Contacts of the helix formed by residues 150 - 158 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C PRO 4.1 2.0 + - - -
149C VAL* 1.3 73.1 - - - +
151C LEU* 1.3 57.8 + - - +
152C GLU* 3.1 26.5 + - - +
153C LEU* 2.6 47.3 + - + +
154C VAL* 2.9 13.7 + - - +
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Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C VAL* 4.0 20.3 + - + -
150C ASP* 1.3 75.2 + - - +
152C GLU* 1.3 61.3 + - + +
154C VAL* 3.7 7.4 - - + -
155C ALA* 3.2 22.0 + - - +
188C GLN* 4.6 8.5 - - - +
192C LYS* 4.1 35.8 - - + +
195C LEU* 4.1 24.7 - - + -
385C PRO* 6.0 0.2 - - - +
386C LEU* 3.8 25.5 - - + +
387C TYR* 4.3 14.8 - - + +
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Residues in contact with GLU 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ASP* 3.0 19.5 + - - +
151C LEU* 1.3 79.1 - - + +
153C LEU* 1.3 61.5 + - - +
155C ALA* 3.6 5.9 + - - +
156C LYS* 3.3 36.8 + - - +
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Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C ASP* 2.6 34.2 + - + +
152C GLU* 1.3 73.6 - - - +
154C VAL* 1.3 57.7 + - + +
155C ALA 3.1 0.2 - - - -
156C LYS* 3.1 18.5 + - + -
157C GLN* 2.7 63.1 + - + +
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Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C VAL* 3.8 25.1 - - + -
150C ASP 2.9 18.0 + - - +
151C LEU* 3.9 8.1 - - + +
153C LEU* 1.3 75.9 - - + +
155C ALA* 1.3 54.3 + - - +
157C GLN* 3.3 8.6 + - - +
158C ASN* 2.9 48.8 + - - +
195C LEU 4.2 4.9 - - - +
196C TYR* 3.8 39.5 - - + +
199C HIS* 5.3 0.4 - - + -
386C LEU* 3.7 24.2 - - + -
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Residues in contact with ALA 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C LEU 3.2 16.3 + - - +
152C GLU* 3.9 6.7 - - - +
153C LEU 3.1 0.6 - - - -
154C VAL* 1.3 74.2 - - - +
156C LYS* 1.3 66.1 + - + +
158C ASN* 3.1 22.5 + - - +
159C PRO* 3.4 5.9 - - - +
385C PRO* 4.4 17.9 - - + -
386C LEU* 4.0 21.4 - - + +
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Residues in contact with LYS 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ASN* 3.4 20.3 + - - -
152C GLU* 3.3 23.9 + - - +
153C LEU* 3.1 24.0 + - + +
155C ALA* 1.3 77.1 - - + +
157C GLN* 1.3 61.2 + - - +
158C ASN 3.4 0.3 + - - -
159C PRO* 3.5 6.5 - - - +
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Residues in contact with GLN 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLU* 3.0 26.9 - - - +
146B ASN* 5.1 0.9 - - - +
153C LEU* 2.7 46.0 + - + +
154C VAL* 3.5 12.0 - - - +
156C LYS* 1.3 79.0 - - - +
158C ASN* 1.3 66.4 + - - +
159C PRO* 3.2 2.1 - - - +
196C TYR* 3.8 24.6 - - - -
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Residues in contact with ASN 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C VAL* 2.9 40.1 + - - +
155C ALA* 3.1 10.2 + - - +
157C GLN* 1.3 86.2 + - - +
159C PRO* 1.3 66.6 - - - +
160C ASN 3.0 4.5 + - - -
161C VAL* 3.0 29.7 + - + +
196C TYR* 5.1 0.8 + - - -
199C HIS* 4.0 11.7 - - - +
200C PRO* 4.0 21.7 - - - +
203C GLN* 2.8 27.8 + - - +
386C LEU* 4.9 3.8 - - + +
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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