Contacts of the strand formed by residues 135 - 140 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C TYR 3.2 0.4 - - - -
134C SER* 1.3 77.0 - - - +
136C VAL* 1.3 64.3 + - - +
137C VAL* 4.2 0.4 - - - -
162C CYS* 3.2 37.5 - - + -
198C GLU 3.4 3.4 - - - -
199C MET* 3.1 21.3 - - - -
201C GLU 3.1 27.8 - - - -
203C VAL* 3.3 18.6 - - + -
227C LEU 3.4 1.6 - - - +
228C SER* 3.2 3.5 - - - -
229C MET* 2.7 43.4 + - + +
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Residues in contact with VAL 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C TYR* 4.3 19.7 - - + +
135C CYS* 1.3 78.4 - - - +
137C VAL* 1.3 62.7 - - - +
138C LYS* 4.1 1.3 + - + +
162C CYS* 5.0 0.2 - - - -
196C THR 3.8 0.9 - - - +
197C ILE* 3.4 3.7 - - - -
198C GLU* 2.8 51.0 + - + +
226C THR* 4.6 17.3 - - + -
227C LEU 3.1 4.3 - - - +
228C SER* 3.8 21.1 - - - +
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Residues in contact with VAL 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136C VAL* 1.3 76.6 - - - +
138C LYS* 1.3 68.1 + - - +
139C MET* 3.9 25.7 - - + +
162C CYS* 3.8 26.5 - - - -
167C VAL* 4.1 20.9 - - + -
195C VAL* 4.5 4.5 - - + -
196C THR 3.5 7.4 - - - +
197C ILE* 4.4 7.9 - - + -
225C VAL 3.7 0.7 - - - +
226C THR* 3.0 6.4 - - - -
227C LEU* 2.7 51.6 + - + +
229C MET* 4.2 14.6 - - + -
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Residues in contact with LYS 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C VAL* 4.1 1.7 + - + -
137C VAL* 1.3 73.5 - - - +
139C MET* 1.3 67.6 + - - +
191C GLU 3.7 20.5 + - - -
194C ALA* 3.8 25.1 + - - +
195C VAL* 3.3 5.5 - - - +
196C THR* 2.8 53.2 + - + +
224C THR* 4.2 27.9 - - - +
225C VAL 3.6 7.6 - - - +
226C THR* 4.2 15.7 - - + -
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Residues in contact with MET 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C VAL* 3.9 23.3 - - + +
138C LYS* 1.3 80.4 - - - +
140C PRO* 1.3 75.1 - - + +
143C GLU* 4.7 2.9 - - - -
144C PHE* 3.8 32.3 - - + -
147C ILE* 5.1 0.2 - - - -
167C VAL* 4.4 0.4 - - + -
169C PHE* 3.3 32.1 - - + -
182C LEU* 3.6 22.0 - - + -
194C ALA 3.8 3.6 - - - -
195C VAL* 4.1 10.5 - - + -
224C THR* 3.3 6.8 - - - -
225C VAL* 2.9 44.3 + - + +
227C LEU* 4.0 11.4 - - + -
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Residues in contact with PRO 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C MET* 1.3 88.7 - - + +
141C SER* 1.3 64.5 + - - +
142C GLY 4.5 1.3 - - - +
143C GLU* 3.1 23.5 + - + +
144C PHE* 3.0 20.3 + - - +
192C GLU 3.3 23.1 - - - +
193C GLU* 3.9 12.6 - - - +
194C ALA 3.2 17.5 - - - +
195C VAL* 4.1 8.1 - - + -
223C SER 3.3 11.7 - - - +
224C THR* 4.1 0.7 - - + -
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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