Contacts of the helix formed by residues 136 - 149 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C HIS* 4.2 17.9 - - - +
30C HIS* 4.4 17.0 - - + -
133C GLU* 5.4 6.3 - - + +
134C GLY 3.4 4.8 + - - +
135C VAL* 1.3 75.9 - - - +
137C VAL* 1.3 67.5 + - - +
138C GLN* 3.7 11.2 - - - -
139C THR* 3.3 32.6 - - - -
140C GLU* 3.0 21.0 + - - +
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Residues in contact with VAL 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C VAL 4.0 0.2 + - - -
136C CYS* 1.3 73.2 - - - +
138C GLN* 1.3 66.3 + - - +
140C GLU* 2.9 26.0 + - + +
141C THR* 2.9 15.2 + - - -
144C ARG* 5.7 0.2 - - - +
789C GLY 3.4 14.8 - - - +
790C GLY* 3.2 38.1 - - - +
791C GLN* 4.1 7.4 - - + +
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Residues in contact with GLN 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ALA 4.6 2.7 - - - +
27C HIS* 3.5 42.1 + - + +
28C VAL* 4.8 0.3 + - - +
107C GLY 3.5 21.7 + - - +
108C HIS* 5.1 11.3 + - - -
109C VAL* 3.7 30.6 - - + +
136C CYS* 3.3 8.8 - - - -
137C VAL* 1.3 78.6 - - - +
139C THR* 1.3 68.8 + - - +
141C THR* 3.0 17.3 + - - -
142C VAL* 3.2 18.1 + - + +
785C ARG* 5.6 5.3 - - - +
790C GLY 5.6 0.9 - - - -
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Residues in contact with THR 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 3.9 17.8 - - + +
26C ALA* 4.0 1.3 - - - -
27C HIS* 3.4 22.9 + - - +
30C HIS* 5.1 1.2 + - - -
127C VAL* 3.8 28.9 - - + -
128C VAL 4.1 13.2 + - - +
129C VAL* 5.1 2.0 - - + -
135C VAL* 4.9 7.6 - - + -
136C CYS* 3.3 25.0 - - - -
138C GLN* 1.3 78.9 - - - +
140C GLU* 1.3 63.1 + - - +
142C VAL* 4.0 2.4 - - - +
143C LEU* 3.0 22.8 + - + +
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Residues in contact with GLU 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C VAL* 4.0 16.5 - - + +
136C CYS 3.0 11.8 + - - +
137C VAL* 2.9 25.3 + - - +
139C THR* 1.3 79.1 - - - +
141C THR* 1.3 59.0 + - - +
143C LEU* 3.4 7.0 + - - +
144C ARG* 3.1 48.4 + - - +
188C ILE* 3.3 32.2 - - + +
791C GLN* 4.4 13.4 + - - -
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Residues in contact with THR 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 5.0 5.2 - - + -
137C VAL 2.9 9.9 + - - -
138C GLN* 3.5 9.0 - - - -
140C GLU* 1.3 74.4 - - - +
142C VAL* 1.3 67.6 + - - +
144C ARG* 2.9 44.6 + - + +
145C GLN* 3.1 7.5 + - + +
790C GLY 3.5 16.7 + - - -
791C GLN* 3.7 8.7 + - - +
792C ALA 4.8 2.0 - - - +
793C PHE* 3.6 43.1 - - + -
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 3.6 37.7 - - + -
109C VAL* 4.7 19.7 - - + -
115C VAL* 4.2 28.3 - - + -
119C LEU* 4.5 7.4 - - + -
138C GLN* 3.2 19.6 + - + +
139C THR* 4.8 0.7 - - - -
141C THR* 1.3 77.4 - - + +
143C LEU* 1.3 58.3 + - - +
145C GLN* 3.1 10.0 + - - +
146C ALA* 2.7 27.2 + - - +
793C PHE* 5.4 0.9 - - + -
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Residues in contact with LEU 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 4.4 5.6 - - + +
125C ALA* 6.2 0.4 - - + -
127C VAL* 3.8 33.7 - - + -
135C VAL* 6.0 2.5 - - + -
139C THR* 3.0 20.7 + - + +
140C GLU* 3.5 6.5 - - - +
142C VAL* 1.3 76.0 - - - +
144C ARG* 1.3 51.7 + - - +
146C ALA* 3.1 13.0 + - + +
147C LEU* 2.8 50.0 + - + +
153C PRO* 4.1 15.9 - - + -
185C VAL* 4.4 13.9 - - + -
188C ILE* 3.9 32.3 - - + -
189C VAL* 4.3 12.8 - - + -
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Residues in contact with ARG 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C VAL* 5.7 0.2 - - - +
140C GLU* 3.1 40.7 + - - +
141C THR* 2.9 45.2 + - + +
143C LEU* 1.3 75.2 - - - +
145C GLN* 1.3 69.1 + - - +
147C LEU* 3.0 13.8 + - - +
148C GLY* 2.9 19.8 + - - -
188C ILE* 4.8 2.2 - - + +
192C TYR* 3.7 54.4 + - + +
736C PRO* 3.8 17.2 - - - +
760C ARG* 4.8 3.8 + - - -
765C LEU* 4.1 21.5 - - + +
791C GLN* 3.3 30.3 + - - +
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Residues in contact with GLN 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C VAL* 5.7 0.9 - - + -
116C THR* 4.3 12.6 + - + +
119C LEU* 3.9 14.8 - - + -
141C THR* 3.1 12.4 + - + +
142C VAL* 3.3 12.1 - - + +
144C ARG* 1.3 83.8 - - - +
146C ALA* 1.3 63.9 - - - +
148C GLY* 2.9 12.7 + - - -
149C GLU* 3.2 15.6 + - + +
734C GLN* 3.5 32.6 + - - +
765C LEU* 5.0 4.0 - - - +
793C PHE* 3.3 48.0 - - + +
795C GLN* 5.0 3.0 + - - -
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Residues in contact with ALA 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 4.2 12.1 - - + -
119C LEU* 3.6 23.5 - - + +
125C ALA* 5.2 0.9 - - + -
142C VAL 2.7 16.3 + - - +
143C LEU* 3.4 16.4 - - + +
145C GLN* 1.3 71.3 - - - +
147C LEU* 1.3 65.0 + - + +
149C GLU* 3.0 8.4 + - - +
151C ILE* 2.9 44.7 + - + +
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Residues in contact with LEU 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C LEU* 2.8 30.0 + - + +
144C ARG 3.3 6.7 - - - +
146C ALA* 1.3 73.2 - - + +
148C GLY* 1.3 59.4 + - - +
150C ARG* 2.9 21.3 + - - +
151C ILE 3.8 18.8 - - - +
153C PRO* 4.3 19.1 - - + -
188C ILE* 3.7 18.2 - - + +
189C VAL* 3.7 26.5 - - + -
192C TYR* 3.8 26.6 - - + +
193C ALA* 4.0 23.1 - - + +
194C ASP* 4.7 2.4 - - - +
197C LEU* 5.0 2.7 - - + +
200C VAL* 4.6 2.7 - - + -
760C ARG* 3.6 8.3 + - - -
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Residues in contact with GLY 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ARG 2.9 12.9 + - - -
145C GLN* 2.9 6.8 + - - -
147C LEU* 1.3 78.1 - - - +
149C GLU* 1.3 52.7 + - - +
150C ARG* 3.1 1.1 + - - +
355C GLN* 2.5 30.9 + - - +
760C ARG* 3.1 28.0 + - - +
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Residues in contact with GLU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C THR* 3.9 8.6 - - + +
119C LEU* 4.4 18.6 - - + +
120C ARG* 2.9 57.1 + - - +
145C GLN* 3.7 12.1 - - + +
146C ALA 3.0 8.7 + - - +
148C GLY* 1.3 77.7 - - - +
150C ARG* 1.3 70.3 + - - +
151C ILE* 3.9 9.0 - - + -
352C ARG* 3.1 31.2 + - - +
355C GLN* 3.4 12.3 + - - +
356C LEU* 4.1 10.0 - - - +
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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