Contacts of the helix formed by residues 136 - 141 (chain A) in PDB entry 1Z2M
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 PRO 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A HIS* 3.8 23.8 - - + +
41A PHE* 3.7 14.8 - - + -
100A LEU 3.6 13.2 - - - +
101A THR 3.8 11.4 - - - +
102A GLN 3.2 11.0 - - - +
103A THR* 4.1 2.5 - - + -
134A GLN 4.3 2.9 - - - +
135A LEU* 1.3 97.0 - - + +
137A LEU* 1.3 66.6 + - - +
139A GLU* 2.9 42.8 + - + +
140A TYR* 3.8 4.8 - - - -
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 5.4 0.4 - - + -
98A VAL* 3.6 40.6 - - + -
99A ARG 3.8 4.3 - - - +
100A LEU* 3.4 10.9 + - + +
102A GLN* 2.9 33.2 + - + +
103A THR 4.4 0.4 - - - +
104A VAL* 4.2 26.5 - - + +
107A LEU* 4.0 27.6 - - + -
131A LEU* 5.2 5.4 - - + -
136A PRO* 1.3 72.2 - - - +
138A GLY* 1.3 62.9 + - - +
139A GLU 3.0 1.4 + - - -
140A TYR* 3.0 22.2 + - + +
141A GLY 4.0 0.9 + - - -
142A LEU* 4.0 29.5 + - + +
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Residues in contact with GLY 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.5 28.7 - - - +
100A LEU* 2.7 47.7 + - - +
136A PRO 3.2 0.4 - - - -
137A LEU* 1.3 72.9 - - - +
139A GLU* 1.3 61.5 + - - +
140A TYR 3.1 1.3 + - - -
141A GLY* 3.4 11.7 + - - -
142A LEU 5.3 0.2 - - - -
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A HIS* 4.5 0.2 - - - +
40A ALA* 3.8 17.7 + - - +
41A PHE* 3.3 46.6 + - - +
129A LYS* 5.6 0.9 + - - -
135A LEU* 4.6 19.5 - - + +
136A PRO* 2.9 31.3 + - + +
138A GLY* 1.3 78.1 - - - +
140A TYR* 1.3 71.4 + - + +
141A GLY 3.5 0.6 + - - -
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Residues in contact with TYR 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A VAL* 4.0 18.8 - - + -
126A PHE* 3.5 26.1 - - + -
127A GLU* 5.3 0.3 - - - +
129A LYS* 4.4 29.5 + - + +
130A PRO 3.9 9.0 - - - -
131A LEU* 3.5 35.9 - - + -
132A GLU* 3.0 25.3 + - - +
135A LEU* 3.1 29.8 - - + +
136A PRO 3.8 17.3 - - - -
137A LEU* 3.0 13.8 + - + +
139A GLU* 1.3 85.4 - - + +
141A GLY* 1.3 63.9 + - - +
142A LEU* 3.4 8.6 + - + -
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Residues in contact with GLY 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 6.2 1.3 - - - -
126A PHE* 4.2 8.7 - - - -
138A GLY 3.4 12.6 + - - -
139A GLU 3.5 1.8 + - - -
140A TYR* 1.3 77.9 - - - +
142A LEU* 1.3 64.2 + - - +
143A LYS* 3.6 17.1 + - - +
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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