Contacts of the strand formed by residues 143 - 152 (chain A) in PDB entry 4AEJ
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 ALA 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ARG* 1.3 78.7 - - - +
144A SER* 1.3 64.3 + - - +
211A ARG* 3.6 2.5 - - - +
212A THR* 3.0 31.9 + - + +
215A ALA* 3.7 23.3 - - + +
218A LEU* 3.7 18.4 - - + +
242A VAL* 4.9 0.9 - - + -
243A CYS 3.1 13.2 - - - +
244A PHE* 3.8 14.8 - - + -
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Residues in contact with SER 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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79A GLU* 4.0 16.6 + - - -
143A ALA* 1.3 78.1 - - - +
145A GLN* 1.3 63.4 + - - +
209A GLU* 4.7 4.7 - - - -
210A TYR 3.2 13.0 - - - -
211A ARG* 4.0 33.6 + - - -
218A LEU* 3.6 4.8 - - - +
241A PRO 3.9 0.3 - - - +
242A VAL* 3.7 0.9 - - - -
243A CYS* 2.8 37.3 + - - +
1246A GOL 4.7 6.2 - - - -
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Residues in contact with GLN 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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119A TYR* 2.8 28.5 + - - -
144A SER* 1.3 78.2 - - - +
146A GLN* 1.3 70.0 + - - +
147A ILE* 4.0 3.6 - - - +
208A PHE 4.0 0.2 - - - +
209A GLU* 3.4 3.8 - - - +
210A TYR 3.0 31.2 + - - -
218A LEU* 4.0 9.2 - - + +
219A PRO* 3.5 9.5 - - - +
220A ILE* 2.9 44.6 + - + +
239A VAL* 3.5 8.1 - - - +
240A GLY 2.8 21.8 + - - +
241A PRO 3.4 16.6 - - - +
242A VAL* 3.8 8.9 - - - +
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Residues in contact with GLN 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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145A GLN* 1.3 77.2 - - - +
147A ILE* 1.3 61.3 + - - +
148A THR* 5.6 1.4 + - - +
192A LEU* 3.7 22.8 - - + +
207A VAL* 3.8 15.3 - - + +
208A PHE 3.2 11.2 - - - +
209A GLU* 3.9 23.0 + - + +
211A ARG* 5.6 0.2 - - - +
240A GLY* 2.8 37.9 + - - -
241A PRO 4.5 2.4 + - - -
1246A GOL 4.4 16.3 + - - +
1248A GOL 5.2 1.7 + - - -
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Residues in contact with ILE 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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117A PHE* 5.1 2.0 - - + -
145A GLN* 4.0 5.2 - - - +
146A GLN* 1.3 81.3 - - - +
148A THR* 1.3 66.1 + - - +
149A TYR 4.8 0.4 - - - +
171A LEU* 4.3 12.1 - - + -
207A VAL* 3.5 2.9 - - - +
208A PHE* 2.8 46.0 + - + +
220A ILE* 3.4 40.8 - - + -
223A ILE* 4.3 17.0 - - + -
237A VAL* 3.6 26.0 - - + -
238A ASP 3.6 2.9 - - - +
239A VAL* 3.8 29.8 - - + -
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Residues in contact with THR 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 GLN* 5.6 1.2 + - - +
147A ILE* 1.3 75.7 - - - +
149A TYR* 1.3 60.7 + - - +
150A HIS* 3.9 15.3 + - + +
205A LYS* 3.8 39.4 + - + +
206A THR 3.5 6.5 - - - +
207A VAL* 3.6 17.9 - - + +
237A VAL* 3.3 7.6 - - - +
238A ASP* 2.9 47.9 + - - +
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Residues in contact with TYR 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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147A ILE* 4.1 1.2 + - + -
148A THR* 1.3 71.2 - - - +
150A HIS* 1.3 60.3 + - - +
151A CYS* 3.8 24.9 + - + -
154A SER* 2.7 26.4 + - - -
155A ILE 4.6 1.3 + - - -
156A ALA* 3.5 27.6 - - + -
169A LEU* 3.6 17.5 - - + -
196A CYS* 3.9 0.3 - - - -
205A LYS* 3.1 4.5 - - - -
206A THR 2.9 38.5 + - - +
208A PHE* 4.0 15.9 - - + -
223A ILE* 4.1 14.6 - - + -
225A PRO* 3.8 27.4 - - + +
228A ILE* 3.8 2.6 - - - +
235A PHE* 3.4 38.5 - + + +
236A GLY 3.6 7.9 - - - -
237A VAL* 4.6 1.6 - - + +
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Residues in contact with HIS 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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89A VAL 5.9 0.2 - - - -
91A ARG* 3.5 32.2 + - + +
148A THR* 3.9 17.7 - - + +
149A TYR* 1.3 73.2 - - - +
151A CYS* 1.3 58.8 + - - +
203A TRP* 3.9 13.5 - - + -
204A SER 3.3 9.0 + - - +
205A LYS* 3.8 19.2 - - + +
235A PHE* 3.2 10.7 - - - +
236A GLY* 2.8 51.4 + - - +
237A VAL 4.4 0.7 - - - -
238A ASP* 2.6 37.6 + - - -
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Residues in contact with CYS 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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149A TYR* 3.8 9.6 - - + -
150A HIS* 1.3 74.6 - - - +
152A LYS* 1.3 59.4 + - - +
153A ASN 4.2 0.4 - - - -
154A SER* 3.4 20.9 - - - +
196A CYS* 2.0 54.7 - - - -
202A GLU 3.6 1.7 - - - +
203A TRP* 3.3 7.7 - - - -
204A SER* 2.7 54.3 + - - -
234A GLU 3.8 2.9 - - - -
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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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151A CYS* 1.3 74.3 - - - +
153A ASN* 1.3 82.0 + - - +
154A SER* 3.2 0.6 + - - -
201A GLY* 3.4 24.5 - - - +
202A GLU 3.5 16.2 - - - +
203A TRP* 3.7 34.7 - - + +
232A ASP* 4.2 10.4 + - - +
233A GLN* 3.6 0.2 - - - -
234A GLU* 3.0 58.9 + - + +
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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