Contacts of the strand formed by residues 68 - 75 (chain L) in PDB entry 3E8E
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 HIS 68 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46L ILE* 3.5 28.2 - - + +
59L LEU* 3.7 20.2 - - + +
60L VAL 3.4 5.0 + - - +
61L LYS* 4.6 10.5 - - + +
66L GLY 4.1 10.9 + - - -
67L ASN* 1.3 74.6 - - - +
69L TYR* 1.3 74.8 + - - +
122L TYR* 4.3 13.2 + - + +
321L PRO* 3.6 31.9 + - + -
322L GLY* 3.5 27.4 - - - +
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Residues in contact with TYR 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43L PHE* 4.3 4.0 - + - -
59L LEU* 3.4 4.3 - - - +
60L VAL* 2.7 41.6 + - + +
62L HIS* 3.8 30.5 - + + -
65L THR* 4.7 1.5 - - + +
67L ASN* 3.6 38.1 + - + -
68L HIS* 1.3 79.8 - - - +
70L ALA* 1.3 57.9 + - - +
107L GLU* 3.5 36.4 + - + +
108L PHE* 4.5 13.8 - + - -
119L VAL* 3.6 22.7 - - + -
120L MET 3.5 17.5 - - - +
121L GLU* 4.6 4.5 - - + -
122L TYR* 3.8 9.0 - - - -
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Residues in contact with ALA 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49L LEU* 4.6 1.1 - - + -
57L VAL* 4.4 5.8 - - + -
58L MET 3.3 7.9 - - - +
59L LEU* 4.6 1.1 - - - +
69L TYR* 1.3 73.8 - - - +
71L MET* 1.3 59.6 + - - +
119L VAL* 3.5 4.2 - - - +
120L MET* 2.9 49.9 + - + +
121L GLU 4.1 1.1 - - - +
122L TYR* 3.8 9.6 - - + +
351L G98 3.8 38.1 - - + +
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Residues in contact with MET 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L LEU* 4.0 20.6 - - + -
43L PHE* 3.4 37.7 - - + -
45L ARG* 5.5 2.0 - - - -
56L ARG 3.8 0.2 - - - +
57L VAL* 3.4 3.5 - - - -
58L MET* 2.7 43.1 + - + +
60L VAL* 4.0 22.7 - - + -
70L ALA* 1.3 73.8 - - - +
72L LYS* 1.3 64.1 + - - +
73L ILE* 3.7 19.4 + - + +
110L PHE* 3.9 9.6 - - + -
117L TYR* 4.1 11.0 - - + -
118L MET 3.4 8.5 - - - +
119L VAL* 3.4 27.6 - - + -
120L MET* 3.8 1.8 - - - -
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Residues in contact with LYS 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L PHE* 5.5 0.2 - - - -
56L ARG 3.6 8.1 - - - +
57L VAL* 4.3 8.3 - - + -
71L MET* 1.3 71.7 - - - +
73L ILE* 1.3 61.5 + - - +
74L LEU* 3.8 15.8 - - + +
91L GLU* 2.9 34.0 + - - +
116L LEU 3.5 0.9 - - - +
117L TYR* 3.3 7.1 - - - -
118L MET* 2.9 49.4 + - + +
120L MET* 3.3 11.8 - - + +
184L ASP* 3.4 13.1 + - - -
186L GLY* 4.8 1.8 - - - -
351L G98 3.3 69.3 + - + +
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Residues in contact with ILE 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L LEU* 5.8 0.7 - - + -
45L ARG* 4.7 3.4 - - + +
55L GLY* 3.0 4.7 - - - -
56L ARG* 2.8 42.4 + - + +
58L MET* 4.0 25.4 - - + -
71L MET* 4.2 17.9 - - + +
72L LYS* 1.3 74.8 - - - +
74L LEU* 1.3 64.2 + - - +
115L ASN* 3.8 22.4 - - + +
116L LEU 3.4 3.1 - - - -
117L TYR* 3.6 33.4 - - + -
335L ILE* 3.7 37.5 - - + -
351L G98 4.7 0.5 - - - -
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Residues in contact with LEU 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L PHE* 3.6 30.7 - - + +
72L LYS* 3.8 24.2 - - + +
73L ILE* 1.3 76.3 - - - +
75L ASP* 1.3 62.2 + - - +
76L LYS 3.4 0.3 + - - -
79L VAL* 4.2 8.7 - - + -
88L THR* 3.4 33.4 - - + -
91L GLU* 4.7 2.0 - - - +
115L ASN* 3.1 9.6 - - - -
116L LEU* 2.8 57.9 + - + +
118L MET* 3.2 32.5 - - + -
351L G98 4.8 1.8 - - + -
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Residues in contact with ASP 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L PHE 2.9 16.5 + - - +
55L GLY* 4.4 1.9 - - - -
73L ILE* 4.2 1.0 + - - +
74L LEU* 1.3 68.5 - - - +
76L LYS* 1.3 67.9 + - - +
77L GLN* 3.3 18.3 + - - +
78L LYS* 3.3 45.9 + - + +
79L VAL* 3.0 24.4 + - - +
114L SER* 3.4 11.3 - - - +
115L ASN* 3.3 13.6 + - - +
336L ARG* 4.8 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