Contacts of the helix formed by residues 142 - 149 (chain A) in PDB entry 4Z7Z
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 GLY 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASN 3.4 3.6 + - - -
141A PRO* 1.3 75.6 - - - +
143A LEU* 1.3 63.8 + - - -
144A MET 3.4 2.7 - - - -
145A ALA* 3.4 9.3 + - - +
146A ALA* 3.1 22.3 + - - +
196A THR* 4.0 3.1 - - - -
197A THR 3.8 9.6 - - - -
198A PRO 5.3 2.0 - - - -
402A ACY 5.0 1.8 + - - +
17D ORP 3.9 25.7 + - - -
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Residues in contact with LEU 143 (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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111A PHE* 3.6 30.1 - - + -
116A GLU* 3.8 32.5 - - + +
119A LEU* 3.6 29.4 - - + +
120A LEU* 4.1 18.2 - - + -
142A GLY* 1.3 71.2 - - - -
144A MET* 1.3 57.5 + - - +
146A ALA* 3.4 3.5 + - - +
147A TYR* 2.9 28.4 + - - +
196A THR* 4.1 15.5 - - + -
197A THR 4.2 1.4 + - - -
198A PRO* 4.2 23.3 + - + +
16D A 6.2 0.2 - - - +
17D ORP 5.5 1.0 + - - -
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Residues in contact with MET 144 (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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111A PHE* 3.8 32.1 - - + -
142A GLY 3.4 0.4 - - - -
143A LEU* 1.3 75.0 - - - +
145A ALA* 1.4 62.1 + - - +
147A TYR* 3.3 5.9 + - - +
148A LYS* 2.9 52.3 + - - +
153A PRO* 3.6 30.1 - - + +
154A GLY* 4.4 7.9 - - - +
155A PRO* 4.8 14.6 - - + -
17C C 5.8 3.8 - - - +
17D ORP 4.8 12.1 + - - +
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Residues in contact with ALA 145 (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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124A LEU* 3.8 22.0 - - + +
141A PRO* 4.3 2.2 - - + -
142A GLY* 3.4 21.0 + - - +
144A MET* 1.4 73.4 - - - +
146A ALA* 1.3 57.0 + - - +
149A GLY* 2.8 34.5 + - - -
150A HIS 3.6 15.0 + - - +
152A TYR 4.9 2.5 - - - +
153A PRO* 3.5 21.9 - - + +
402A ACY 5.9 2.7 - - + -
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Residues in contact with ALA 146 (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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119A LEU* 3.6 19.7 - - + +
122A LYS* 2.9 34.0 + - + +
123A THR 5.0 9.8 - - - +
124A LEU* 5.4 0.4 - - - -
141A PRO* 4.5 4.3 - - + +
142A GLY 3.1 15.6 + - - +
143A LEU* 3.6 5.2 - - - +
145A ALA* 1.3 75.3 - - - +
147A TYR* 1.4 60.0 + - - +
149A GLY* 3.8 6.1 + - - -
196A THR* 3.5 27.1 - - + +
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Residues in contact with TYR 147 (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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111A PHE* 3.2 43.7 - + + -
112A ASN* 3.4 30.2 + - + +
114A VAL* 3.7 16.8 - - + +
119A LEU* 3.8 19.9 - - + +
122A LYS* 3.1 20.9 + - - +
143A LEU 2.9 17.6 + - - +
144A MET* 3.4 13.2 - - - +
145A ALA 3.3 0.2 - - - -
146A ALA* 1.4 76.6 - - - +
148A LYS* 1.3 93.1 + - + +
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Residues in contact with LYS 148 (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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144A MET* 2.9 35.8 + - - +
147A TYR* 1.3 99.2 - - + +
149A GLY* 1.3 61.9 + - - +
150A HIS* 3.3 21.4 + - + +
153A PRO* 3.9 17.7 - - + -
175A HIS* 3.8 30.3 + - + +
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Residues in contact with GLY 149 (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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122A LYS* 5.7 1.6 - - - -
123A THR 5.5 2.2 - - - -
124A LEU* 3.4 17.9 - - - +
125A PRO* 4.5 11.5 - - - +
145A ALA 2.8 12.7 + - - -
146A ALA* 3.8 5.6 + - - -
147A TYR 3.4 2.2 - - - -
148A LYS* 1.3 77.7 - - - +
150A HIS* 1.3 66.4 + - - +
151A HIS* 5.3 0.3 - - - -
178A ASP* 4.6 0.7 - - - +
179A HIS* 4.8 7.4 - - - -
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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