Contacts of the strand formed by residues 140 - 145 (chain C) in PDB entry 6PUO
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 140 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ASP* 3.1 4.3 + - - -
130C ILE* 2.9 44.9 + - + +
131C VAL* 6.0 0.4 - - - -
132C PHE* 3.6 28.1 - - + -
136C SER* 4.7 10.5 - - - -
138C LYS* 4.0 29.7 + - - +
139C VAL* 1.3 75.5 - - - +
141C LYS* 1.3 65.9 + - - +
279C SER 3.3 20.5 + - - -
280C ASN* 4.7 2.9 - - - +
281C HIS 3.3 27.1 - - - +
282C SER* 3.8 18.4 - - - +
284C PHE* 4.3 7.9 - - + -
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Residues in contact with LYS 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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128C GLY 3.7 6.5 - - - +
129C ASP* 4.3 21.3 - - + -
139C VAL* 5.4 9.0 - - - +
140C LYS* 1.3 77.4 - - - +
142C TYR* 1.3 60.3 + - - +
161C HIS 5.3 1.6 + - - -
162C TRP* 3.6 53.5 + - + +
282C SER 3.8 4.0 + - - -
283C HIS* 3.4 26.0 - - + +
284C PHE* 2.9 23.8 + - - +
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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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63C ILE* 6.1 0.2 - - - +
126C ALA* 3.1 28.3 + - + -
127C PHE 3.4 5.8 + - - -
128C GLY* 2.9 53.9 + - - +
129C ASP 3.4 29.2 - - - -
130C ILE* 4.0 13.9 - - + -
140C LYS 4.6 1.1 - - - +
141C LYS* 1.3 78.3 - - - +
143C VAL* 1.3 66.3 + - - +
144C ARG* 6.2 0.2 - - + -
162C TRP* 4.0 5.1 - - - -
244C TRP* 5.5 0.4 - + - -
253C LEU* 3.5 50.5 + - + +
259C SER* 4.3 6.3 - - - -
262C ALA* 4.7 0.5 - - - +
284C PHE* 3.1 27.6 - - + +
286C LEU* 4.3 18.6 - - + -
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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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63C ILE* 4.4 17.3 - - + -
67C ILE* 4.7 11.4 - - + -
124C THR* 5.2 1.1 - - + -
127C PHE* 3.7 26.0 - - + +
142C TYR* 1.3 78.4 - - - +
144C ARG* 1.3 68.6 + - - +
145C VAL* 4.0 17.9 + - + -
154C ILE* 6.4 0.4 - - + -
157C LEU* 4.4 11.7 - - + -
162C TRP* 4.3 14.6 - - + -
284C PHE 3.0 11.5 + - - +
285C ILE* 3.6 14.4 - - + -
286C LEU* 2.9 30.7 + - - +
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Residues in contact with ARG 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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67C ILE* 4.3 1.7 - - - +
69C LYS* 3.4 37.7 - - + +
70C LYS 3.9 9.7 + - - -
93C TYR* 5.2 3.8 + - - -
124C THR* 3.3 25.4 + - + +
125C ASP* 5.5 0.8 - - - +
126C ALA* 3.7 33.4 + - + +
127C PHE* 4.7 0.8 - - - +
143C VAL* 1.3 80.0 - - - +
145C VAL* 1.3 72.1 + - - +
244C TRP* 3.1 50.7 - - + +
254C ILE* 5.2 8.7 - - - +
286C LEU* 3.3 11.9 - - + +
288C ASP* 2.6 34.6 + - + -
290C GLY* 5.8 0.6 - - - -
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Residues in contact with VAL 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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67C ILE* 4.0 20.6 - - + -
68C LYS 3.7 6.1 - - - -
69C LYS* 5.0 0.7 - - - -
143C VAL* 4.0 20.4 - - + -
144C ARG* 1.3 80.4 - - - +
146C SER* 1.3 70.6 + - - +
149C THR* 4.6 10.5 - - - +
154C ILE* 5.2 12.8 - - + -
285C ILE* 4.3 14.6 - - + -
286C LEU 2.9 7.2 + - - +
287C VAL* 3.8 24.2 - - + -
288C ASP* 2.9 31.4 + - - +
301C LEU* 4.5 7.6 - - + -
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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