Contacts of the helix formed by residues 139 - 151 (chain D) in PDB entry 2ZU6
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 ASN 139 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B THR* 4.8 9.9 - - - +
238B LYS* 4.5 14.4 - - - +
136D GLY 4.5 6.0 + - - +
137D GLY* 3.0 2.0 - - - -
138D THR* 1.3 99.2 + - - +
140D VAL* 1.3 64.7 + - - +
141D ARG 3.2 2.5 - - - -
142D ALA* 3.0 24.2 + - + +
143D GLU* 3.1 11.7 + - - +
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Residues in contact with VAL 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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2D ACY 5.3 8.1 - - - +
136D GLY* 4.2 18.0 - - - -
137D GLY 2.8 25.1 + - - +
138D THR 3.5 3.3 - - - +
139D ASN* 1.3 73.2 - - - +
141D ARG* 1.3 67.1 + - - +
142D ALA 2.9 0.7 + - - -
143D GLU* 2.9 10.9 + - - +
144D VAL* 2.8 42.0 + - + +
161D ARG* 4.7 3.8 - - - +
165D MET* 5.1 1.6 - - + -
249E GLU* 4.3 19.1 - - - +
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Residues in contact with ARG 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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234B THR 5.9 0.2 - - - -
237B GLU* 3.9 27.1 - - - -
238B LYS* 5.0 10.1 - - + +
241B ASP* 2.6 41.5 + - - +
278B TYR* 3.8 15.2 - - - +
281B SER* 2.8 36.3 + - - -
282B TYR* 3.4 15.4 - - - -
2D ACY 3.5 38.7 + - + +
138D THR 4.9 1.6 + - - +
139D ASN 3.1 1.6 + - - -
140D VAL* 1.3 79.2 - - - +
142D ALA* 1.3 58.1 + - - +
144D VAL* 3.4 2.1 + - - +
145D GLN* 3.0 49.4 + - - +
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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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234B THR* 4.6 21.3 - - + +
139D ASN* 3.0 20.4 + - + +
140D VAL 3.0 0.4 - - - -
141D ARG* 1.3 77.3 - - - +
143D GLU* 1.3 69.5 + - - +
145D GLN* 3.1 11.6 + - - +
146D LYS* 3.0 20.5 + - - +
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Residues in contact with GLU 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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132D HIS* 3.2 36.0 + - + +
134D CYS* 3.7 2.8 - - - +
135D ILE* 2.5 39.3 + - - +
136D GLY* 3.1 23.4 + - - -
139D ASN 3.1 9.3 + - - +
140D VAL* 2.9 12.1 + - - +
142D ALA* 1.3 79.6 - - - +
144D VAL* 1.3 58.6 + - + +
146D LYS* 3.0 20.0 + - - +
147D LEU* 3.1 20.0 + - + +
161D ARG* 4.6 0.7 - - - -
165D MET* 3.4 22.7 - - + +
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Residues in contact with VAL 144 (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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2D ACY 4.5 13.7 - - + +
140D VAL* 2.8 29.7 + - + +
141D ARG* 3.9 4.7 - - - +
143D GLU* 1.3 77.2 - - + +
145D GLN* 1.3 62.8 + - + +
147D LEU* 3.8 8.5 - - - +
148D GLN* 3.4 24.6 + - - +
165D MET* 3.2 33.9 - - + -
170D TYR* 3.5 45.9 - - + +
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Residues in contact with GLN 145 (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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234B THR* 5.0 6.9 + - - -
237B GLU* 3.5 24.3 + - - +
275B CYS* 4.9 9.0 - - - +
277B THR* 5.8 0.4 + - - -
141D ARG* 3.0 48.1 + - + +
142D ALA* 3.1 8.9 + - - +
144D VAL* 1.3 76.1 - - + +
146D LYS* 1.3 53.4 + - - +
148D GLN* 3.1 14.0 + - - +
149D MET* 2.7 44.2 + - + +
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Residues in contact with LYS 146 (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 SER* 6.3 2.9 - - - -
131D CYS 5.1 3.4 + - - -
132D HIS* 3.3 49.8 + - + +
142D ALA 3.0 10.0 + - - +
143D GLU* 3.0 10.9 + - - +
145D GLN* 1.3 71.8 - - - +
147D LEU* 1.3 70.6 + - + +
149D MET* 2.7 3.8 + - - +
150D GLU* 2.7 63.7 + - + +
152D PRO* 4.1 11.9 - - + -
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Residues in contact with LEU 147 (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 HIS* 3.9 32.1 - - + -
134D CYS* 4.3 4.5 - - - -
143D GLU* 3.1 19.7 + - + +
144D VAL* 3.8 10.3 - - - +
146D LYS* 1.3 79.3 - - + +
148D GLN* 1.3 58.5 + - - +
151D ALA* 3.0 29.8 + - - +
152D PRO* 4.1 10.8 - - + -
155D ILE* 4.8 6.3 - - + -
165D MET* 3.4 44.0 - - + -
170D TYR* 4.0 13.3 - - + +
171D LEU* 3.3 33.5 - - + +
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Residues in contact with GLN 148 (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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144D VAL* 3.4 13.1 + - - +
145D GLN* 3.1 16.2 + - - +
146D LYS 2.8 4.6 + - - -
147D LEU* 1.3 80.5 - - - +
149D MET* 1.3 61.6 + - + +
151D ALA* 4.6 1.9 + - - +
168D ARG 5.3 0.2 + - - -
169D ARG 4.3 8.5 + - - +
170D TYR* 3.5 48.3 - - - +
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Residues in contact with MET 149 (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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99D LYS* 3.2 23.3 + - - -
145D GLN* 2.7 27.5 + - + +
146D LYS 2.7 3.9 + - - +
148D GLN* 1.3 74.6 - - + +
150D GLU* 1.3 70.5 + - + +
151D ALA 3.8 0.7 - - - -
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Residues in contact with GLU 150 (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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99D LYS* 4.3 20.3 - - - +
130D SER* 4.9 2.3 + - - -
146D LYS* 2.7 59.3 + - + +
149D MET* 1.3 85.8 - - + +
151D ALA* 1.3 70.9 + - - +
152D PRO* 3.0 7.0 - - + +
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Residues in contact with ALA 151 (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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99D LYS* 3.9 17.3 - - + +
100D ALA* 3.5 23.6 + - - +
101D THR* 3.7 9.4 - - - +
130D SER* 4.8 0.2 + - - -
147D LEU 3.0 17.0 + - - +
148D GLN 4.6 2.0 + - - +
149D MET 3.8 1.0 - - - -
150D GLU* 1.3 74.8 - - - +
152D PRO* 1.3 75.3 - - - +
153D HIS* 3.6 2.1 + - - -
171D LEU* 5.6 2.0 - - + -
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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