Contacts of the helix formed by residues 123 - 135 (chain A) in PDB entry 1DC2
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 HIS 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ALA 2.6 26.9 + - - +
87A ARG* 2.7 33.5 + - - -
88A GLU 3.4 5.4 - - - -
89A GLY* 3.0 20.2 + - - -
118A ALA* 2.7 24.6 + - - +
121A LEU* 3.4 33.6 - - + +
122A GLY* 1.3 79.5 + - - -
124A ARG* 1.3 50.9 + - - +
125A ASP* 3.2 4.0 - - - -
126A VAL* 2.6 26.8 + - + -
127A ALA 2.5 32.8 + - - -
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Residues in contact with ARG 124 (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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118A ALA 4.0 0.4 + - - -
119A GLU* 4.9 18.7 - - + +
122A GLY* 3.5 6.5 + - - -
123A HIS* 1.3 77.0 - - - +
125A ASP* 1.3 71.2 + - - +
126A VAL 2.8 0.3 + - - -
127A ALA* 2.9 9.8 + - - -
128A ARG* 2.7 49.5 + - - +
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Residues in contact with ASP 125 (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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91A LEU* 3.0 27.3 - - + +
123A HIS* 3.2 1.4 - - - -
124A ARG* 1.3 81.3 + - - +
126A VAL* 1.3 64.0 + - + +
128A ARG* 4.4 5.7 - - - +
129A TYR* 3.3 15.2 + - - +
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Residues in contact with VAL 126 (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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86A ALA* 3.3 21.3 - - + -
89A GLY* 3.8 25.1 - - - +
91A LEU* 4.0 17.0 - - + +
94A LEU* 3.0 38.8 - - + -
123A HIS* 2.6 32.4 + - + +
125A ASP* 1.3 78.8 - - + +
127A ALA* 1.3 55.0 + - - +
128A ARG 3.2 0.2 - - - -
129A TYR* 4.5 0.2 - - - -
130A LEU* 2.6 40.7 + - + +
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Residues in contact with ALA 127 (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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115A VAL* 2.8 32.2 - - - +
118A ALA* 3.5 10.4 - - - +
119A GLU* 3.3 51.1 - - + +
123A HIS 2.5 16.3 + - - +
124A ARG* 3.5 4.5 - - - +
126A VAL* 1.3 72.9 - - - +
128A ARG* 1.3 63.8 + - + +
130A LEU* 3.2 2.4 - - - +
131A ARG* 3.0 5.9 + - - +
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Residues in contact with ARG 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 5.9 4.3 - - + -
124A ARG* 2.7 46.4 + - - +
125A ASP* 4.4 4.7 - - - +
127A ALA* 1.3 72.2 - - + +
129A TYR* 1.3 65.3 + - - +
130A LEU 2.9 1.4 + - - -
131A ARG* 3.0 20.8 + - - +
132A ALA* 3.3 9.8 + - - +
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Residues in contact with TYR 129 (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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91A LEU* 3.6 31.9 - - + -
94A LEU* 4.5 17.9 - - + -
95A VAL* 4.1 22.2 - - + +
98A HIS* 4.6 12.0 + - - +
104A LEU* 5.6 0.4 - - + -
125A ASP 3.3 18.2 + - - +
126A VAL 3.4 2.9 + - - +
128A ARG* 1.3 79.5 - - - +
130A LEU* 1.3 65.3 + - + +
132A ALA* 3.2 10.2 + - + +
133A ALA* 2.9 38.7 + - + +
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Residues in contact with LEU 130 (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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82A VAL* 4.0 3.1 - - + -
86A ALA* 3.5 22.7 - - + -
94A LEU* 2.9 31.4 - - + -
104A LEU* 3.0 28.5 - - + -
114A PRO* 3.4 16.2 - - + +
115A VAL* 3.3 32.8 - - + +
118A ALA* 3.9 1.6 - - + -
126A VAL 2.6 24.6 + - - +
127A ALA 3.2 6.1 - - - +
129A TYR* 1.3 77.0 - - + +
131A ARG* 1.3 55.6 + - - +
133A ALA* 2.9 1.4 + - - +
134A ALA* 2.5 39.5 + - + +
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Residues in contact with ARG 131 (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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115A VAL* 3.0 34.7 - - + +
116A ASP* 4.9 5.0 + - - -
119A GLU* 3.9 25.0 + - - -
127A ALA 4.0 3.4 - - - -
128A ARG* 3.0 13.6 + - - +
130A LEU* 1.3 79.5 - - - +
132A ALA* 1.3 58.4 + - - +
134A ALA* 4.7 1.8 - - - -
135A GLY* 2.9 34.1 + - - +
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Residues in contact with ALA 132 (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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128A ARG 3.3 6.6 + - - +
129A TYR* 3.2 15.6 + - + +
130A LEU 3.0 0.6 - - - -
131A ARG* 1.3 81.9 - - - +
133A ALA* 1.3 59.6 + - - +
135A GLY* 4.1 4.2 + - - -
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Residues in contact with ALA 133 (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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98A HIS* 3.4 38.2 - - + +
104A LEU* 3.5 24.6 - - + +
129A TYR* 2.9 34.0 + - + +
130A LEU 2.9 3.0 + - - +
132A ALA* 1.3 77.8 - - - +
134A ALA* 1.3 60.8 + - - +
135A GLY 3.5 0.2 - - - -
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Residues in contact with ALA 134 (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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104A LEU* 2.7 35.4 - - + +
105A ASP* 2.7 29.1 - - - +
113A LEU* 4.7 15.5 - - + -
114A PRO* 5.6 1.8 - - + -
115A VAL* 5.1 2.7 - - + -
130A LEU* 2.5 24.7 + - + +
131A ARG* 4.7 1.8 - - - -
133A ALA* 1.3 73.9 - - - +
135A GLY* 1.3 69.1 + - - +
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Residues in contact with GLY 135 (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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105A ASP* 4.1 5.8 - - - +
113A LEU* 5.0 6.9 - - - +
131A ARG* 2.9 26.6 + - - +
132A ALA 4.1 4.3 + - - -
133A ALA 3.5 1.8 - - - -
134A ALA* 1.3 91.8 - - - +
136A GLY* 1.3 59.4 + - - -
138A ARG* 5.6 1.1 - - - -
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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