Contacts of the helix formed by residues 136 - 149 (chain E) in PDB entry 1ZM9
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 CYS 136 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27E HIS* 4.0 24.2 - - - +
30E HIS* 4.0 17.3 - - + -
133E GLU* 5.3 6.5 - - + +
134E GLY 3.4 5.0 + - - +
135E VAL* 1.3 78.2 - - - +
137E VAL* 1.3 67.0 + - - +
138E GLN* 3.3 7.4 + - - +
139E THR* 3.3 33.1 - - - -
140E GLU* 3.2 20.8 + - - +
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Residues in contact with VAL 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E VAL 4.0 0.2 + - - -
136E CYS* 1.3 73.4 - - - +
138E GLN* 1.3 54.2 + - - +
140E GLU* 3.2 14.6 + - + +
141E THR* 2.8 43.5 + - - +
144E ARG* 5.4 2.7 - - - +
785E ARG* 5.8 5.8 - - - +
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Residues in contact with GLN 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ALA 5.1 1.3 - - - +
27E HIS* 4.0 35.1 + - + +
28E VAL* 5.1 0.3 + - - +
107E GLY 3.4 19.8 - - - +
108E HIS* 4.6 1.4 - - - +
109E VAL* 3.0 38.2 + - + +
136E CYS* 3.3 9.2 - - - +
137E VAL* 1.3 79.3 - - - +
139E THR* 1.3 67.9 + - - +
141E THR* 3.1 8.6 + - - -
142E VAL* 3.0 29.4 + - + +
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Residues in contact with THR 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ILE* 3.7 22.2 - - + +
26E ALA* 3.9 2.4 - - - +
27E HIS* 3.3 24.6 + - - +
30E HIS* 4.8 1.2 + - - -
127E VAL* 3.5 30.5 - - + -
128E VAL 4.5 8.4 + - - +
129E VAL* 5.1 2.7 - - + -
135E VAL* 4.7 9.4 - - + -
136E CYS* 3.3 21.4 - - - -
138E GLN* 1.3 78.9 - - - +
140E GLU* 1.3 56.0 + - - +
142E VAL* 3.8 7.1 + - - -
143E LEU* 3.2 25.8 + - - +
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Residues in contact with GLU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E VAL* 3.9 22.0 - - + +
136E CYS 3.2 14.5 + - - +
137E VAL* 3.2 17.9 - - - +
138E GLN 3.0 0.2 - - - -
139E THR* 1.3 77.0 - - - +
141E THR* 1.3 64.4 + - - +
143E LEU* 3.4 7.3 - - - +
144E ARG* 3.1 43.4 + - - +
188E ILE* 3.3 36.5 - - + +
192E TYR* 5.1 0.5 + - - -
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Residues in contact with THR 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E VAL* 4.9 14.8 - - + -
137E VAL* 2.8 26.4 + - - +
138E GLN* 3.3 9.6 - - - -
140E GLU* 1.3 74.2 - - - +
142E VAL* 1.3 68.9 + - - +
144E ARG* 2.7 47.0 + - + +
145E GLN* 3.2 11.1 + - + +
793E PHE* 5.7 7.6 - - + -
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Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ILE* 3.4 43.3 - - + -
26E ALA 6.1 1.1 - - - +
109E VAL* 4.2 24.7 - - + -
115E VAL* 4.6 22.0 - - + -
119E LEU* 4.9 4.3 - - + -
138E GLN* 3.2 19.5 - - + +
139E THR* 3.9 2.9 - - - +
141E THR* 1.3 80.0 - - - +
143E LEU* 1.3 56.9 + - - +
145E GLN* 2.8 31.2 - - - +
146E ALA* 2.9 7.8 + - - +
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Residues in contact with LEU 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ILE* 4.4 3.3 - - + +
125E ALA* 6.1 0.4 - - + -
127E VAL* 3.7 33.4 - - + -
135E VAL* 5.8 4.9 - - + -
139E THR 3.2 14.2 + - - +
140E GLU* 3.4 11.9 - - + +
141E THR 3.0 0.4 - - - -
142E VAL* 1.3 75.2 - - - +
144E ARG* 1.3 67.5 + - - +
145E GLN 2.8 1.3 + - - -
146E ALA* 3.0 12.9 + - + +
147E LEU* 2.8 42.5 + - + +
153E PRO* 4.1 15.9 - - + -
185E VAL* 4.7 11.7 - - + -
188E ILE* 3.7 25.4 - - + -
189E VAL* 4.5 14.4 - - + -
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Residues in contact with ARG 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E VAL* 4.4 4.0 + - - +
140E GLU* 3.1 40.8 + - - +
141E THR* 2.7 57.0 + - - +
143E LEU* 1.3 71.5 - - - +
145E GLN* 1.3 61.4 + - - +
147E LEU* 3.3 12.8 - - - +
148E GLY* 3.0 22.9 + - - -
188E ILE* 5.0 0.2 - - - +
192E TYR* 3.2 55.6 + - + +
790E GLY 4.8 14.0 + - - -
791E GLN* 5.8 5.6 - - - +
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Residues in contact with GLN 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E VAL* 5.7 4.0 - - + -
116E THR* 3.8 25.2 + - - +
119E LEU* 3.5 17.0 - - + +
141E THR* 3.2 12.0 + - + +
142E VAL* 2.8 19.7 + - - +
143E LEU 2.8 0.8 - - - -
144E ARG* 1.3 79.3 - - - +
146E ALA* 1.3 66.4 + - - +
147E LEU 2.9 1.1 - - - -
148E GLY* 2.6 15.7 + - - -
149E GLU* 2.9 15.6 + - - +
793E PHE* 2.8 58.4 - - + -
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Residues in contact with ALA 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E ILE* 4.9 3.4 - - + -
119E LEU* 3.9 10.9 - - + +
125E ALA* 4.7 8.3 - - + -
142E VAL 2.9 14.2 + - - +
143E LEU* 3.0 19.0 + - + +
145E GLN* 1.3 70.6 - - - +
147E LEU* 1.3 56.9 + - - +
149E GLU* 3.0 18.1 + - - +
150E ARG 3.0 10.2 + - - -
151E ILE* 3.0 48.4 + - + +
153E PRO* 6.4 0.4 - - + -
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Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E LEU* 2.8 42.8 + - + +
144E ARG* 3.3 8.5 - - - +
146E ALA* 1.3 74.3 - - - +
148E GLY* 1.3 64.6 + - - +
150E ARG* 3.2 10.4 + - - +
151E ILE 4.6 13.2 - - - +
153E PRO* 4.9 7.0 - - + -
188E ILE* 3.6 15.5 - - + +
189E VAL* 4.3 11.9 - - + +
192E TYR* 3.1 48.5 - - + +
193E ALA* 4.2 19.9 - - + +
194E ASP* 3.5 18.4 + - - +
197E LEU* 5.2 4.2 - - + +
200E VAL* 5.2 0.9 - - + -
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Residues in contact with GLY 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E ARG 3.0 10.1 + - - -
145E GLN* 2.6 15.2 + - - -
147E LEU* 1.3 74.2 - - - +
149E GLU* 1.3 59.1 + - - -
150E ARG* 3.3 3.0 + - - +
192E TYR 5.3 0.9 - - - -
194E ASP* 4.8 4.2 - - - +
355E GLN* 3.3 23.0 + - - +
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Residues in contact with GLU 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E THR* 3.9 7.7 - - + +
119E LEU* 4.0 22.7 - - + -
120E ARG* 3.3 55.5 + - - +
145E GLN* 2.9 15.7 + - - +
146E ALA 3.0 8.0 + - - +
148E GLY* 1.3 78.7 - - - +
150E ARG* 1.3 66.6 + - - +
151E ILE* 3.8 13.2 - - + -
352E ARG* 2.8 37.0 + - - +
355E GLN* 4.5 10.5 + - - +
356E LEU* 4.4 5.4 - - - +
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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