Contacts of the strand formed by residues 153 - 163 (chain O) in PDB entry 3DXA
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 153 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176N MET* 3.5 32.5 - - + -
179N MET* 5.1 3.6 - - - -
181N PHE* 3.6 36.3 - - - -
147O GLU* 3.6 5.4 - - - +
148O ILE* 3.3 26.9 + - - +
151O THR* 3.1 30.9 + - - +
152O GLN* 1.3 81.5 - - - +
154O ALA* 1.3 64.0 + - - +
208O ARG* 3.7 33.8 - - + +
209O VAL 3.6 10.1 - - - +
211O ALA* 3.7 5.3 - - - +
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Residues in contact with ALA 154 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143O PRO* 3.8 25.4 - - + -
147O GLU* 3.7 1.8 - - - -
148O ILE* 4.6 2.7 - - + -
153O LYS* 1.3 77.6 - - - +
155O THR* 1.3 62.1 + - - +
156O LEU* 3.6 3.1 + - + +
207O LEU 3.7 0.7 - - - +
208O ARG* 3.5 3.5 - - - -
209O VAL* 2.8 40.3 + - + +
211O ALA* 4.4 4.5 - - - -
214O TRP* 3.8 27.1 - - + -
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Residues in contact with THR 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136N LEU* 3.9 11.8 - - - +
148N LEU* 3.3 28.6 - - + +
150N THR* 5.2 4.3 + - - +
174N LEU* 5.3 5.2 - - + -
185N SER* 5.8 0.9 - - - -
143O PRO* 3.5 18.9 - - - +
147O GLU* 2.7 34.7 + - - +
154O ALA* 1.3 69.4 - - - +
156O LEU* 1.3 68.5 + - - +
157O VAL* 4.2 0.4 - - + +
206O ARG* 4.2 17.7 - - + -
207O LEU 3.7 3.4 - - - +
208O ARG* 3.0 28.2 + - + -
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Residues in contact with LEU 156 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140O VAL* 4.7 9.6 - - + -
141O PHE 4.0 7.2 - - - +
142O GLU* 5.2 0.9 - - - -
143O PRO* 4.0 24.5 - - + -
154O ALA* 3.9 13.0 - - + +
155O THR* 1.3 74.5 - - - +
157O VAL* 1.3 61.9 + - - +
172O TRP* 4.3 17.5 - - + -
206O ARG* 3.3 6.6 - - - +
207O LEU* 2.7 51.6 + - + +
209O VAL* 4.4 7.6 - - + -
214O TRP* 4.0 20.9 - - + -
221O PHE* 3.7 39.0 - - + -
252O ALA* 4.9 3.4 - - + -
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Residues in contact with VAL 157 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136N LEU* 3.2 28.7 - - + -
146N VAL* 4.2 8.3 - - + -
148N LEU* 4.0 28.0 - - + -
187N VAL* 4.0 28.7 - - + -
140O VAL* 3.1 6.2 - - - +
141O PHE* 3.0 34.3 + - + -
155O THR 4.2 0.7 - - - +
156O LEU* 1.3 80.9 - - - +
158O CYS* 1.3 71.5 + - - +
159O LEU* 4.3 2.5 - - + -
172O TRP* 4.0 3.4 - - - -
205O SER 3.2 13.7 - - - +
206O ARG* 4.6 3.1 - - + -
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Residues in contact with CYS 158 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138O VAL* 3.8 13.2 - - - -
139O ALA 3.7 13.0 - - - -
140O VAL* 4.7 0.7 - - - -
157O VAL* 1.3 75.3 - - - +
159O LEU* 1.3 66.4 + - - +
160O ALA 4.1 0.7 - - - -
170O LEU* 4.5 4.8 - - + +
172O TRP* 3.5 16.4 - - + -
203O LEU 3.7 1.0 - - - +
204O SER* 3.3 5.2 - - - -
205O SER* 2.8 36.1 + - - +
223O CYS* 2.0 50.3 - - - -
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Residues in contact with LEU 159 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142N SER* 5.7 0.2 + - - -
146N VAL* 3.6 29.2 - - + -
187N VAL* 4.4 4.7 - - + -
189N TRP* 3.3 63.0 - - + +
137O GLU 3.8 3.3 - - - +
139O ALA* 3.2 30.7 + - - +
141O PHE* 3.7 14.9 - - + -
157O VAL* 4.8 1.6 - - + -
158O CYS* 1.3 75.2 - - - +
160O ALA* 1.3 61.2 + - - +
161O THR* 3.9 10.3 + - + +
203O LEU 3.5 2.7 - - - +
204O SER* 3.5 32.1 - - - -
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Residues in contact with ALA 160 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136O PRO* 4.7 3.6 - - + -
137O GLU 3.8 4.7 - - - -
138O VAL* 3.8 10.1 - - + -
158O CYS* 4.1 1.6 - - - -
159O LEU* 1.3 70.3 - - - +
161O THR* 1.3 68.9 + - - +
163O PHE* 3.2 12.7 - - + -
170O LEU* 4.6 7.0 - - + -
203O LEU* 2.9 31.7 + - + +
225O VAL* 3.6 36.6 - - + -
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Residues in contact with THR 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189N TRP* 4.0 19.0 + - + -
136O PRO* 4.5 0.2 - - - -
137O GLU* 2.7 43.2 + - - +
159O LEU* 4.4 8.4 + - + +
160O ALA* 1.3 89.8 - - - +
162O GLY* 1.3 56.0 + - - +
163O PHE* 4.1 3.6 - - - -
192O GLU* 3.5 15.2 + - - -
202O ALA* 2.9 27.6 - - + -
203O LEU 3.9 2.0 - - - +
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Residues in contact with GLY 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O PHE* 3.9 0.3 - - - +
135O PRO 3.1 11.3 - - - +
137O GLU* 4.2 8.3 + - - +
161O THR* 1.3 71.3 + - - -
163O PHE* 1.3 60.1 + - - -
192O GLU* 3.2 16.7 + - - -
200O ARG* 3.2 31.8 + - - +
201O TYR 3.2 12.3 - - - -
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Residues in contact with PHE 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O PHE* 3.8 1.8 - - - +
135O PRO 3.3 24.0 - - - +
136O PRO* 3.7 12.1 - - + -
160O ALA* 3.2 29.2 - - + -
161O THR* 4.1 2.9 - - - -
162O GLY* 1.3 76.2 - - - -
164O TYR* 1.3 61.5 + - - +
165O PRO 3.6 7.9 - - - -
166O ASP* 3.8 18.2 - - + -
168O VAL* 3.4 45.1 - - + -
189O PRO* 4.2 6.1 - - + -
200O ARG* 4.4 1.6 - - - -
201O TYR* 2.9 41.2 + - + +
202O ALA* 3.6 15.7 - - - -
203O LEU* 3.8 13.9 - - + -
227O PHE* 4.7 3.1 - - + -
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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