Contacts of the helix formed by residues 164 - 170 (chain E) in PDB entry 4GOO
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 SER 164 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34E PRO 5.5 0.2 - - - -
55E ILE* 4.4 9.3 - - - +
163E GLU* 1.3 78.0 - - - +
165E TYR* 1.3 76.4 + - - +
166E ALA* 2.7 8.0 + - - -
167E ASP* 2.8 25.4 + - - -
168E SER* 3.1 10.6 + - - -
301E 0Y2 3.4 23.6 + - - -
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Residues in contact with TYR 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E PRO* 4.1 8.5 - - + -
35E PHE* 3.8 26.9 - + + -
164E SER* 1.3 77.4 + - - +
166E ALA* 1.3 74.9 + - + +
168E SER* 3.7 8.3 - - - -
169E MET* 2.9 46.2 + - - +
201E PHE* 3.8 27.1 - + - -
205E GLN* 3.5 33.0 - - + +
208E HIS* 2.8 38.3 + + - +
209E LEU* 4.3 13.7 - - + -
212E ILE* 3.8 16.4 - - + -
301E 0Y2 3.3 26.3 + - - +
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Residues in contact with ALA 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E SER* 2.7 9.3 + - - -
165E TYR* 1.3 93.0 - - + +
167E ASP* 1.3 65.1 + - - +
169E MET* 3.4 2.8 + - - +
170E ALA* 3.3 18.5 + - - +
208E HIS* 4.4 9.2 - - + -
212E ILE* 3.9 24.7 - - + +
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Residues in contact with ASP 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E GLU* 3.8 24.6 - - - +
164E SER* 2.8 28.2 + - - +
166E ALA* 1.3 71.5 - - - +
168E SER* 1.3 65.6 + - - +
170E ALA* 3.1 15.3 + - - +
171E ARG* 3.5 13.3 + - - +
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Residues in contact with SER 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E VAL* 3.9 16.6 - - - +
34E PRO* 3.2 23.7 - - - +
51E ILE* 5.4 1.1 - - - -
53E ALA* 3.5 31.0 - - - -
163E GLU* 3.2 14.7 + - - -
164E SER 3.1 8.6 + - - -
165E TYR* 3.1 11.5 + - - -
167E ASP* 1.3 75.8 - - - +
169E MET* 1.3 66.9 + - - +
171E ARG* 3.0 24.2 + - - +
172E ALA 4.0 0.2 + - - -
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Residues in contact with MET 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E VAL* 4.9 4.9 - - - -
34E PRO* 3.7 25.6 - - + -
165E TYR* 2.9 26.2 + - - +
166E ALA 3.8 3.8 - - - +
167E ASP 3.2 0.2 - - - -
168E SER* 1.3 83.3 + - - +
170E ALA* 1.3 57.6 + - - +
172E ALA* 3.5 18.9 + - - +
178E VAL* 4.4 7.2 - - + -
180E CYS* 4.4 9.0 - - - -
209E LEU* 3.4 34.1 - - + +
212E ILE* 3.9 28.0 - - + -
213E ALA* 4.1 11.7 - - + +
216E LEU* 3.7 37.8 - - + +
223E VAL* 4.9 0.9 - - + -
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Residues in contact with ALA 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E ALA 3.3 10.2 + - - +
167E ASP* 3.1 11.5 + - - +
168E SER 3.1 1.4 - - - -
169E MET* 1.3 75.0 - - - +
171E ARG* 1.3 66.2 + - - +
172E ALA 3.2 7.4 + - - +
216E LEU* 5.7 1.1 - - - -
219E ARG* 5.4 7.0 + - - +
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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