Contacts of the helix formed by residues 165 - 174 (chain R) in PDB entry 5A0Q
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 ALA 165 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31R THR* 3.2 28.7 - - + -
160R ALA* 3.4 18.8 - - + +
161R ILE 3.4 2.2 - - - -
162R GLY 3.2 32.0 + - - +
163R ARG 3.1 2.8 + - - -
164R GLY* 1.3 76.5 - - - +
166R LYS* 1.3 59.2 + - + +
167R SER 3.3 0.2 - - - -
168R VAL* 3.2 4.9 + - - +
169R ARG* 2.8 29.3 + - - +
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Residues in contact with LYS 166 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27R LYS* 4.1 36.4 - - + +
160R ALA 5.3 1.3 - - - +
161R ILE* 6.3 0.4 - - - -
162R GLY 4.5 11.2 - - - +
164R GLY* 3.2 2.9 - - - +
165R ALA* 1.3 78.8 - - + +
167R SER* 1.3 59.1 + - - +
169R ARG* 3.1 43.5 + - - +
170R GLU* 3.1 31.0 + - - +
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Residues in contact with SER 167 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164R GLY* 3.4 18.4 + - - -
165R ALA 3.3 0.2 - - - -
166R LYS* 1.3 78.2 - - - +
168R VAL* 1.4 56.5 + - - +
170R GLU* 3.5 10.4 + - - +
171R PHE* 3.0 25.0 + - - +
198R VAL* 4.5 15.2 - - - +
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Residues in contact with VAL 168 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31R THR* 4.5 4.9 - - + -
33R VAL* 4.1 10.1 - - + -
160R ALA* 3.8 22.2 - - + -
164R GLY 3.4 8.4 + - - +
165R ALA* 3.3 11.7 - - - +
166R LYS 3.2 0.2 - - - -
167R SER* 1.4 74.7 - - - +
169R ARG* 1.4 57.7 + - - +
170R GLU 3.3 0.2 - - - -
171R PHE* 3.2 5.8 + - + +
172R LEU* 2.8 29.5 + - + +
194R ALA* 3.3 44.9 - - + +
195R LEU* 4.2 9.6 - - + -
198R VAL* 4.0 15.0 - - + -
199R VAL* 4.3 4.0 - - + -
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Residues in contact with ARG 169 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156R TRP* 4.8 17.4 - - + -
159R ASN* 3.2 29.6 - - - +
160R ALA* 3.5 31.6 + - + +
165R ALA 2.8 9.3 + - - +
166R LYS* 3.1 55.2 + - - +
168R VAL* 1.4 73.4 - - - +
170R GLU* 1.4 58.1 + - - +
172R LEU* 3.2 13.2 + - + +
173R GLU* 2.8 53.2 + - - +
56S SER* 4.9 6.9 + - - -
58S LEU* 4.5 2.6 - - + +
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Residues in contact with GLU 170 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166R LYS 3.1 12.8 + - - +
167R SER* 3.7 11.2 - - - +
169R ARG* 1.4 83.7 - - - +
171R PHE* 1.4 59.4 + - - +
173R GLU* 3.2 31.6 + - - +
174R LYS* 3.3 18.3 + - - +
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Residues in contact with PHE 171 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167R SER 3.0 15.7 + - - +
168R VAL* 3.2 12.3 + - - +
170R GLU* 1.4 72.8 - - - +
172R LEU* 1.3 67.5 + - + +
174R LYS* 3.4 30.7 - - - +
175R ASN* 3.0 47.6 + - + +
193R LYS* 3.8 31.6 - - + -
194R ALA* 3.6 35.7 - - + -
197R GLU* 3.1 39.3 - - + -
198R VAL* 4.0 16.6 - - + -
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Residues in contact with LEU 172 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33R VAL* 4.1 22.2 - - + -
34R GLY 4.5 2.2 - - - +
35R VAL* 4.2 15.9 - - + -
158R ALA* 4.2 10.3 - - + -
159R ASN 4.8 5.6 - - - +
160R ALA* 5.0 0.7 - - + -
168R VAL* 2.8 22.8 + - + +
169R ARG* 3.3 13.7 - - - +
171R PHE* 1.3 81.0 - - + +
173R GLU* 1.3 54.9 + - - +
175R ASN* 2.9 5.3 + - + +
176R TYR* 2.7 39.7 + - + +
190R LEU* 3.0 39.7 - - + +
193R LYS* 6.1 0.4 - - - -
194R ALA* 4.4 14.1 - - + -
58S LEU* 4.1 10.3 - - + -
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Residues in contact with GLU 173 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156R TRP* 6.0 0.9 - - - -
169R ARG* 2.8 47.9 + - - +
170R GLU* 3.2 24.9 + - - +
172R LEU* 1.3 74.7 - - - +
174R LYS* 1.4 59.5 + - - +
175R ASN 3.6 0.2 + - - -
176R TYR* 4.0 10.2 + - - +
56S SER* 5.9 0.2 - - - -
57S PRO* 3.9 34.1 - - + +
58S LEU* 3.8 23.9 - - + +
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Residues in contact with LYS 174 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170R GLU 3.3 9.6 + - - +
171R PHE* 3.4 48.4 - - - +
173R GLU* 1.4 76.2 - - - +
175R ASN* 1.3 70.3 + - - +
176R TYR 3.7 0.4 - - - -
197R GLU* 5.5 2.6 + - - -
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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