Contacts of the helix formed by residues 152 - 162 (chain B) in PDB entry 4DHI
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B LEU* 5.6 0.7 - - - -
149B GLY 5.7 1.3 - - - +
150B VAL 3.6 6.5 + - - +
151B HIS* 1.3 77.2 - - - +
153B GLU* 1.3 64.9 + - - +
154B GLU* 3.5 16.5 + - - +
155B ALA* 3.1 23.0 + - - +
156B VAL* 3.0 23.1 + - - +
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Residues in contact with GLU 153 (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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80B ARG* 5.7 0.9 + - - -
102B LEU* 3.9 21.3 - - + +
103B LYS* 6.0 1.6 - - - -
152B THR* 1.3 73.6 - - - +
154B GLU* 1.3 75.4 + - - +
156B VAL* 3.2 7.9 + - - +
157B TYR* 3.0 61.1 + - + -
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Residues in contact with GLU 154 (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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152B THR* 3.7 18.6 - - - +
153B GLU* 1.3 87.7 + - - +
155B ALA* 1.3 64.6 + - - +
157B TYR* 3.3 6.6 + - - +
158B THR* 3.1 26.3 + - - -
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Residues in contact with ALA 155 (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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150B VAL 5.6 0.2 - - - +
151B HIS* 4.1 18.8 - - + +
152B THR* 3.1 29.5 + - - +
154B GLU* 1.3 76.4 - - - +
156B VAL* 1.3 62.2 + - - +
158B THR* 3.3 8.6 + - - -
159B ILE* 3.1 29.9 + - + +
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Residues in contact with VAL 156 (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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98B ILE* 3.8 28.0 - - + -
102B LEU* 4.0 17.3 - - + -
142B PHE* 4.0 13.7 - - + -
146B ILE* 3.9 28.3 - - + -
151B HIS* 3.9 11.2 - - + -
152B THR 3.0 14.1 + - - +
153B GLU* 3.5 8.7 - - - +
154B GLU 3.2 0.2 - - - -
155B ALA* 1.3 76.5 - - - +
157B TYR* 1.3 61.4 + - + +
159B ILE* 3.2 10.0 + - - +
160B LEU* 3.0 34.5 + - + +
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Residues in contact with TYR 157 (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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44B VAL* 4.5 15.3 - - + -
45B ALA 5.5 0.2 - - - -
80B ARG* 3.5 33.4 + - - -
95B VAL* 4.8 5.4 - - + -
98B ILE* 6.2 0.9 - - + -
99B GLU* 3.0 35.0 + - + +
102B LEU* 4.2 11.7 - - + +
153B GLU* 3.0 58.0 + - + +
154B GLU* 3.3 5.3 + - - +
156B VAL* 1.3 77.9 - - + +
158B THR* 1.3 61.9 + - - +
160B LEU* 3.3 21.3 + - + +
161B ASN* 3.1 33.7 + - - +
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Residues in contact with THR 158 (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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154B GLU 3.1 14.0 + - - -
155B ALA* 3.6 11.2 - - - -
156B VAL 3.2 0.2 - - - -
157B TYR* 1.3 76.2 - - - +
159B ILE* 1.3 64.9 + - + +
161B ASN* 3.1 15.3 + - - +
162B ASP* 3.2 14.7 + - + +
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Residues in contact with ILE 159 (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 PHE* 5.5 2.0 - - + -
142B PHE* 3.9 29.4 - - + -
151B HIS* 3.6 36.6 - - + +
155B ALA* 3.1 18.7 + - + +
156B VAL 3.6 5.8 - - - +
158B THR* 1.3 76.7 - - + +
160B LEU* 1.3 62.8 + - - +
161B ASN 3.1 1.4 + - - -
162B ASP* 3.2 23.6 + - - +
165B SER* 3.7 21.5 - - - +
166B ALA 3.7 5.5 + - - -
169B ILE* 4.1 11.4 - - + -
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Residues in contact with LEU 160 (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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43B LEU* 3.8 5.0 - - - +
44B VAL* 3.8 24.6 - - + +
91B ARG* 4.7 1.2 + - - +
94B LEU* 3.9 22.9 - - + -
95B VAL* 4.5 17.5 - - + -
98B ILE* 3.9 26.2 - - + -
142B PHE* 4.3 3.4 - - + -
156B VAL* 3.0 36.3 + - + +
157B TYR* 3.8 21.3 - - + +
158B THR 3.3 0.4 - - - -
159B ILE* 1.3 75.4 - - - +
161B ASN* 1.3 59.1 + - - +
162B ASP 3.6 0.2 - - - -
166B ALA* 3.3 21.1 - - + +
169B ILE* 4.2 20.9 - - + -
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Residues in contact with ASN 161 (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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42B PRO* 3.5 9.0 - - + +
43B LEU* 3.1 21.4 + - - +
44B VAL* 2.9 53.0 + - - +
157B TYR* 3.1 26.8 + - - +
158B THR* 3.1 7.2 + - - +
159B ILE 3.1 0.6 - - - -
160B LEU* 1.3 78.6 - - - +
162B ASP* 1.3 59.6 + - - +
163B ASP* 3.6 4.7 + - - +
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Residues in contact with ASP 162 (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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158B THR* 3.2 12.0 + - + +
159B ILE* 3.2 12.0 + - - +
161B ASN* 1.3 76.5 - - - +
163B ASP* 1.3 68.6 + - - +
164B GLY* 3.1 6.3 + - - -
165B SER* 3.1 31.9 + - - +
166B ALA* 2.7 24.7 + - - +
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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