Contacts of the helix formed by residues 123 - 140 (chain A) in PDB entry 2D3Y
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ARG* 3.7 23.1 - - - +
121A LYS 4.9 0.9 - - - +
122A PRO* 1.3 76.5 - - - +
124A PRO* 1.3 76.1 - - + +
125A GLU* 3.5 8.9 + - - +
126A GLU* 2.8 38.6 + - - +
127A LEU* 2.9 23.2 + - - +
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Residues in contact with PRO 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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122A PRO 4.6 0.9 - - - +
123A THR* 1.3 88.9 - - + +
125A GLU* 1.3 55.7 + - - +
127A LEU* 3.3 14.1 + - + +
128A ARG* 2.8 52.3 + - - +
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Residues in contact with GLU 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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123A THR* 3.1 8.6 - - - +
124A PRO* 1.3 81.0 - - - +
126A GLU* 1.3 58.2 + - + +
128A ARG* 3.3 27.6 + - + +
129A ALA* 3.0 27.4 + - + +
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Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A CYS* 4.0 21.8 - - + +
18A ARG* 2.8 53.1 + - - +
19A LEU* 3.5 34.0 + - + +
113A VAL* 4.3 3.3 - - + +
122A PRO* 3.2 10.3 - - + +
123A THR* 2.8 30.4 + - - +
125A GLU* 1.3 75.4 - - + +
127A LEU* 1.3 65.2 + - - +
129A ALA* 3.1 2.8 + - - +
130A CYS* 3.0 26.0 + - - +
220A SF4 5.0 0.3 - - - -
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Residues in contact with LEU 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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58A LEU* 4.5 0.4 - - + -
112A ALA* 3.9 20.8 - - + +
113A VAL* 3.5 26.7 - - + -
122A PRO* 4.1 14.4 - - + +
123A THR 2.9 20.2 + - - +
124A PRO* 3.3 15.9 + - + +
126A GLU* 1.3 78.2 - - - +
128A ARG* 1.3 62.6 + - + +
130A CYS* 3.5 1.4 + - - +
131A ALA* 3.3 21.8 + - - +
153A ILE* 3.7 37.7 - - + -
157A ALA* 5.1 5.8 - - + -
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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
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124A PRO* 2.8 47.8 + - - +
125A GLU* 3.6 30.6 + - + +
126A GLU 3.3 0.4 - - - -
127A LEU* 1.3 77.6 - - + +
129A ALA* 1.3 61.2 - - - +
131A ALA* 3.5 17.8 - - - +
132A ARG* 4.5 2.6 + - - -
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Residues in contact with ALA 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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15A LEU* 4.8 6.5 - - + -
16A CYS* 3.8 20.9 - - - -
125A GLU* 3.0 15.2 + - + +
126A GLU 3.1 8.0 + - - +
128A ARG* 1.3 79.4 - - - +
130A CYS* 1.3 61.7 + - - +
131A ALA 3.1 1.6 + - - -
132A ARG* 3.0 43.9 + - - +
220A SF4 3.9 7.0 - - - -
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Residues in contact with CYS 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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112A ALA 3.3 14.6 - - - +
113A VAL* 4.0 5.2 - - + -
114A ARG* 3.3 60.2 + - - -
126A GLU 3.0 15.5 + - - +
127A LEU 3.5 1.5 + - - +
129A ALA* 1.3 72.0 - - - +
131A ALA* 1.3 59.0 + - - +
132A ARG 3.0 2.9 - - - -
133A TRP* 2.8 24.3 + - - +
134A THR 3.2 6.9 + - - -
220A SF4 2.4 35.6 - - - -
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Residues in contact with ALA 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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112A ALA 5.2 0.4 - - - -
127A LEU 3.3 12.0 + - - +
128A ARG* 3.5 17.5 - - - +
129A ALA 3.1 1.0 - - - -
130A CYS* 1.3 77.6 - - - +
132A ARG* 1.3 61.3 + - - +
133A TRP 3.1 0.2 - - - -
134A THR* 3.2 13.1 + - - -
135A GLU* 3.0 29.1 + - + +
161A HIS* 5.4 0.2 + - - -
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Residues in contact with ARG 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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15A LEU* 3.4 40.8 - - - +
128A ARG 4.5 2.2 + - - -
129A ALA* 3.0 30.0 + - - +
130A CYS 3.0 0.8 - - - -
131A ALA* 1.3 78.7 - - - +
133A TRP* 1.3 85.8 + - + +
135A GLU* 3.5 18.0 + - - +
136A VAL* 3.3 26.0 + - - +
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Residues in contact with TRP 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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1A MET* 4.8 3.8 - - + -
6A PHE* 4.0 20.6 - + + -
9A THR* 3.7 42.0 - - + -
10A LEU* 3.6 32.1 - - + -
13A CYS* 3.4 34.2 - - + +
15A LEU* 5.5 0.4 - - + -
114A ARG* 3.7 20.2 - - - +
130A CYS* 2.8 10.8 + - - +
132A ARG* 1.3 97.2 - - + +
134A THR* 1.3 59.3 + - - +
135A GLU 3.2 1.8 - - - -
136A VAL* 3.3 17.5 + - + +
137A GLU* 2.8 33.1 + - - +
220A SF4 3.9 21.5 - - - -
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Residues in contact with THR 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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56A PHE* 3.8 24.6 - - + -
112A ALA* 4.0 4.7 + - - -
114A ARG* 3.1 28.2 + - - +
130A CYS 3.2 5.0 + - - -
131A ALA* 3.2 15.6 + - - -
133A TRP* 1.3 76.9 - - - +
135A GLU* 1.3 58.7 + - - +
137A GLU* 4.5 0.7 - - - +
138A LEU* 2.9 52.4 + - + +
157A ALA* 5.6 2.2 - - + +
158A LEU* 5.4 1.1 - - + -
161A HIS* 4.0 18.2 - - + +
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Residues in contact with GLU 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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131A ALA* 3.0 21.7 + - + +
132A ARG* 3.5 18.1 - - - +
133A TRP 3.2 0.2 - - - -
134A THR* 1.3 77.3 - - - +
136A VAL* 1.3 64.0 + - + +
138A LEU* 4.5 0.7 - - - +
139A GLY* 3.1 20.6 + - - -
161A HIS* 3.9 25.5 + - + +
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Residues in contact with VAL 136 (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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1A MET* 3.9 42.0 - - + +
6A PHE* 3.5 28.7 - - + -
132A ARG 3.4 14.6 - - - +
133A TRP* 3.3 17.1 + - + +
135A GLU* 1.3 78.3 - - + +
137A GLU* 1.3 62.1 + - - +
139A GLY* 3.2 10.0 + - - -
140A LEU* 3.4 17.2 + - + +
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Residues in contact with GLU 137 (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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6A PHE* 3.7 24.7 - - + -
45A GLY* 3.0 22.5 + - - -
108A TYR* 2.6 35.4 + - + +
110A THR* 2.6 31.4 + - + +
114A ARG* 2.9 20.9 + - - +
133A TRP 2.8 20.6 + - - +
134A THR 4.1 1.3 - - - +
136A VAL* 1.3 74.0 - - - +
138A LEU* 1.3 64.7 + - + +
140A LEU* 3.2 20.0 + - + +
141A LEU* 3.8 10.4 + - + +
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Residues in contact with LEU 138 (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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54A LEU* 4.1 24.2 - - + -
56A PHE* 5.5 2.5 - - + -
110A THR* 5.2 7.2 - - + -
114A ARG* 6.1 0.7 - - - +
134A THR* 2.9 36.3 + - + +
135A GLU 4.5 0.7 - - - +
137A GLU* 1.3 76.3 - - + +
139A GLY* 1.3 61.7 + - - +
141A LEU* 3.1 30.4 + - + +
142A PRO* 5.0 0.7 - - - +
144A VAL* 5.8 0.4 - - + -
147A TYR* 4.0 34.8 + - + +
158A LEU* 4.3 12.3 - - + -
161A HIS* 3.7 35.9 - - + +
162A PHE* 4.6 0.7 - - + -
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Residues in contact with GLY 139 (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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135A GLU 3.1 18.6 + - - -
136A VAL* 3.2 4.0 + - - -
137A GLU 3.1 0.6 - - - -
138A LEU* 1.3 77.0 - - - +
140A LEU* 1.3 60.7 + - - +
141A LEU 3.2 1.4 + - - -
142A PRO* 4.1 10.6 - - - +
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Residues in contact with LEU 140 (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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1A MET 3.2 25.4 - - - +
2A ASP* 4.0 10.1 - - - -
3A ARG* 3.8 32.5 - - + +
6A PHE* 3.8 28.0 - - + -
49A PRO 4.0 7.1 - - - +
136A VAL* 3.6 15.7 - - + +
137A GLU* 3.2 10.2 + - + +
138A LEU 3.1 1.2 - - - -
139A GLY* 1.3 78.4 - - - +
141A LEU* 1.3 66.4 + - + +
142A PRO* 3.3 11.7 - - - +
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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