4 - - + +
192A VAL 3.3 4.3 - - - +
193A TYR* 3.6 37.0 - - + +
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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