Contacts of the strand formed by residues 139 - 145 (chain C) in PDB entry 6S6A
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 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C ARG 3.3 2.5 + - - +
64C ILE* 3.4 8.4 - - + -
65C LEU 3.0 23.9 + - - -
137C THR* 3.5 9.3 + - - +
138C GLY* 1.3 79.5 - - - +
140C LEU* 1.3 58.9 - - - +
141C ILE* 4.2 0.4 - - + -
171C MET* 4.5 1.8 - - - +
172C ASN* 3.2 18.2 - - + +
174C GLU* 4.6 2.2 - - + -
232C VAL* 3.9 22.0 - - + -
236C LEU* 3.6 21.5 - - + -
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Residues in contact with LEU 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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65C LEU* 3.3 13.5 - - + +
67C MET* 3.3 49.8 - - + -
134C PHE* 4.4 10.3 - - + -
139C ALA* 1.3 72.8 - - - +
141C ILE* 1.3 64.9 + - - +
142C TYR* 4.2 5.8 - - + +
160C THR* 4.4 17.9 - - - +
161C VAL* 4.5 9.2 - - + -
164C ALA* 4.7 0.9 - - + -
171C MET* 3.8 17.4 - - + +
172C ASN 2.8 9.9 + - - +
173C PHE* 3.5 24.6 - - + +
174C GLU* 2.9 30.0 + - - +
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Residues in contact with ILE 141 (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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64C ILE* 3.7 27.6 - - + -
65C LEU 2.9 10.1 + - - +
66C LEU* 3.4 16.2 - - + +
67C MET 3.0 25.5 + - - +
140C LEU* 1.3 73.9 - - - +
142C TYR* 1.3 57.9 + - - +
143C VAL* 3.7 2.4 + - + -
174C GLU* 3.1 15.7 - - + -
176C PHE* 3.5 52.5 - - + -
229C PHE* 3.8 25.4 - - + -
232C VAL* 4.1 16.2 - - + -
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Residues in contact with TYR 142 (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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67C MET* 3.4 15.5 - - + -
68C GLY* 3.6 15.8 - - - -
69C LEU* 3.7 30.7 - - - +
140C LEU* 3.8 10.6 + - + +
141C ILE* 1.3 69.7 - - - +
143C VAL* 1.3 75.8 + - - +
144C ILE* 3.6 22.9 - - + -
153C ALA* 3.6 20.7 + - + -
156C ARG* 3.8 7.6 - - + +
157C LEU* 4.0 41.5 - - + -
160C THR* 4.0 16.2 - - + -
161C VAL* 5.5 3.4 - - + -
174C GLU 2.8 12.3 + - - +
175C VAL* 3.3 10.5 - - + +
176C PHE 2.9 26.7 + - - -
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Residues in contact with VAL 143 (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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66C LEU* 3.7 37.2 - - + -
67C MET 2.8 19.5 + - - +
68C GLY* 3.6 3.1 - - - -
69C LEU 4.6 0.3 + - - -
72C SER* 3.4 39.1 - - - +
73C GLY 4.5 0.7 - - - +
74C LYS* 4.4 2.7 - - + +
77C ILE* 3.9 17.7 - - + -
141C ILE* 4.2 5.6 - - + +
142C TYR* 1.3 87.6 - - - +
144C ILE* 1.3 59.9 + - - +
176C PHE* 3.5 8.1 - - + +
178C HIS* 3.8 24.5 - - + -
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Residues in contact with ILE 144 (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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72C SER* 4.8 0.2 - - - -
142C TYR* 3.6 18.4 + - + -
143C VAL* 1.3 71.1 - - - +
145C ASP* 1.3 75.2 + - - +
146C ALA* 4.3 1.3 - - - +
150C TYR* 3.8 21.1 - - + -
153C ALA* 4.2 18.4 - - + +
154C LEU* 5.2 6.3 - - + +
157C LEU* 4.1 17.5 - - + -
175C VAL* 3.8 26.9 - - + -
176C PHE 2.8 12.2 + - - +
177C ILE* 4.8 2.7 - - + -
178C HIS* 3.0 30.4 + - - +
195C ILE* 4.1 29.2 - - + -
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Residues in contact with ASP 145 (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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71C ARG* 3.8 16.2 + - - +
72C SER* 4.2 18.5 + - - +
144C ILE* 1.3 76.8 - - - +
146C ALA* 1.3 60.9 + - - +
147C GLN* 3.0 23.9 + - - +
148C ASP* 3.4 40.5 + - + +
149C ASP 4.8 1.0 - - - +
150C TYR* 4.6 3.3 - - - +
153C ALA* 5.5 2.0 - - - +
178C HIS 4.1 1.8 - - - -
179C LYS* 2.9 37.9 + - - +
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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