Contacts of the helix formed by residues 140 - 148 (chain A) in PDB entry 4Z4H
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 LEU 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.6 23.6 - - + -
50A PRO* 3.1 37.9 - - + +
52A ILE* 3.3 21.1 + - + +
54A ILE* 3.9 33.2 - - + -
138A VAL* 4.5 1.1 - - + +
139A SER* 1.3 70.7 - - - +
141A GLN* 1.3 57.4 + - - +
143A LEU* 3.3 12.5 + - + +
144A HIS* 2.6 31.5 + - - -
158A THR* 3.7 22.2 - - + +
162A LEU* 4.2 19.1 - - + -
397A PHE* 5.2 4.5 - - + +
399A ILE* 5.9 0.4 - - + -
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Residues in contact with GLN 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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51A LYS* 3.2 48.8 + - + +
52A ILE* 5.9 0.7 - - - -
53A ASP* 6.5 0.2 - - - -
139A SER* 4.0 8.3 - - - +
140A LEU* 1.3 75.8 - - - +
142A ALA* 1.3 61.5 + - - +
143A LEU 3.0 6.1 + - - -
144A HIS* 3.2 21.2 + - - +
145A ASP* 3.2 29.7 + - - +
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Residues in contact with ALA 142 (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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139A SER* 3.1 26.5 + - - +
141A GLN* 1.3 77.5 - - - +
143A LEU* 1.3 56.7 + - - +
145A ASP* 3.9 13.7 - - - +
146A ALA* 3.2 24.1 + - - +
151A LEU* 4.0 14.4 - - + +
155A PRO* 4.3 9.9 - - + +
158A THR* 5.7 0.4 - - - +
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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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49A ILE* 5.1 6.1 - - + -
139A SER 3.8 1.2 + - - -
140A LEU* 3.3 14.9 + - + +
141A GLN 3.0 0.8 - - - -
142A ALA* 1.3 76.4 - - - +
144A HIS* 1.3 60.4 + - + +
145A ASP 3.1 1.1 - - - -
146A ALA* 3.2 2.0 + - + +
147A LEU* 2.9 36.8 + - + +
154A VAL* 4.2 14.4 - - + -
155A PRO* 4.3 12.3 - - + +
158A THR* 3.8 23.3 - - + -
159A ILE* 3.7 24.5 - - + -
162A LEU* 3.5 33.2 - - + -
213A MET* 4.0 20.4 - - + -
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Residues in contact with HIS 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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49A ILE* 3.0 42.1 + - + +
50A PRO 3.7 14.8 - - - -
51A LYS* 4.1 8.3 + - + +
140A LEU 2.6 27.7 + - - -
141A GLN* 3.2 19.4 + - - +
143A LEU* 1.3 77.6 - - + +
145A ASP* 1.3 58.7 + - - +
147A LEU* 3.6 10.7 + - + +
148A SER* 3.0 26.5 + - - -
150A ARG* 5.5 0.2 - - - -
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Residues in contact with ASP 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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141A GLN* 3.2 37.4 + - - +
142A ALA* 3.9 14.4 - - - +
143A LEU 3.1 0.4 - - - -
144A HIS* 1.3 77.2 - - - +
146A ALA* 1.3 63.0 + - - +
148A SER* 3.1 16.3 + - - +
150A ARG* 3.4 36.6 + - + +
151A LEU* 3.1 26.9 + - + -
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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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142A ALA 3.2 9.8 + - - +
143A LEU* 3.2 7.1 + - + +
145A ASP* 1.3 79.4 - - - +
147A LEU* 1.3 59.1 + - - +
148A SER 3.0 12.1 - - - +
151A LEU* 3.7 17.5 - - + +
153A SER 3.4 23.9 - - - +
154A VAL* 3.9 11.3 - - + +
155A PRO* 3.5 22.7 - - + -
743A PRO* 4.5 3.1 - - - +
744A THR* 4.4 12.1 - - - +
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Residues in contact with LEU 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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143A LEU* 2.9 25.5 + - + +
144A HIS* 3.8 9.0 - - + +
146A ALA* 1.3 75.2 - - - +
148A SER* 1.3 59.5 + - - +
154A VAL* 5.2 1.3 - - + -
208A PRO* 3.5 29.6 - - + -
209A SER 3.2 27.3 - - - +
210A LEU 4.3 13.2 - - - +
211A TRP 5.2 5.4 - - - +
212A LYS* 4.0 5.4 - - - -
213A MET* 3.6 43.5 - - + +
743A PRO* 4.2 16.8 - - + +
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Residues in contact with SER 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 HIS 3.0 18.5 + - - -
145A ASP* 3.1 10.4 + - - +
146A ALA 3.0 15.2 - - - +
147A LEU* 1.3 79.1 - - - +
149A GLY* 1.3 65.9 + - - +
150A ARG* 3.1 27.9 + - - +
151A LEU 4.2 3.1 - - - +
743A PRO* 5.7 0.9 - - - +
744A THR* 5.0 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