Contacts of the helix formed by residues 131 - 143 (chain D) in PDB entry 4HYY
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 GLY 131 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D THR* 1.3 81.4 - - - +
132D LYS* 1.3 64.7 + - - +
133D THR 3.3 0.9 - - - -
134D GLN* 3.6 16.6 - - - +
135D LEU* 2.8 27.5 + - - +
303D LEU* 4.0 9.0 - - - -
311D ARG* 3.3 13.6 - - - +
328D PHE* 4.7 6.1 - - - -
330D ILE* 4.4 7.6 - - - -
335D ILE* 4.2 0.9 - - - +
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Residues in contact with LYS 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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124D ALA* 4.0 17.5 - - + +
125D PHE* 4.1 7.6 - - - -
126D GLY 3.3 23.9 + - - +
127D GLU 3.5 11.5 + - - -
128D PHE* 3.4 48.1 - - + +
130D THR* 2.5 13.2 + - - -
131D GLY* 1.3 75.8 - - - +
133D THR* 1.3 60.7 + - - +
135D LEU* 3.3 11.1 + - - +
136D SER* 3.1 16.9 + - - -
265D PHE* 4.4 0.3 - - - -
267D THR* 3.9 19.4 - - + +
268D ASN 3.4 26.6 + - - +
269D GLN* 4.7 11.9 - - - +
303D LEU* 3.9 15.8 - - + +
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Residues in contact with THR 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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128D PHE* 2.5 40.3 - - + -
132D LYS* 1.3 78.1 - - - +
134D GLN* 1.3 70.0 + - - +
135D LEU 3.2 0.3 + - - -
136D SER* 3.3 9.1 - - - -
137D HIS* 2.9 48.9 + - + +
164D THR* 4.0 20.4 + - + +
223D ASP* 3.4 18.7 + - - +
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Residues in contact with GLN 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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128D PHE* 6.5 0.2 - - + -
130D THR 5.1 2.5 - - - +
131D GLY* 3.6 16.4 - - - +
133D THR* 1.3 83.3 - - + +
135D LEU* 1.3 56.7 + - - +
137D HIS* 3.4 6.3 + - - +
138D THR* 2.9 31.0 + - - -
169D ARG* 2.8 40.8 + - - +
173D ILE* 5.1 0.2 - - - +
330D ILE* 3.3 40.4 - - + +
331D THR 4.2 4.9 + - - -
334D GLY* 4.7 5.9 - - - -
335D ILE* 3.6 13.9 + - + -
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Residues in contact with LEU 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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103D THR* 4.3 29.4 - - + +
108D PHE* 4.0 30.1 - - + -
116D ILE* 5.3 2.0 - - + -
124D ALA* 4.5 9.0 - - + -
131D GLY 2.8 21.3 + - - +
132D LYS 3.4 4.3 - - - +
134D GLN* 1.3 71.6 - - - +
136D SER* 1.3 67.0 + - - +
138D THR* 3.1 1.5 + - - -
139D LEU* 2.9 51.5 + - + +
265D PHE* 3.4 27.6 - - + -
301D ILE* 6.3 0.2 - - + -
303D LEU* 4.7 6.1 - - + -
328D PHE* 6.1 0.7 - - + -
335D ILE* 3.7 13.5 - - + -
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Residues in contact with SER 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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132D LYS 3.1 12.3 + - - -
133D THR* 3.3 11.7 + - - -
135D LEU* 1.3 79.5 - - - +
137D HIS* 1.3 64.4 + - - -
139D LEU* 3.5 1.0 + - - -
140D CYS* 3.2 25.9 + - - -
158D PHE* 3.9 25.1 - - - -
221D ILE* 3.7 14.0 - - - +
223D ASP* 4.2 8.4 - - - +
265D PHE* 3.7 18.7 - - - -
267D THR* 3.8 9.5 - - - +
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Residues in contact with HIS 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 THR* 2.9 38.4 + - + +
134D GLN* 3.4 8.1 + - - +
135D LEU 3.2 0.8 - - - -
136D SER* 1.3 83.1 - - - +
138D THR* 1.3 64.6 + - - +
140D CYS* 3.1 20.9 + - - +
141D VAL* 3.6 1.9 + - - +
158D PHE* 5.2 2.0 - + - -
164D THR 3.7 16.8 - - - -
165D PHE* 3.7 18.0 - + - -
166D ARG* 2.9 38.7 + - + +
169D ARG* 3.8 20.7 + - + +
170D LEU* 3.3 30.3 - - + +
173D ILE* 3.9 13.4 - - + +
223D ASP* 6.0 0.7 - - - -
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Residues in contact with THR 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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103D THR 3.3 26.0 - - - +
104D GLY* 4.6 0.7 - - - -
134D GLN 2.9 16.1 + - - -
135D LEU* 3.1 5.4 + - - -
137D HIS* 1.3 74.5 - - - +
139D LEU* 1.3 57.6 + - - +
141D VAL* 2.8 22.3 + - - +
142D THR* 3.0 25.0 + - + -
173D ILE* 3.9 17.5 - - + -
177D PHE* 4.7 2.7 - - + -
334D GLY* 3.3 7.2 - - - -
335D ILE* 2.8 37.7 + - - +
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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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101D ILE* 4.2 10.5 - - + -
102D THR 3.7 20.6 - - - +
103D THR* 4.4 3.4 - - - -
116D ILE* 3.7 27.1 - - + -
135D LEU* 2.9 38.7 + - + +
136D SER* 3.8 4.3 - - - +
138D THR* 1.3 76.1 - - - +
140D CYS* 1.3 64.8 + - - +
141D VAL 3.1 0.9 + - - -
142D THR* 3.4 5.8 - - - +
143D ALA* 3.1 28.9 + - - +
219D LEU* 3.6 17.6 - - + +
221D ILE* 4.4 0.9 - - + -
265D PHE* 3.6 40.2 - - + -
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Residues in contact with CYS 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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136D SER 3.2 21.4 + - - -
137D HIS* 3.1 12.0 + - - +
139D LEU* 1.3 75.2 - - - +
141D VAL* 1.3 60.1 + - - +
144D GLN* 3.1 23.6 + - - -
156D ILE* 3.3 21.3 - - - +
158D PHE* 3.6 29.2 - - - -
165D PHE* 4.1 13.9 - - - -
170D LEU* 3.6 19.1 - - + -
188D VAL* 4.1 14.3 - - + +
221D ILE* 4.0 5.2 - - - -
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Residues in contact with VAL 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 HIS 4.0 7.6 - - - +
138D THR 2.8 7.8 + - - +
140D CYS* 1.3 80.5 - - - +
142D THR* 1.3 56.7 + - - +
143D ALA 3.1 2.0 - - - -
144D GLN* 2.7 35.2 + - - +
145D LEU* 3.6 9.8 + - + +
170D LEU* 4.0 19.1 - - + +
173D ILE* 3.8 28.7 - - + -
174D ALA* 4.4 13.9 - - - -
177D PHE* 4.2 24.2 - - + -
179D VAL* 5.6 0.9 - - + -
184D VAL* 4.3 23.1 - - + -
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Residues in contact with THR 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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101D ILE* 3.6 7.1 - - - +
102D THR* 2.9 46.7 + - + +
104D GLY 4.2 3.6 - - - +
138D THR* 3.0 18.9 + - + +
139D LEU* 3.4 16.6 - - - -
141D VAL* 1.3 74.2 - - - +
143D ALA* 1.3 61.7 + - - +
145D LEU* 3.1 31.4 + - + +
151D TYR* 4.4 2.1 - - - -
177D PHE* 3.8 32.8 - - + -
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Residues in contact with ALA 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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101D ILE* 3.6 22.0 - - + -
139D LEU 3.1 17.9 + - - +
141D VAL 3.0 0.6 + - - -
142D THR* 1.3 81.8 + - - +
144D GLN* 1.3 57.2 + - - +
145D LEU 3.3 0.2 - - - -
151D TYR* 2.6 27.1 + - - +
153D GLY* 3.4 2.1 - - - -
154D GLY 2.9 14.9 + - - +
156D ILE* 3.7 22.2 - - + -
218D LYS* 5.3 1.3 - - + -
219D LEU* 4.0 9.0 - - + -
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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