Contacts of the strand formed by residues 86 - 93 (chain B) in PDB entry 3LPK
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 GLN 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B THR* 3.2 2.9 - - - -
81B VAL* 2.9 45.6 + - + +
84B PRO* 3.9 7.6 + - + +
85B PRO* 1.3 73.8 - - - +
87B THR* 1.3 65.2 + - - +
88B LEU* 3.6 5.6 + - + +
112B TYR 3.8 4.9 - - - +
113B TYR* 3.6 14.0 - - - -
114B GLN* 2.8 55.3 + - - +
117B LEU* 4.1 14.2 + - - +
118B SER* 4.1 17.6 - - - -
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Residues in contact with THR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU* 3.5 39.7 - - + +
79B MET 3.5 5.8 - - - +
80B THR* 3.9 12.8 - - + +
85B PRO* 3.9 4.5 + - - +
86B GLN* 1.3 71.2 - - - +
88B LEU* 1.3 74.6 + - - +
111B ARG* 3.3 32.8 + - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU* 3.7 1.7 - - - +
79B MET* 2.9 36.2 + - - +
81B VAL* 4.0 22.0 - - + -
86B GLN* 3.6 9.8 + - + +
87B THR* 1.3 89.9 - - - +
89B ASN* 1.3 61.9 + - - +
90B ILE* 3.8 13.7 + - + +
101B VAL* 3.9 32.8 - - + -
102B GLY 5.0 0.2 - - - +
111B ARG* 3.8 20.4 - - + +
112B TYR* 4.2 20.6 - - - +
113B TYR* 4.2 12.3 - - + +
177B GLU* 3.6 20.0 - - + +
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Residues in contact with ASN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ARG* 4.1 3.2 - - - +
76B TYR* 3.5 26.3 - - + -
77B VAL 3.7 1.6 - - - -
78B GLU* 3.8 25.5 + - - +
88B LEU* 1.3 71.2 - - - +
90B ILE* 1.3 64.6 + - - +
111B ARG* 3.2 14.0 + - - +
175B ASN* 3.0 35.5 + - - +
176B TRP* 3.4 3.3 - - - -
177B GLU* 2.8 37.2 + - - +
455B TLA 2.9 25.0 + - - +
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Residues in contact with ILE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B TYR* 3.5 4.7 - - - +
77B VAL* 2.7 44.2 + - + +
79B MET* 3.5 34.1 - - + -
81B VAL* 6.3 0.4 - - + -
88B LEU* 3.9 18.8 - - + +
89B ASN* 1.3 83.7 - - - +
91B LEU* 1.3 65.6 + - - +
92B VAL 3.4 0.3 + - - -
99B PHE* 4.1 4.9 - - + -
101B VAL* 3.9 19.1 - - + -
178B GLY* 3.6 18.8 - - - +
179B ILE* 3.4 9.2 - - - +
180B LEU* 3.3 37.2 - - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B GLN 4.4 0.2 - - - +
74B GLY* 3.6 27.8 - - - -
75B TYR 3.4 19.1 - - - +
76B TYR* 3.8 4.5 - - - +
90B ILE* 1.3 70.3 - - - +
92B VAL* 1.3 68.5 + - - +
93B ASP* 3.4 4.2 + - + -
176B TRP* 3.8 35.4 - - + +
178B GLY 2.9 19.5 + - - +
179B ILE* 4.0 17.7 - - + +
180B LEU* 2.8 30.5 + - - +
290B SER 5.3 4.0 - - - +
291B GLY* 5.1 2.7 - - - -
456B Z76 3.8 32.3 - - + -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 4.1 17.7 - - + -
75B TYR* 2.8 26.4 + - + +
77B VAL* 4.0 26.0 - - + +
90B ILE 4.1 1.1 - - - +
91B LEU* 1.3 73.2 - - - +
93B ASP* 1.3 55.2 + - - +
180B LEU* 4.3 5.8 - - + -
182B LEU* 3.6 25.6 - - + -
213B LEU* 4.0 23.8 - - + -
215B LEU* 6.0 1.3 - - + -
235B MET* 4.1 12.6 - - + -
290B SER* 2.7 35.6 + - - +
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 4.4 2.9 - - + +
92B VAL* 1.3 75.2 - - - +
94B THR* 1.3 57.9 + - - +
95B GLY* 2.8 20.8 + - - -
96B SER* 2.5 23.9 + - - +
179B ILE* 3.4 25.6 - - + +
180B LEU 3.1 15.7 + - - +
181B GLY* 3.4 2.6 - - - -
182B LEU* 2.8 24.7 + - - -
289B ASP* 3.0 14.6 - - - +
290B SER* 3.5 1.1 - - - -
291B GLY* 3.1 14.5 - - - +
456B Z76 2.6 20.2 + - - +
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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