Contacts of the strand formed by residues 135 - 140 (chain F) in PDB entry 6S1M
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F TYR* 4.1 0.5 - - - +
134F SER* 1.3 84.1 - - - +
136F VAL* 1.3 65.4 + - - +
137F VAL* 5.2 0.2 - - - -
162F CYS* 3.2 44.2 - - + -
198F GLU 3.1 4.5 - - - +
199F MET* 3.3 28.3 - - - -
201F GLU 3.4 12.6 - - - -
203F VAL* 4.5 4.3 - - + -
227F LEU 3.5 1.4 - - - +
228F SER* 3.3 3.5 - - - -
229F MET* 2.9 44.7 + - + +
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Residues in contact with VAL 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F GLU* 6.0 0.9 - - - +
133F TYR* 4.4 14.6 - - + +
135F CYS* 1.3 78.2 - - - +
137F VAL* 1.3 65.0 + - - +
138F LYS* 4.2 2.4 + - + +
196F THR 3.7 1.4 - - - +
197F ILE* 3.6 2.6 - - - -
198F GLU* 3.0 56.1 + - + +
226F THR* 4.5 16.8 - - + +
227F LEU 3.2 4.0 - - - +
228F SER* 3.4 24.7 - - - +
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Residues in contact with VAL 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136F VAL* 1.3 77.7 - - - +
138F LYS* 1.3 65.6 + - - +
139F MET* 3.6 25.5 - - + +
162F CYS* 4.3 15.0 - - - -
167F VAL* 4.3 22.7 - - + -
195F VAL* 4.3 8.5 - - + -
196F THR 3.4 8.3 - - - +
197F ILE* 4.3 18.4 - - + -
225F VAL 3.6 1.6 - - - +
226F THR* 3.0 4.8 - - - -
227F LEU* 2.6 50.6 + - + +
229F MET* 4.4 11.7 - - + -
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Residues in contact with LYS 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F VAL* 4.1 3.2 + - + +
137F VAL* 1.3 72.3 - - - +
139F MET* 1.3 68.2 + - - +
191F GLU 3.7 17.6 + - - -
192F GLU* 4.8 5.3 - - - +
194F ALA* 3.7 23.0 + - - +
195F VAL* 3.4 5.7 - - - +
196F THR* 3.0 56.9 + - - +
224F THR* 4.1 25.7 - - + +
225F VAL 3.5 3.1 - - - -
226F THR* 4.1 19.1 - - + +
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Residues in contact with MET 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F VAL* 3.6 22.4 - - + +
138F LYS* 1.3 79.1 - - - +
140F PRO* 1.3 84.0 - - + +
143F GLU* 4.3 2.5 - - - +
144F PHE* 3.9 25.4 - - + -
147F ILE* 4.5 2.5 - - - -
169F PHE* 4.0 14.4 - - + -
182F LEU* 3.6 20.4 - - + -
192F GLU 5.1 0.4 - - - -
194F ALA 3.8 5.6 - - - -
195F VAL* 4.0 13.0 - - + -
224F THR* 3.3 6.2 - - - -
225F VAL* 2.9 38.7 + - + +
227F LEU* 3.3 35.4 - - + -
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Residues in contact with PRO 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139F MET* 1.3 96.1 - - + +
141F SER* 1.3 65.0 + - - +
142F GLY* 4.3 2.5 - - - +
143F GLU* 3.4 32.3 - - + +
144F PHE* 3.2 16.3 + - - +
192F GLU 3.2 23.8 - - - +
193F GLU* 3.7 17.9 - - - +
194F ALA 3.7 10.8 - - - +
195F VAL* 4.4 1.1 - - + -
223F SER 3.4 10.1 - - - +
224F THR* 4.2 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