Contacts of the helix formed by residues 104 - 110 (chain D) in PDB entry 2V32
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 ARG 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D CYS* 3.7 29.6 + - - +
101D ASP* 2.9 23.5 + - - -
102D GLU* 2.7 32.4 + - - +
103D THR* 1.3 78.1 + - - +
105D GLU* 1.3 64.7 + - - +
106D LEU 3.2 2.7 - - - -
107D ALA* 4.2 5.8 - - + -
108D VAL* 3.1 31.7 + - + +
119D THR* 3.5 25.9 - - - +
123D MET* 3.1 31.6 - - - +
124D PRO* 2.8 49.5 + - + +
125D LEU* 3.9 8.5 - - - +
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Residues in contact with GLU 105 (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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12D PHE* 5.9 2.1 - - - +
13D GLU 5.1 8.4 - - - +
101D ASP* 3.4 4.4 + - - +
103D THR* 3.0 34.4 + - - +
104D ARG* 1.3 77.5 - - - +
106D LEU* 1.3 68.3 + - + +
108D VAL* 3.7 3.6 - - - +
109D LYS* 2.8 29.5 + - - +
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Residues in contact with LEU 106 (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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10D PRO* 5.7 1.3 - - + -
12D PHE* 3.7 55.6 - - + -
13D GLU 5.7 1.3 - - - +
14D ALA* 4.7 3.8 - - + -
69D LEU* 3.6 23.6 - - + -
99D ILE* 4.4 8.1 - - + -
101D ASP* 3.0 19.1 + - + +
105D GLU* 1.3 87.1 - - + +
107D ALA* 1.3 66.7 + - - +
108D VAL 3.0 1.8 - - - -
109D LYS* 4.2 13.5 - - + +
110D LEU* 2.9 36.5 + - + +
112D MET* 3.7 11.2 - - + +
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Residues in contact with ALA 107 (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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71D CYS* 4.3 5.8 - - - -
101D ASP* 3.0 16.8 + - - +
104D ARG* 3.8 14.1 - - + +
106D LEU* 1.3 75.6 - - - +
108D VAL* 1.3 58.7 + - - +
111D GLY 3.4 0.5 + - - -
112D MET* 2.9 44.4 + - + +
113D VAL* 3.7 21.2 + - + +
125D LEU 5.1 0.4 - - - -
126D THR* 3.6 21.1 - - + +
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Residues in contact with VAL 108 (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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2D GLY 4.4 3.5 + - - -
104D ARG* 3.1 24.0 + - + +
105D GLU* 3.8 3.1 - - - +
106D LEU 3.0 0.4 - - - -
107D ALA* 1.3 78.1 - - - +
109D LYS* 1.3 68.3 + - - +
110D LEU 3.2 1.3 - - - -
111D GLY* 3.0 13.0 + - - -
113D VAL* 4.0 19.1 - - + -
124D PRO* 5.6 5.4 - - + -
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Residues in contact with LYS 109 (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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2D GLY 3.3 23.4 + - - +
3D ILE* 5.4 0.2 - - - +
10D PRO* 4.1 35.4 - - + +
12D PHE* 6.4 0.4 - - + -
105D GLU 2.8 21.2 + - - +
106D LEU* 4.1 13.7 - - + +
108D VAL* 1.3 74.9 - - - +
110D LEU* 1.3 62.8 + - + +
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Residues in contact with LEU 110 (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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2D GLY* 3.9 12.4 - - - -
3D ILE* 4.4 8.9 + - + -
9D PHE* 3.5 42.4 - - + -
10D PRO* 3.8 26.9 - - + -
12D PHE* 5.4 1.6 - - + -
34D LEU* 4.2 8.5 - - + -
106D LEU* 2.9 27.3 + - + +
109D LYS* 1.3 79.1 - - + +
111D GLY* 1.3 64.4 + - - +
112D MET* 3.2 26.5 + - + -
131D PHE* 3.6 32.8 - - + -
144D LEU* 5.1 1.0 - - - +
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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