Contacts of the helix formed by residues 124 - 143 (chain D) in PDB entry 2HR3
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 ASP 124 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D LEU* 1.3 75.4 - - - +
125D GLU* 1.3 65.2 + - - +
126D SER* 2.8 35.6 + - - -
127D GLU* 2.9 35.6 + - - +
128D ARG* 3.1 19.6 + - - +
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D ASP* 1.3 74.5 - - - +
126D SER* 1.3 56.8 + - - +
128D ARG* 3.3 23.7 + - - +
129D ALA* 2.9 30.8 + - - +
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D ASP* 2.8 22.6 - - - -
125D GLU* 1.3 80.9 - - - +
127D GLU* 1.3 56.4 + - - +
129D ALA* 3.4 8.5 - - - +
130D LEU* 3.1 28.6 + - - +
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Residues in contact with GLU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU* 3.7 25.1 - - + +
140C ARG* 2.8 36.9 + - - -
123D LEU* 3.2 14.4 - - + -
124D ASP* 2.9 42.4 + - - +
126D SER* 1.3 72.8 - - - +
128D ARG* 1.3 59.8 + - - +
130D LEU* 3.4 9.5 - - + +
131D LEU* 3.0 32.4 + - - +
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Residues in contact with ARG 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ASP* 6.2 0.9 - - - -
9C LEU* 6.5 0.9 - - + -
119D MSE 3.3 32.5 + - + +
120D HIS* 3.7 39.0 + - - +
123D LEU* 2.6 45.0 + - + -
124D ASP* 3.1 12.4 + - - +
125D GLU* 3.3 29.5 - - - +
127D GLU* 1.3 73.7 - - - +
129D ALA* 1.3 56.7 + - - +
131D LEU* 3.8 5.5 - - - +
132D ALA* 2.6 38.5 + - - +
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Residues in contact with ALA 129 (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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125D GLU 2.9 14.0 + - - +
126D SER* 3.4 11.7 - - - +
128D ARG* 1.3 76.7 - - - +
130D LEU* 1.3 51.2 + - - +
132D ALA* 3.2 6.8 + - - +
133D ALA* 2.8 35.3 + - - +
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Residues in contact with LEU 130 (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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130C LEU* 3.6 25.7 - - + +
133C ALA* 4.3 26.2 - - + +
134C ALA* 4.3 5.4 - - + +
137C LEU* 4.1 19.7 - - + -
126D SER 3.1 13.0 + - - +
127D GLU* 3.4 13.5 - - + +
129D ALA* 1.3 79.0 - - - +
131D LEU* 1.3 58.7 + - - +
133D ALA* 3.2 5.9 + - + +
134D ALA* 2.8 31.8 + - - +
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Residues in contact with LEU 131 (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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13C LEU* 4.0 31.0 - - + +
16C GLN* 4.8 1.7 - - - +
134C ALA* 4.0 26.0 - - + +
137C LEU* 4.3 12.3 - - + -
138C LEU* 3.7 26.2 - - + -
141C LEU* 4.0 8.5 - - + -
119D MSE 4.4 6.5 - - + -
123D LEU* 3.6 31.4 - - + -
127D GLU 3.0 18.1 + - - +
128D ARG* 3.8 3.8 - - - +
130D LEU* 1.3 72.1 - - - +
132D ALA* 1.3 62.0 + - - +
134D ALA* 4.3 3.8 - - + -
135D GLY* 2.9 30.5 + - - -
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Residues in contact with ALA 132 (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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9C LEU* 5.9 7.2 - - + -
16C GLN* 5.3 1.4 + - - +
119D MSE 6.0 0.2 - - - +
128D ARG 2.6 23.4 + - - +
129D ALA* 3.3 8.1 - - - +
131D LEU* 1.3 73.6 - - - +
133D ALA* 1.3 55.2 + - - +
135D GLY* 5.5 0.2 - - - -
136D PRO* 2.9 26.2 - - - +
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Residues in contact with ALA 133 (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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130C LEU* 3.9 21.7 - - + +
129D ALA 2.8 16.8 + - - +
130D LEU* 3.6 11.0 - - + +
132D ALA* 1.3 72.7 - - - +
134D ALA* 1.3 60.5 + - - +
136D PRO* 3.3 13.2 - - - +
137D LEU* 4.3 7.6 - - - +
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Residues in contact with ALA 134 (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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130C LEU* 3.9 17.9 - - + +
131C LEU* 3.7 14.2 - - + +
134C ALA* 3.5 26.5 - - + -
130D LEU 2.8 17.0 + - - +
131D LEU* 4.0 4.7 - - + +
133D ALA* 1.3 76.0 - - - +
135D GLY* 1.3 56.7 + - - +
136D PRO 3.2 2.7 - - - -
137D LEU* 2.8 33.4 + - - +
138D LEU* 3.5 4.5 + - + +
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Residues in contact with GLY 135 (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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13C LEU* 4.9 3.1 - - - -
16C GLN* 3.1 32.0 - - - +
131D LEU* 2.9 15.2 + - - -
134D ALA* 1.3 75.4 - - - +
136D PRO* 1.3 69.3 - - - +
138D LEU* 2.8 32.0 + - - +
139D THR 3.4 0.3 + - - -
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Residues in contact with PRO 136 (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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16C GLN* 3.9 15.5 - - - +
132D ALA 2.9 23.3 - - - +
133D ALA 3.3 12.6 - - - +
135D GLY* 1.3 88.2 - - - +
137D LEU* 1.3 62.2 + - + +
138D LEU 3.1 0.2 - - - -
139D THR* 3.3 11.9 + - - +
140D ARG* 3.1 19.6 + - - +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU* 4.1 12.0 - - + +
127C GLU* 3.5 53.8 - - + +
130C LEU* 4.0 17.5 - - + -
131C LEU* 3.9 18.2 - - + -
133D ALA 4.3 9.9 - - - +
134D ALA 2.8 17.7 + - - +
136D PRO* 1.3 73.1 - - + +
138D LEU* 1.3 59.4 + - - +
139D THR 3.2 0.2 - - - -
140D ARG* 3.4 29.0 - - - +
141D LEU* 3.0 31.9 + - - +
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Residues in contact with LEU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 5.0 3.1 - - + -
16C GLN* 3.9 17.9 - - + +
17C VAL* 3.7 35.0 - - + -
20C LEU* 4.0 28.9 - - + +
131C LEU* 3.7 23.1 - - + -
138C LEU* 4.8 7.4 - - + -
13D LEU* 4.2 15.3 - - + -
17D VAL* 4.4 7.4 - - + -
134D ALA* 4.0 6.1 - - + +
135D GLY* 2.8 18.5 + - - +
137D LEU* 1.3 77.9 - - - +
139D THR* 1.3 58.0 + - - +
141D LEU* 3.3 9.1 + - + +
142D ALA* 3.0 26.9 + - - +
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Residues in contact with THR 139 (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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16C GLN* 3.1 32.7 + - - +
19C THR* 5.6 5.5 - - + +
135D GLY 3.4 0.4 + - - -
136D PRO* 3.3 13.3 + - - +
138D LEU* 1.3 77.2 - - - +
140D ARG* 1.3 64.5 + - - +
142D ALA* 3.2 16.5 + - - +
143D GLN* 3.2 38.2 + - + +
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Residues in contact with ARG 140 (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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122C CYS* 3.1 37.3 + - + +
123C LEU* 4.0 4.6 - - + +
127C GLU* 2.7 44.1 + - - -
136D PRO 3.1 12.8 + - - +
137D LEU* 3.4 28.1 - - - +
138D LEU 3.3 0.2 - - - -
139D THR* 1.3 74.6 - - - +
141D LEU* 1.3 65.1 + - - +
143D GLN* 3.3 12.3 + - + +
144D PHE* 3.3 18.4 + - - +
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Residues in contact with LEU 141 (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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20C LEU* 4.1 21.1 - - + -
114C TRP* 3.1 21.5 - - + -
115C LEU* 4.3 4.5 - - + -
118C ALA* 3.8 13.0 - - + -
119C MSE 3.7 37.2 - - + +
122C CYS* 3.8 13.2 - - - -
123C LEU* 3.9 8.3 - - + -
131C LEU* 4.0 23.6 - - + -
13D LEU* 4.0 18.4 - - + -
137D LEU 3.0 16.5 + - - +
138D LEU* 3.5 7.9 - - + +
140D ARG* 1.3 79.1 - - - +
142D ALA* 1.3 56.8 + - - +
144D PHE* 3.0 18.6 + - - +
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Residues in contact with ALA 142 (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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19C THR* 3.7 39.3 - - + +
20C LEU* 4.0 14.5 - - - +
23C ARG* 2.7 35.4 + - + +
138D LEU 3.0 14.2 + - - +
139D THR* 3.2 10.9 + - - +
141D LEU* 1.3 74.5 - - - +
143D GLN* 1.3 55.5 + - + +
144D PHE 3.4 0.4 - - - -
145D GLU* 4.8 0.2 - - - +
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Residues in contact with GLN 143 (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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19C THR* 6.3 0.7 - - + -
23C ARG* 4.0 2.0 - - - +
139D THR* 3.2 35.6 + - + +
140D ARG* 3.7 9.4 - - - +
141D LEU 3.2 0.6 - - - -
142D ALA* 1.3 76.8 - - + +
144D PHE* 1.3 63.9 + - - +
145D GLU* 3.4 14.6 + - - +
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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
------------------------------------------------------------
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