Contacts of the helix formed by residues 139 - 147 (chain B) in PDB entry 4ZPK
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 ASP 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B HIS 3.2 15.3 - - - +
137B PRO 2.8 3.0 - - - -
138B CYS* 1.3 84.3 - - - +
140B HIS* 1.3 55.3 + - - +
141B GLU 3.1 2.7 - - - -
142B GLU* 2.8 29.0 + - + +
143B ILE* 2.8 29.6 + - + +
169B PHE 5.4 0.4 - - - +
170B MET* 3.6 4.9 - - - -
171B ARG* 2.7 63.7 + - - +
299B LYS* 3.8 19.4 + - - +
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Residues in contact with HIS 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 3.0 47.2 + + + +
135B THR* 2.3 45.6 + - - -
136B HIS 3.1 13.5 - - - -
137B PRO* 3.3 27.4 - - + +
139B ASP* 1.3 75.8 - - - +
141B GLU* 1.3 63.0 + - - +
143B ILE* 3.7 6.0 - - - +
144B ARG* 2.9 34.6 + - - +
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B CYS* 3.3 33.8 + - - +
140B HIS* 1.3 87.7 + - - +
142B GLU* 1.3 62.7 + - + +
144B ARG* 3.4 12.4 - - + +
145B GLU* 2.9 28.6 + - - +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B CYS 5.0 2.9 - - - +
139B ASP* 2.8 20.7 + - + +
141B GLU* 1.3 76.7 - - + +
143B ILE* 1.3 62.9 + - + +
145B GLU* 3.1 9.8 + - - +
146B ASN* 3.0 36.7 + - - +
168B PHE* 4.0 5.8 - - + +
169B PHE 3.1 29.6 + - - +
295B ASN* 4.8 8.3 + - - +
299B LYS* 3.1 28.0 + - - -
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Residues in contact with ILE 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B VAL* 6.4 0.7 - - + -
131B ILE* 4.7 8.1 - - + -
132B PHE* 4.4 8.3 - - + -
135B THR* 3.7 27.4 - - + +
139B ASP* 2.8 35.6 + - + +
140B HIS* 3.7 7.0 - - + +
142B GLU* 1.3 76.1 - - + +
144B ARG* 1.3 57.2 + - - +
146B ASN* 2.8 26.4 + - - +
147B LEU* 2.9 30.5 + - + +
168B PHE* 4.4 8.5 - - + -
170B MET* 3.5 44.0 - - + -
222B LEU* 5.9 2.2 - - + -
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ASP* 6.1 1.4 - - - +
132B PHE* 3.5 40.8 - - + -
140B HIS* 2.9 29.5 + - - +
141B GLU* 3.3 12.6 + - - +
143B ILE* 1.3 74.4 - - - +
145B GLU* 1.3 62.7 + - - +
147B LEU* 3.3 24.0 + - - +
148B THR* 4.1 11.0 + - + +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B GLU 2.9 12.8 + - - +
142B GLU* 3.3 9.4 - - - +
144B ARG* 1.3 77.6 - - - +
146B ASN* 1.3 95.8 + - - +
147B LEU 3.0 1.2 + - - -
148B THR* 3.4 20.2 + - - +
166B ARG* 4.7 5.8 + - - -
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Residues in contact with ASN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B GLU* 3.0 27.1 + - - +
143B ILE 2.8 9.2 + - - +
145B GLU* 1.3 91.9 + - - +
147B LEU* 1.3 59.8 + - - +
148B THR 3.4 0.2 - - - -
166B ARG* 3.0 43.0 + - - +
167B ASP 4.6 2.9 + - - +
168B PHE* 3.2 65.1 - - + +
199B VAL* 4.4 0.9 - - - +
222B LEU* 4.1 8.5 - - + +
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B VAL* 4.0 10.1 - - + -
103B THR 3.3 19.7 - - - +
104B GLN* 3.9 35.6 + - - +
106B GLY* 4.1 10.8 - - - -
131B ILE* 4.7 0.7 - - + -
132B PHE* 4.1 26.0 - - + -
143B ILE* 2.9 24.1 + - + +
144B ARG* 3.6 11.9 - - - +
145B GLU 3.0 1.2 + - - -
146B ASN* 1.3 79.6 - - - +
148B THR* 1.3 59.7 + - - +
199B VAL* 4.3 13.6 - - - +
222B LEU* 3.6 35.3 - - + +
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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