Contacts of the helix formed by residues 145 - 159 (chain D) in PDB entry 4ZHF
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 145 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B SO4 5.6 6.3 - - - +
144D LEU* 1.3 79.6 - - - +
146D SER* 1.3 65.9 - - - +
147D GLU* 3.7 10.8 + - - +
148D LEU* 3.2 32.8 + - + +
149D LYS* 3.1 20.2 + - - +
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Residues in contact with SER 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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144D LEU 3.8 1.0 + - - -
145D THR* 1.3 71.2 - - - +
147D GLU* 1.3 56.7 + - - +
149D LYS* 3.2 14.2 + - - +
150D GLU* 2.8 32.9 + - - +
147E GLU* 3.5 28.6 + - - +
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Residues in contact with GLU 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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145D THR* 3.1 11.3 + - - +
146D SER* 1.3 79.0 - - - +
148D LEU* 1.3 58.9 + - + +
150D GLU* 3.4 5.1 + - - +
151D ASN* 3.0 47.6 + - - +
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Residues in contact with LEU 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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117D GLN* 6.2 0.2 - - + -
118D HIS* 4.1 38.8 - - + +
137D LEU* 4.5 7.9 - - + +
144D LEU* 4.1 36.8 - - + -
145D THR* 3.2 25.3 + - + +
147D GLU* 1.3 81.7 - - + +
149D LYS* 1.3 58.9 + - - +
151D ASN* 3.3 16.8 + - + +
152D PHE* 3.0 27.0 + - - +
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Residues in contact with LYS 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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34D VAL* 4.5 10.9 - - + +
137D LEU* 4.1 12.6 - - + -
143D GLU* 5.2 5.5 + - - -
144D LEU* 3.4 29.4 + - + +
145D THR 3.1 14.8 + - - +
146D SER* 3.8 10.5 - - - +
148D LEU* 1.3 77.5 - - - +
150D GLU* 1.3 56.3 + - - +
152D PHE* 3.2 8.7 + - - +
153D ILE* 3.0 34.7 + - + +
168D PHE* 3.9 37.2 - - + +
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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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146D SER 2.8 17.7 + - - +
147D GLU* 3.7 6.5 - - - +
149D LYS* 1.3 74.3 - - - +
151D ASN* 1.3 58.8 + - - +
153D ILE* 3.3 12.7 + - - +
154D ARG* 2.9 50.8 + - - +
145E THR* 3.3 36.7 - - + +
146E SER* 3.3 28.3 + - - -
147E GLU* 3.8 10.7 + - - +
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Residues in contact with ASN 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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120D MET* 5.3 3.7 - - + +
147D GLU* 3.0 38.3 + - - +
148D LEU* 3.3 20.8 + - + +
150D GLU* 1.3 76.1 - - - +
152D PHE* 1.3 57.6 + - - +
154D ARG* 2.7 38.9 + - - +
155D PHE* 2.9 28.9 + - - +
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Residues in contact with PHE 152 (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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35D GLY* 3.8 8.7 - - - -
36D LEU 3.7 22.7 - - - -
37D ALA* 3.7 11.4 - - + -
120D MET* 3.8 26.5 - - - -
135D ILE* 3.6 42.4 - - + -
137D LEU* 3.8 31.2 - - + -
148D LEU 3.0 12.7 + - - +
149D LYS 3.4 6.3 - - - +
150D GLU 3.2 0.2 - - - -
151D ASN* 1.3 75.3 - - - +
153D ILE* 1.3 59.9 + - - +
155D PHE* 3.4 1.2 + - - +
156D SER* 2.9 38.5 + - - -
166D ILE* 3.9 20.0 - - + -
168D PHE* 4.0 20.4 - + - -
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Residues in contact with ILE 153 (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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149D LYS* 3.0 22.4 + - + +
150D GLU* 3.6 16.2 - - - +
152D PHE* 1.3 74.9 - - - +
154D ARG* 1.3 66.6 + - - +
156D SER* 3.3 1.2 + - - -
157D LYS* 3.0 58.5 + - + +
163D GLU* 4.0 9.6 - - + +
166D ILE* 4.1 19.1 - - + -
168D PHE* 3.9 27.8 - - + -
146E SER* 3.3 32.8 - - - +
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Residues in contact with ARG 154 (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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150D GLU* 2.9 46.1 + - - +
151D ASN* 2.7 38.5 + - - +
153D ILE* 1.3 77.8 - - - +
155D PHE* 1.3 61.1 + - - +
157D LYS* 3.3 8.9 + - - +
158D SER* 3.1 20.9 + - - -
145E THR* 6.1 0.4 - - - +
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Residues in contact with PHE 155 (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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15D LYS 4.0 9.6 - - - -
16D VAL* 4.5 4.5 - - + -
17D PRO* 3.7 27.4 - - + -
111D VAL* 4.0 30.1 - - + -
120D MET* 3.9 30.1 - - + -
122D PHE* 5.6 0.4 - - + -
135D ILE* 4.0 22.7 - - + -
151D ASN 2.9 16.3 + - - +
152D PHE 3.8 3.6 - - - +
153D ILE 3.3 0.2 - - - -
154D ARG* 1.3 77.1 - - - +
156D SER* 1.3 64.5 + - - +
158D SER* 2.7 33.9 + - - -
159D LEU* 3.3 30.6 + - + +
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Residues in contact with SER 156 (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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37D ALA* 3.3 25.5 - - - +
135D ILE* 4.0 14.7 - - - +
152D PHE* 2.9 33.3 + - - -
153D ILE 3.6 4.7 - - - -
155D PHE* 1.3 77.3 - - - +
157D LYS* 1.3 61.4 + - - +
159D LEU* 3.1 13.4 + - - +
160D GLY 3.5 0.5 + - - -
161D LEU* 3.3 23.2 + - - +
166D ILE* 3.7 20.2 - - - -
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Residues in contact with LYS 157 (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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153D ILE* 3.0 38.2 + - - +
154D ARG* 3.6 9.8 - - - +
155D PHE 3.2 0.2 - - - -
156D SER* 1.3 72.8 - - - +
158D SER* 1.3 56.2 + - - +
159D LEU 3.0 5.2 - - - -
160D GLY* 2.8 20.6 + - - -
161D LEU 3.1 26.5 - - - +
162D PRO* 4.4 2.2 - - + -
163D GLU* 2.8 43.9 + - - +
166D ILE* 3.8 7.9 - - + -
149E LYS* 4.6 9.7 - - - +
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Residues in contact with SER 158 (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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15D LYS* 3.9 26.5 + - - +
154D ARG* 3.1 13.0 + - - -
155D PHE* 2.7 34.3 + - - -
157D LYS* 1.3 75.0 - - - +
159D LEU* 1.3 63.9 + - - +
160D GLY 3.4 0.4 + - - -
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Residues in contact with LEU 159 (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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8D ILE* 5.0 0.2 - - - +
9D PRO 4.6 3.8 - - - +
11D PRO* 3.9 34.0 - - + +
15D LYS* 3.6 29.8 - - + +
16D VAL* 4.1 3.1 - - + -
122D PHE* 4.1 18.2 - - + -
133D PHE* 3.8 22.2 - - + -
135D ILE* 3.8 23.8 - - + -
155D PHE* 3.6 37.2 - - + +
156D SER 3.1 7.3 + - - +
157D LYS 3.0 1.2 - - - -
158D SER* 1.3 88.1 - - - +
160D GLY* 1.3 56.2 + - - +
161D LEU 3.5 1.8 - - - -
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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