Contacts of the helix formed by residues 87 - 94 (chain D) in PDB entry 2G4C
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 SER 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70D LEU* 6.0 1.3 - - - -
83D LYS 5.9 0.4 - - - -
84D GLN* 3.6 20.4 + - - -
85D GLN 3.4 2.4 + - - -
86D LEU* 1.3 76.9 - - - +
88D ARG* 1.3 100.7 + - - +
90D SER* 3.4 15.0 + - - -
91D LEU* 3.0 29.9 + - - +
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Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D SER* 1.3 93.9 + - - +
89D ASP* 1.3 105.2 + - - +
91D LEU* 4.1 4.7 - - - +
92D LEU* 3.5 30.4 + - - +
295D TRP* 5.3 15.8 - - + -
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Residues in contact with ASP 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ARG* 1.3 116.1 + - - +
90D SER* 1.3 56.2 + - - +
92D LEU* 3.4 3.2 + - - +
93D SER* 2.7 41.3 + - - -
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Residues in contact with SER 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D GLN 5.4 0.2 + - - -
85D GLN* 3.5 25.0 + - - -
87D SER* 3.4 14.0 + - - -
88D ARG* 5.7 0.2 + - - -
89D ASP* 1.3 77.1 - - - +
91D LEU* 1.3 53.6 + - - +
93D SER* 2.9 8.0 + - - -
94D GLY 2.7 13.9 + - - -
95D CYS* 2.6 52.6 + - - +
96D HIS* 4.2 2.5 - - - -
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D LEU* 4.0 14.6 - - + -
79D LEU* 4.4 13.9 - - + -
86D LEU* 3.3 51.8 - - + -
87D SER 3.0 18.5 + - - +
88D ARG* 4.1 5.2 - - - +
90D SER* 1.3 75.9 - - - +
92D LEU* 1.3 61.4 + - + +
94D GLY* 3.4 7.3 + - - -
96D HIS* 3.5 32.8 + - + +
234D LYS* 4.6 4.9 + - - -
343D ASP* 6.0 0.5 - - - +
347D LEU* 3.9 37.0 - - + +
351D TYR* 6.1 4.5 - - + +
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Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ARG* 3.5 15.5 + - + +
89D ASP* 3.4 4.5 + - - +
90D SER 3.3 0.2 - - - -
91D LEU* 1.3 74.5 - - + +
93D SER* 1.3 57.3 + - - +
94D GLY 2.6 15.2 + - - -
234D LYS* 3.4 12.9 + - - +
293D PHE* 4.7 5.6 - - + -
295D TRP* 3.5 37.0 - - + +
298D GLU* 3.7 25.1 - - + +
344D ARG* 2.8 55.7 + - + +
347D LEU* 4.5 13.0 - - + -
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Residues in contact with SER 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ASP* 2.7 27.3 + - - -
90D SER* 2.9 11.1 + - - -
92D LEU* 1.3 71.8 - - - +
94D GLY* 1.3 60.5 + - - +
95D CYS* 3.1 19.1 + - - +
218D VAL* 4.2 30.3 - - - +
232D GLY* 4.4 5.5 - - - -
234D LYS* 4.7 6.5 - - - +
344D ARG* 4.7 1.3 - - - +
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Residues in contact with GLY 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D SER 2.7 5.5 + - - -
91D LEU 3.7 8.3 - - - -
92D LEU 2.6 10.1 + - - -
93D SER* 1.3 79.7 - - - +
95D CYS* 1.3 55.7 + - - +
96D HIS* 3.4 18.1 + - - +
232D GLY* 4.6 0.2 - - - -
233D GLU* 3.0 38.6 + - - +
234D LYS* 4.1 10.1 - - - -
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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