Contacts of the helix formed by residues 150 - 158 (chain A) in PDB entry 4EE5
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 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A VAL* 1.3 76.3 - - - +
151A LEU* 1.3 59.8 + - - +
152A GLU* 3.3 20.1 + - - +
153A LEU* 3.0 47.9 + - + +
154A VAL* 3.0 16.0 + - - +
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Residues in contact with LEU 151 (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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149A VAL* 4.0 7.6 + - + -
150A ASP* 1.3 70.9 + - - +
152A GLU* 1.3 56.4 + - - +
154A VAL* 3.6 7.4 - - + +
155A ALA* 2.7 35.7 + - - +
188A GLN* 4.7 8.7 - - - +
192A LYS* 3.7 49.7 - - + +
195A LEU* 3.8 28.9 - - + -
386A LEU* 3.7 16.7 - - + +
387A TYR* 4.2 13.7 - - + +
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Residues in contact with GLU 152 (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 ASP* 3.3 16.1 + - - +
151A LEU* 1.3 77.6 - - - +
153A LEU* 1.3 56.4 + - - +
155A ALA* 3.4 8.5 - - - +
156A LYS* 3.1 36.2 + - + +
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Residues in contact with LEU 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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150A ASP* 3.0 32.0 + - + +
152A GLU* 1.3 75.3 - - - +
154A VAL* 1.3 54.7 + - + +
155A ALA 3.1 1.1 - - - -
156A LYS* 3.0 19.5 + - + +
157A GLN* 2.7 64.1 + - + +
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Residues in contact with VAL 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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149A VAL* 3.7 24.5 - - + -
150A ASP 3.0 14.3 + - - +
151A LEU* 3.2 11.2 + - + +
153A LEU* 1.3 76.2 - - + +
155A ALA* 1.3 57.7 + - - +
157A GLN* 3.3 9.9 + - - +
158A ASN* 2.9 50.9 + - - +
195A LEU 4.2 5.4 - - - +
196A TYR* 3.9 38.4 - - + +
199A HIS* 5.4 0.4 - - + -
386A LEU* 3.7 18.6 - - + -
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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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151A LEU 2.7 19.7 + - - +
152A GLU* 3.4 9.4 - - - +
154A VAL* 1.3 73.5 - - - +
156A LYS* 1.3 57.7 + - - +
158A ASN 3.1 25.7 + - - +
159A PRO* 3.5 4.3 - - - +
385A PRO* 4.4 16.6 - - + -
386A LEU* 3.9 23.1 - - + +
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Residues in contact with LYS 156 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A GLU* 3.1 21.0 + - - +
153A LEU* 3.0 22.5 + - + +
155A ALA* 1.3 73.2 - - + +
157A GLN* 1.3 63.6 + - + +
158A ASN 3.1 1.3 - - - -
159A PRO* 3.3 16.8 - - - +
146C ASN* 4.7 6.4 - - - +
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Residues in contact with GLN 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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153A LEU* 2.7 55.2 + - + +
154A VAL* 3.7 8.3 - - - +
156A LYS* 1.3 71.6 - - - +
158A ASN* 1.3 66.7 + - - +
159A PRO* 3.2 8.0 - - - +
196A TYR* 3.7 27.2 - - - -
146C ASN* 4.7 10.1 + - - -
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Residues in contact with ASN 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 VAL* 2.9 41.2 + - - +
155A ALA* 3.3 7.7 - - - +
156A LYS 3.1 0.8 - - - -
157A GLN* 1.3 90.2 + - - +
159A PRO* 1.3 58.5 - - - +
160A ASN 3.1 2.9 - - - -
161A VAL* 2.9 38.8 + - + +
196A TYR* 5.2 0.8 + - - -
199A HIS* 4.2 7.4 - - - +
200A PRO* 3.7 28.5 - - - +
203A GLN* 3.1 24.4 + - - +
386A LEU* 4.8 6.6 - - + +
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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