Contacts of the helix formed by residues 125 - 142 (chain D) in PDB entry 3HYW
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 125 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D ARG* 3.5 24.3 + - - +
45D PHE* 3.7 10.5 - - - -
109D LEU* 4.3 12.8 - - + -
123D ILE 3.8 0.9 - - - +
124D CYS* 1.3 82.1 - - - +
126D ALA* 1.3 59.3 + - - +
127D GLU* 3.6 16.0 + - - +
128D HIS* 3.0 38.4 + - + +
129D ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D TYR* 3.6 12.5 + - + +
45D PHE* 3.5 26.0 - - + -
48D LEU* 3.8 11.1 - - + +
55D PHE* 3.6 37.0 - - + -
125D THR* 1.3 73.4 - - - +
127D GLU* 1.3 58.9 + - - +
129D ALA* 3.2 2.9 + - - +
130D LEU* 2.9 37.2 + - + +
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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
----------------------------------------------------------
36D ARG* 3.1 36.4 + - - +
38D TYR* 2.6 30.9 + - - -
55D PHE* 5.6 0.2 - - - -
125D THR* 3.6 9.5 - - - +
126D ALA* 1.3 77.2 + - - +
128D HIS* 1.3 62.9 + - + +
130D LEU* 3.5 10.3 + - + +
131D GLU* 3.3 24.8 + - - +
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Residues in contact with HIS 128 (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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109D LEU* 4.1 18.5 - - + +
111D PHE* 4.1 19.4 - + - -
117D GLU* 5.4 7.2 - - + -
122D SER* 3.1 35.2 + - - +
125D THR* 3.0 32.7 + - + +
127D GLU* 1.3 75.3 - - + +
129D ALA* 1.3 61.5 + - - +
131D GLU* 3.3 11.1 + - - +
132D THR* 2.9 31.4 + - - -
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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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45D PHE* 3.5 26.7 - - + +
48D LEU* 4.0 12.8 - - + -
49D ALA* 3.3 23.4 - - + +
122D SER 3.7 6.0 + - - -
123D ILE* 4.4 7.0 - - - +
125D THR 2.9 18.0 + - - +
126D ALA* 3.5 6.1 - - - +
128D HIS* 1.3 76.4 - - - +
130D LEU* 1.3 58.8 + - - +
132D THR* 3.3 1.3 + - - -
133D GLN* 3.1 22.5 + - - +
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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
----------------------------------------------------------
48D LEU* 3.8 32.5 - - + +
55D PHE* 4.6 23.6 - - + +
126D ALA 2.9 23.5 + - - +
127D GLU* 3.8 8.5 - - + +
129D ALA* 1.3 73.5 - - - +
131D GLU* 1.3 65.1 + - - +
133D GLN* 3.5 10.2 + - + +
134D LYS* 3.4 29.8 + - - +
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D THR* 5.3 2.0 - - + -
127D GLU 3.3 14.4 + - - +
128D HIS* 3.3 15.6 + - - +
130D LEU* 1.3 74.6 - - - +
132D THR* 1.3 63.6 + - - +
134D LYS* 3.1 44.5 + - - +
135D LYS* 3.2 20.3 + - - +
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Residues in contact with THR 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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49D ALA* 3.9 18.8 - - + -
121D THR* 3.3 33.8 - - - +
122D SER 2.7 27.5 + - - -
123D ILE* 4.0 4.7 - - + -
128D HIS 2.9 10.3 + - - -
129D ALA 3.3 10.1 + - - -
131D GLU* 1.3 76.5 - - - +
133D GLN* 1.3 56.1 + - - +
135D LYS* 3.2 3.3 + - - +
136D LEU* 2.9 29.8 + - + +
163D PHE* 4.0 20.9 - - + -
247D PHE* 4.2 4.0 - - + -
249D MET* 4.6 0.2 - - + -
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Residues in contact with GLN 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU 4.1 4.9 - - - +
49D ALA 3.1 27.1 + - - +
50D MET* 3.4 13.4 + - - +
51D GLY* 4.0 17.5 - - - -
129D ALA 3.1 11.3 + - - +
130D LEU* 3.7 13.7 - - + +
131D GLU 3.3 0.4 - - - -
132D THR* 1.3 74.7 - - - +
134D LYS* 1.3 64.6 + - + +
136D LEU* 3.3 8.2 + - - +
137D GLN* 3.0 48.3 + - - +
140D TYR* 5.1 3.8 + - - -
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Residues in contact with LYS 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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130D LEU* 3.4 14.5 + - - +
131D GLU* 3.1 40.7 + - - +
133D GLN* 1.3 79.3 - - + +
135D LYS* 1.3 59.4 + - - +
137D GLN* 3.4 8.9 + - - +
138D GLU* 3.3 29.2 + - - +
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Residues in contact with LYS 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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119D ASN 3.5 25.5 + - - -
120D SER 4.9 1.1 - - - +
121D THR* 3.4 28.7 - - + +
131D GLU 3.2 9.0 + - - +
132D THR 3.2 8.3 + - - +
134D LYS* 1.3 76.4 - - - +
136D LEU* 1.3 65.2 + - - +
138D GLU* 3.3 18.1 + - + +
139D LEU* 3.1 19.1 + - - +
246D LYS 4.4 9.5 + - - -
247D PHE* 3.7 18.0 - - + +
248D THR 3.6 27.3 + - - +
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Residues in contact with LEU 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ALA 3.1 26.7 - - - +
50D MET* 3.8 22.4 - - - -
132D THR* 2.9 18.3 + - + +
133D GLN* 3.3 8.9 + - - +
135D LYS* 1.3 72.7 - - - +
137D GLN* 1.3 60.2 + - - +
139D LEU* 3.0 14.2 + - + +
140D TYR* 2.9 48.9 + - + +
163D PHE* 3.9 9.4 - - + -
167D LEU* 3.7 28.0 - - + -
247D PHE* 3.5 28.5 - - + -
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Residues in contact with GLN 137 (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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133D GLN* 3.0 36.6 + - - +
134D LYS* 3.5 12.8 - - - +
135D LYS 3.3 0.2 - - - -
136D LEU* 1.3 75.1 - - - +
138D GLU* 1.3 61.6 + - + +
140D TYR* 3.4 28.3 + - - +
141D ALA* 3.2 23.2 + - - +
174D ARG* 3.9 16.4 + - - +
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Residues in contact with GLU 138 (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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134D LYS* 3.6 19.1 - - - +
135D LYS* 3.3 18.0 + - + +
136D LEU 3.2 0.6 - - - -
137D GLN* 1.3 77.3 - - + +
139D LEU* 1.3 57.6 - - - +
141D ALA* 4.0 5.5 - - - +
142D ASN* 3.1 24.6 + - - +
246D LYS* 3.2 15.4 + - - +
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Residues in contact with LEU 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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135D LYS 3.1 11.5 + - - +
136D LEU* 3.0 25.6 + - + +
138D GLU* 1.3 75.5 - - - +
140D TYR* 1.3 66.9 + - + +
143D PRO* 3.0 34.8 - - + +
144D GLY 3.4 40.4 - - - +
146D VAL* 3.7 20.9 - - + -
167D LEU* 4.6 10.3 - - + -
171D LEU* 4.8 5.2 - - + -
176D ILE* 5.2 1.0 - - + +
180D VAL* 4.9 5.4 - - + -
246D LYS* 3.8 15.0 - - + +
247D PHE* 3.9 28.7 - - + -
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Residues in contact with TYR 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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50D MET* 3.8 17.3 + - - +
133D GLN* 5.1 3.4 - - - -
136D LEU* 2.9 40.7 + - + +
137D GLN* 3.7 28.3 - - - +
138D GLU 3.4 0.2 - - - -
139D LEU* 1.3 80.7 - - + +
141D ALA* 1.3 62.4 + - - +
143D PRO* 3.7 12.3 - - - +
167D LEU* 4.0 7.2 - - + +
170D GLU* 3.3 19.0 - - + +
171D LEU* 3.7 28.5 - - + -
174D ARG* 3.5 58.8 - - - +
176D ILE* 4.2 14.3 - - + +
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Residues in contact with ALA 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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137D GLN 3.2 16.9 + - - +
138D GLU* 4.0 7.2 - - - +
139D LEU 3.3 0.2 - - - -
140D TYR* 1.3 79.0 - - - +
142D ASN* 1.3 71.6 + - - +
143D PRO* 3.7 5.0 - - - +
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Residues in contact with ASN 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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138D GLU 3.1 11.9 + - - +
139D LEU* 3.1 4.2 - - - +
141D ALA* 1.3 89.8 - - - +
143D PRO* 1.4 67.7 - - - +
144D GLY 3.7 0.2 + - - -
246D LYS* 3.0 34.3 + - + +
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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