Contacts of the strand formed by residues 135 - 140 (chain E) in PDB entry 1AXC
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 CYS 135 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E TYR* 3.9 0.3 - - - +
134E SER* 1.3 78.7 - - - +
136E VAL* 1.3 65.5 + - - +
137E VAL* 5.2 0.2 - - - -
162E CYS* 3.3 46.2 - - + -
198E GLU 3.3 2.9 - - - -
199E MET* 3.4 26.2 - - - -
201E GLU 3.5 10.8 - - - -
203E VAL* 3.8 11.7 - - + -
227E LEU 3.5 1.5 - - - +
228E SER* 3.1 5.0 - - - -
229E MET* 2.8 44.3 + - + +
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Residues in contact with VAL 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E TYR* 4.5 14.6 - - + +
135E CYS* 1.3 80.9 - - - +
137E VAL* 1.3 63.9 + - - +
138E LYS* 4.1 1.5 + - + +
196E THR 3.9 0.3 - - - +
197E ILE* 3.3 4.5 - - - +
198E GLU* 2.7 54.7 + - + +
226E THR* 4.6 15.7 - - + -
227E LEU 3.1 5.6 - - - +
228E SER* 3.7 23.1 - - - +
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Residues in contact with VAL 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E VAL* 1.3 77.4 - - - +
138E LYS* 1.3 68.9 + - - +
139E MET* 3.8 26.4 - - + +
162E CYS* 4.2 17.9 - - - -
167E VAL* 3.9 23.8 - - + -
195E VAL* 4.3 9.0 - - + -
196E THR 3.6 6.1 - - - +
197E ILE* 4.6 4.9 - - + +
225E VAL 3.6 1.4 - - - +
226E THR* 3.0 6.1 - - - -
227E LEU* 2.8 38.9 + - + +
229E MET* 4.0 26.7 - - + -
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Residues in contact with LYS 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E VAL* 4.1 2.8 - - + +
137E VAL* 1.3 74.2 - - - +
139E MET* 1.3 68.5 + - - +
191E GLU 3.6 22.0 + - - -
194E ALA* 4.1 18.5 + - - +
195E VAL* 3.3 2.4 - - - -
196E THR* 2.8 55.8 + - - +
224E THR* 4.2 25.6 - - + +
225E VAL 3.7 2.7 - - - -
226E THR* 3.8 22.0 - - + -
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Residues in contact with MET 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E VAL* 3.8 19.1 - - + -
138E LYS* 1.3 78.3 - - - +
140E PRO* 1.3 70.0 - - + +
143E GLU* 4.9 1.3 - - - -
144E PHE* 4.1 26.5 - - + -
147E ILE* 5.1 0.4 - - - -
167E VAL* 4.8 0.2 - - + -
169E PHE* 3.5 28.5 - - + -
182E LEU* 3.8 22.0 - - + -
194E ALA 3.5 6.7 - - - +
195E VAL* 4.4 9.9 - - + -
224E THR* 3.2 8.2 - - - -
225E VAL* 2.8 48.9 + - + +
227E LEU* 3.7 25.8 - - + -
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Residues in contact with PRO 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E MET* 1.3 90.1 - - + +
141E SER* 1.3 60.9 + - - +
142E GLY* 4.3 1.8 - - - +
143E GLU* 3.0 24.8 + - + +
144E PHE* 3.0 25.6 + - - +
192E GLU 3.0 22.2 - - - +
193E GLU* 4.1 13.7 - - - +
194E ALA 3.4 11.7 - - - +
195E VAL* 4.4 6.7 - - + -
223E SER 3.6 9.6 - - - +
225E VAL* 4.1 0.2 - - - -
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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