Contacts of the helix formed by residues 82 - 88 (chain L) in PDB entry 3EXG
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 THR 82 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37L TYR* 3.7 18.8 - - - +
80L PHE* 3.4 12.9 - - - +
81L MET* 1.3 87.1 - - + +
83L PHE* 1.3 66.2 + - - +
84L ASN* 2.8 30.5 + - - +
85L PHE* 3.1 35.3 + - + +
117L PRO* 3.5 18.8 - - + -
128L HIS* 5.1 8.8 - - + +
173L GLU* 5.6 1.3 - - - +
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Residues in contact with PHE 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80L PHE* 4.1 17.0 - + - -
82L THR* 1.3 71.3 - - - +
84L ASN* 1.3 62.2 + - - +
86L SER* 2.3 50.6 + - - +
87L MET 3.7 1.9 + - - -
114L PHE* 4.1 16.8 - - + -
115L ARG 4.0 1.6 - - - -
116L GLY* 3.2 41.1 - - - -
117L PRO 3.0 19.0 + - - +
118L ASN* 4.0 6.9 - - + +
132L PHE* 3.8 25.0 - - + -
136L TYR* 3.7 18.6 - + - -
168L VAL* 3.8 24.7 - - + -
169L VAL 3.6 6.5 - - - -
170L LEU* 3.5 25.6 - - + -
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Residues in contact with ASN 84 (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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137I ILE* 4.8 7.3 - - + +
91J ASP* 5.3 0.7 - - - +
95J ASN* 4.5 3.1 + - - +
99J LYS* 5.4 0.3 + - - -
82L THR* 2.8 27.5 + - - +
83L PHE* 1.3 79.0 - - - +
85L PHE* 1.3 63.3 + - + +
86L SER 3.3 0.2 + - - -
87L MET* 3.4 25.8 + - - +
88L GLN* 5.6 0.7 - - - +
118L ASN* 6.2 0.4 - - - +
119L GLY 5.3 3.0 + - - +
127L GLN 3.3 24.9 - - - +
128L HIS* 3.2 26.0 + - + +
129L SER* 3.3 2.9 + - - +
130L GLN* 3.2 36.8 + - - +
132L PHE* 3.7 11.3 - - - -
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Residues in contact with PHE 85 (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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136I GLY 4.1 17.0 - - - -
137I ILE* 4.2 26.5 - - + -
138I VAL* 4.8 9.0 - - + -
28L GLU* 5.4 1.6 - - - -
59L GLU* 3.5 42.3 - - + +
80L PHE* 4.6 4.5 - - + -
81L MET* 3.6 28.9 - - + +
82L THR* 3.1 41.6 + - + +
83L PHE 3.1 0.4 - - - -
84L ASN* 1.3 77.6 - - + +
86L SER* 1.3 60.8 + - - +
87L MET 3.3 0.2 - - - -
88L GLN* 3.4 17.4 + - - +
128L HIS* 4.0 22.9 - + - -
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Residues in contact with SER 86 (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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80L PHE* 3.5 41.4 - - - -
82L THR 3.7 1.2 + - - -
83L PHE* 2.3 44.3 + - - +
85L PHE* 1.3 69.3 - - - +
87L MET* 1.3 57.0 + - - -
88L GLN 3.0 2.7 - - - -
89L ALA 2.8 20.6 + - - +
90L ILE* 2.9 13.2 + - - +
93L VAL* 5.8 0.6 - - - +
132L PHE* 5.2 0.9 - - - -
136L TYR* 2.9 23.8 + - - -
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Residues in contact with MET 87 (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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87J MET 4.0 3.8 - - - +
88J GLN 5.2 0.5 - - - +
90J ILE* 3.7 22.6 - - + +
91J ASP* 3.9 19.2 + - + +
94J ILE* 4.1 26.0 - - + -
95J ASN* 2.8 43.1 - - - +
84L ASN* 3.4 13.5 + - + +
85L PHE 3.3 1.2 - - - -
86L SER* 1.3 78.5 + - - +
88L GLN* 1.3 64.0 + - - +
90L ILE* 3.5 23.6 + - + +
130L GLN* 4.6 1.6 - - - +
132L PHE* 3.7 34.3 - - + -
135L TRP* 4.2 15.5 - - + -
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Residues in contact with GLN 88 (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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137I ILE* 3.8 14.5 - - + +
138I VAL 3.5 9.7 - - - +
172I GLN* 3.3 39.6 + - - +
174I GLN* 3.7 4.8 + - - +
60J MET* 4.0 29.5 - - + +
87J MET 4.9 0.9 - - - +
88J GLN 4.6 5.1 - - - +
91J ASP* 4.4 12.3 - - + +
177K GLU* 4.6 4.6 + - - -
59L GLU* 3.8 19.4 - - + +
60L MET* 3.4 37.1 - - - +
84L ASN 5.6 0.4 - - - +
85L PHE* 3.4 16.2 + - - +
86L SER 3.0 0.2 - - - -
87L MET* 1.3 81.8 - - + +
89L ALA* 1.3 57.3 + - - +
90L ILE 3.3 0.8 + - - -
91L ASP 4.7 0.3 + - - -
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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