Contacts of the helix formed by residues 87 - 92 (chain C) in PDB entry 2GD4
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 PHE 87 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C ILE* 3.2 21.7 + - + +
84C SER 3.5 3.9 + - - +
85C THR 3.5 0.4 - - - -
86C ALA* 1.3 79.2 - - + +
88C ALA* 1.3 56.3 + - - +
89C MET 3.2 0.7 - - - -
90C THR* 3.4 11.9 + - - -
91C LYS* 3.1 22.9 + - - +
102C LEU* 3.7 8.7 - - + +
106C PHE* 3.2 37.0 - + + -
108C PHE* 4.8 4.0 - - - -
215C LEU* 3.4 27.4 - - + -
331C LEU* 4.0 19.5 - - + -
335C LEU* 3.2 30.5 - - + -
340C LEU* 3.9 0.9 - - + -
343C LEU* 3.3 35.2 - - + -
344C PHE* 3.6 12.6 - + - -
367C ALA* 3.8 11.2 - - + -
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Residues in contact with ALA 88 (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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84C SER 3.5 3.2 + - - +
85C THR 2.8 17.9 + - - +
86C ALA 2.6 3.4 + - - -
87C PHE* 1.3 73.0 - - - +
89C MET* 1.3 64.0 + - + +
90C THR 3.0 4.9 - - - -
91C LYS* 3.8 12.4 - - - +
92C LEU* 3.3 21.3 + - - +
108C PHE* 4.5 2.7 - - + -
119C ILE* 4.4 8.9 - - + +
120C HIS* 3.9 9.5 + - - +
123C PHE* 3.4 34.5 - - + -
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Residues in contact with MET 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C THR* 4.1 13.5 - - + +
86C ALA* 2.6 12.5 + - - +
88C ALA* 1.3 78.9 - - + +
90C THR* 1.3 59.5 + - - +
92C LEU* 3.6 15.9 - - - +
120C HIS* 3.4 45.1 - - + +
123C PHE* 5.3 0.2 - - + -
146C LEU* 4.8 8.7 - - + -
158C TYR* 2.7 45.7 + - - +
162C SER* 5.0 7.4 - - - +
165C VAL* 3.8 14.4 - - + +
166C TYR* 3.6 48.2 - - + -
354C ILE* 4.6 0.3 - - - +
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Residues in contact with THR 90 (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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86C ALA 3.9 2.4 + - - -
87C PHE* 3.5 20.3 - - - +
88C ALA 3.0 0.2 - - - -
89C MET* 1.3 79.8 - - - +
91C LYS* 1.3 66.0 + - - +
92C LEU 2.7 5.8 + - - -
93C GLY 2.8 15.0 + - - +
94C ALA* 3.2 11.4 + - - +
102C LEU* 3.5 10.1 - - + -
146C LEU* 5.3 3.5 - - - +
158C TYR* 5.0 0.2 - - - -
213C LEU* 6.1 0.9 - - + -
215C LEU* 4.2 16.5 - - - +
343C LEU* 3.5 32.8 - - + -
351C LEU* 3.5 23.3 - - + +
354C ILE* 5.3 5.6 - - + -
364C VAL* 5.0 2.9 - - + -
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Residues in contact with LYS 91 (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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21C CYS 5.1 1.6 - - - +
87C PHE 3.1 13.0 + - - +
88C ALA* 3.8 10.8 - - - +
90C THR* 1.3 79.2 - - - +
92C LEU* 1.3 67.7 + - - +
93C GLY 3.5 0.2 + - - -
94C ALA* 3.5 8.2 + - - +
99C LEU* 3.4 35.3 - - + +
102C LEU* 3.5 15.0 - - + +
103C MET* 3.6 20.6 - - - -
108C PHE* 4.6 10.5 - - + -
116C SER 4.7 5.4 - - - +
117C ASP* 5.2 2.2 - - - +
119C ILE* 4.1 28.9 - - + -
120C HIS* 6.4 0.4 - - + -
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Residues in contact with LEU 92 (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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19C PRO* 4.0 26.0 - - + +
20C MET 4.2 13.3 - - - +
21C CYS 4.7 1.9 - - - +
88C ALA 3.3 13.1 + - - +
89C MET* 3.6 20.9 - - - +
90C THR 2.7 0.6 + - - -
91C LYS* 1.3 85.9 - - - +
93C GLY* 1.3 59.0 + - - +
94C ALA 3.6 1.9 + - - +
120C HIS* 3.5 32.8 - - + +
158C TYR* 3.4 32.1 - - + -
161C ILE* 3.7 36.1 - - + -
162C SER 5.1 0.7 - - - +
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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