Contacts of the helix formed by residues 100 - 106 (chain A) in PDB entry 2GR9
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 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLY 3.0 8.4 + - - -
99A VAL* 1.3 75.0 - - - +
101A ILE* 1.3 69.4 + - - +
102A SER* 3.2 26.5 - - - +
103A SER* 3.0 28.2 + - - -
104A ILE* 3.3 12.6 - - - +
119A ARG* 4.3 2.9 + - - +
164A GLU* 3.3 20.2 - - - +
269A GLN* 4.4 12.9 + - - +
273A ASP* 5.2 4.1 + - - -
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Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL 3.9 0.6 + - - -
100A THR* 1.3 70.3 - - - +
102A SER* 1.3 67.5 + - - +
104A ILE* 3.0 9.4 + - - +
105A GLU* 2.9 28.3 + - - +
117A VAL* 3.4 34.3 - - + +
119A ARG* 3.3 20.4 - - + +
136A ALA* 3.7 29.6 - - + +
137A THR 4.1 9.6 - - - +
138A GLY* 3.7 13.7 - - - -
164A GLU* 2.7 45.8 + - + +
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Residues in contact with SER 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A THR* 3.2 15.7 - - - +
101A ILE* 1.3 77.9 - - - +
103A SER* 1.3 58.5 + - - +
104A ILE 2.5 14.0 + - - -
105A GLU* 2.7 21.2 + - - -
106A LYS* 2.9 44.7 + - - +
164A GLU* 4.9 0.4 + - - -
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A LEU* 4.5 2.1 - - - +
99A VAL* 3.8 10.9 - - - +
100A THR* 3.0 32.0 + - - -
102A SER* 1.3 79.8 + - - +
104A ILE* 1.3 57.5 + - - +
106A LYS* 3.9 5.7 - - - +
107A LYS* 3.2 27.8 - - - +
273A ASP* 5.2 10.1 - - - -
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Residues in contact with ILE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 4.8 7.2 - - + -
75A ILE* 3.3 31.4 - - + -
79A LEU* 3.1 44.3 - - + +
92A VAL* 5.3 0.4 - - + -
94A SER* 4.9 10.8 - - - +
99A VAL* 3.4 16.6 - - + -
100A THR 3.3 14.4 - - - +
101A ILE* 3.0 9.1 + - - +
102A SER 2.5 5.7 + - - -
103A SER* 1.3 77.5 + - - +
105A GLU* 1.3 71.4 + - - +
107A LYS* 3.7 1.4 - - - +
108A LEU* 3.0 31.9 + - + +
117A VAL* 4.4 17.5 - - + -
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ILE* 2.9 19.1 + - - +
102A SER* 2.7 14.8 + - - +
104A ILE* 1.3 72.0 - - - +
106A LYS* 1.3 61.7 + - + +
107A LYS 2.5 17.2 + - - -
108A LEU* 2.6 18.3 + - - -
109A SER* 2.7 17.4 + - - -
115A PRO* 4.1 18.5 - - + +
117A VAL* 3.2 33.0 + - + +
139A THR* 2.5 48.4 + - - +
140A HIS* 3.8 13.5 + - + +
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER* 2.9 42.0 + - - +
103A SER* 3.9 6.3 - - - +
105A GLU* 1.3 76.9 - - + +
107A LYS* 1.3 66.9 + - - +
109A SER* 3.9 9.9 - - - +
139A THR* 6.0 2.5 - - - -
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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