Contacts of the helix formed by residues 152 - 160 (chain A) in PDB entry 4DHZ
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 THR 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU* 5.0 4.0 - - - -
149A GLY* 4.9 7.6 - - - +
150A VAL 3.9 3.3 + - - +
151A HIS* 1.3 74.8 - - - +
153A GLU* 1.3 68.7 + - - +
154A GLU* 3.2 23.6 + - - +
155A ALA* 3.8 8.7 + - - +
156A VAL* 3.1 26.6 + - - +
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Residues in contact with GLU 153 (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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102A LEU* 4.6 25.1 - - + +
103A LYS* 2.8 32.0 + - - -
152A THR* 1.3 78.8 - - - +
154A GLU* 1.3 59.1 + - - +
156A VAL* 4.0 3.0 - - - +
157A TYR* 3.2 49.3 + - + +
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Residues in contact with GLU 154 (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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152A THR* 3.8 15.2 + - - +
153A GLU* 1.3 78.8 - - - +
155A ALA* 1.3 67.0 + - - +
157A TYR* 3.8 6.8 + - - +
158A THR* 2.9 25.4 + - - -
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Residues in contact with ALA 155 (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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150A VAL 5.1 1.8 - - - +
151A HIS* 4.2 16.4 - - + +
152A THR* 3.4 23.7 + - - +
154A GLU* 1.3 83.4 - - + +
156A VAL* 1.3 66.6 + - - +
158A THR* 3.0 9.6 + - - -
159A ILE* 3.0 28.1 + - + +
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Residues in contact with VAL 156 (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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98A ILE* 3.8 28.3 - - + -
102A LEU* 4.6 12.1 - - + -
142A PHE* 4.0 13.0 - - + -
146A ILE* 3.9 21.3 - - + -
151A HIS* 3.8 19.1 - - + -
152A THR 3.1 19.9 + - - +
153A GLU* 4.0 5.2 - - - +
155A ALA* 1.3 76.4 - - - +
157A TYR* 1.3 61.7 + - + +
159A ILE* 3.1 10.4 + - - +
160A LEU* 2.8 38.3 + - + +
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Residues in contact with TYR 157 (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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44A VAL* 4.9 6.7 - - + -
80A ARG* 3.6 31.7 + - - -
95A VAL* 4.5 8.7 - - + -
98A ILE* 4.8 5.2 - - + -
99A GLU* 2.9 35.8 + - + +
102A LEU* 4.8 8.8 - - + +
153A GLU* 3.2 41.6 + - + +
154A GLU* 4.2 6.7 - - - +
155A ALA 3.3 0.6 - - - -
156A VAL* 1.3 76.9 - - + +
158A THR* 1.3 59.5 + - - +
160A LEU* 3.7 26.6 + - + +
161A ASN* 2.6 37.2 + - - +
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Residues in contact with THR 158 (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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154A GLU* 2.9 16.5 + - - -
155A ALA* 3.0 11.9 + - - -
157A TYR* 1.3 74.7 - - - +
159A ILE* 1.3 65.6 + - + +
161A ASN* 3.4 5.3 + - - +
162A ASP* 3.2 21.3 + - - +
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Residues in contact with ILE 159 (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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138A PHE* 5.7 2.7 - - + -
142A PHE* 4.0 23.6 - - + -
151A HIS* 3.6 46.2 - - + +
155A ALA* 3.0 22.0 + - + +
156A VAL* 3.1 5.6 + - - +
158A THR* 1.3 74.2 - - - +
160A LEU* 1.3 57.1 + - - +
161A ASN 3.0 10.3 + - - -
162A ASP* 3.3 20.2 + - - +
165A SER* 3.6 29.4 - - - +
166A ALA 3.7 2.3 + - - -
169A ILE* 4.3 10.5 - - + -
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Residues in contact with LEU 160 (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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43A LEU* 4.1 4.7 - - - +
44A VAL* 3.8 22.9 - - + +
91A ARG* 4.7 2.2 + - + +
94A LEU* 3.4 30.3 - - + -
95A VAL* 4.2 17.3 - - + -
98A ILE* 4.4 13.7 - - + -
142A PHE* 4.8 2.7 - - + -
156A VAL* 2.8 28.1 + - + +
157A TYR* 3.7 37.2 - - + +
158A THR 3.3 0.4 - - - -
159A ILE* 1.3 74.8 - - - +
161A ASN* 1.3 58.1 + - - +
166A ALA* 3.5 20.5 - - + +
169A ILE* 4.5 17.5 - - + -
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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