Contacts of the strand formed by residues 143 - 148 (chain A) in PDB entry 4A04
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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114A LEU* 4.0 7.4 - - + -
120A TRP* 4.3 8.3 - + - +
139A MET* 4.2 12.8 - - + +
141A PRO 3.8 2.4 + - - -
142A THR* 1.3 70.5 - - - +
144A GLN* 1.3 61.4 + - - +
145A VAL* 3.6 20.6 - - + -
160A MET* 3.5 38.4 - - + -
212A SER* 3.7 0.3 - - - -
213A PHE* 3.1 42.2 + + + +
216A LEU* 6.4 0.2 - - + -
239A PRO* 4.4 9.6 - - + -
241A PHE* 3.8 29.6 - + + -
263A PHE 5.3 0.2 - - - -
265A PHE* 3.7 23.6 - + - -
268A THR* 3.7 38.6 - - + -
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Residues in contact with GLN 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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114A LEU* 3.7 5.5 - - - +
115A GLU* 2.8 46.7 + - + +
116A MET* 4.0 22.3 - - - +
142A THR* 3.3 25.5 + - + +
143A PHE* 1.3 78.5 - - - +
145A VAL* 1.3 63.1 + - - +
210A ILE* 3.7 24.7 - - + +
211A VAL 3.4 4.0 - - - -
212A SER* 3.7 19.5 - - - -
214A ASP* 5.9 0.6 - - - +
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A VAL* 3.7 22.7 - - + -
113A GLN 3.3 8.7 - - - +
114A LEU* 4.3 3.1 - - + -
115A GLU* 4.3 5.4 - - - -
143A PHE* 3.6 26.5 - - + -
144A GLN* 1.3 79.3 - - - +
146A LYS* 1.3 58.9 + - - +
147A LEU* 3.9 10.1 - - + -
210A ILE* 3.5 3.6 - - - +
211A VAL* 2.8 53.9 + - + +
213A PHE* 4.9 2.9 - - + -
241A PHE* 3.8 32.3 - - + -
265A PHE* 4.2 8.3 - - + -
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Residues in contact with LYS 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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111A SER 3.8 0.3 - - - +
112A VAL* 3.4 8.0 - - - +
113A GLN* 2.8 40.9 + - + +
115A GLU* 3.5 24.7 - - - +
145A VAL* 1.3 72.9 - - - +
147A LEU* 1.3 65.7 + - - +
148A PHE* 3.7 36.0 - - + -
207A MET 5.8 4.7 - - - +
209A GLN 5.5 2.5 - - - +
210A ILE* 4.3 19.3 - - + +
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Residues in contact with LEU 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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110A VAL* 4.2 7.2 - - + -
111A SER 3.8 0.7 - - - -
112A VAL* 3.8 22.4 - - + -
145A VAL* 3.9 18.8 - - + -
146A LYS* 1.3 79.2 - - - +
148A PHE* 1.3 73.3 + - - +
150A MET* 3.8 32.1 - - + -
158A LEU* 4.1 10.5 - - + -
206A TRP* 4.1 13.5 + - + +
207A MET* 3.4 33.3 + - + +
209A GLN 5.5 1.4 + - - -
211A VAL* 3.8 24.7 - - + -
241A PHE* 4.2 2.0 - - + -
243A VAL* 3.9 14.4 - - + -
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Residues in contact with PHE 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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110A VAL* 3.4 6.8 - - - +
111A SER* 2.8 57.0 + - - +
112A VAL 5.1 0.2 - - - -
113A GLN* 3.9 27.6 - - + -
146A LYS* 3.7 46.0 - - + -
147A LEU* 1.3 80.2 - - - +
149A GLY* 1.3 63.0 + - - +
150A MET* 3.4 4.1 + - - -
207A MET* 3.8 10.8 - - + -
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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