Contacts of the helix formed by residues 165 - 171 (chain C) in PDB entry 6APL
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 GLN 165 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160C LEU* 4.4 1.8 - - + -
163C SER* 3.1 36.5 + - - +
164C ARG* 1.3 78.1 + - - +
166C GLY* 1.3 53.3 + - - +
167C PRO* 3.4 2.2 - - - -
168C ASN* 3.1 32.2 + - - +
169C ILE* 2.8 38.1 + - + +
189C ASP 3.3 14.8 + - - +
323C TYR* 3.6 27.8 - - + -
372C TYR* 3.5 35.0 + - + -
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Residues in contact with GLY 166 (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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165C GLN* 1.3 75.1 - - - +
167C PRO* 1.3 65.1 - - - +
169C ILE* 3.1 2.1 + - - +
170C ASP* 2.8 35.1 + - - +
187C GLU 4.0 2.0 - - - -
188C ARG* 3.2 12.5 + - - -
189C ASP 3.3 2.8 + - - -
190C VAL 4.1 0.7 - - - -
191C GLY* 3.5 29.6 - - - -
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Residues in contact with PRO 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C ARG* 3.7 15.3 - - + +
166C GLY* 1.3 87.6 - - - +
168C ASN* 1.3 67.2 + - - +
170C ASP* 3.9 3.7 - - + +
171C ALA* 3.0 26.7 + - - +
188C ARG* 4.1 6.5 - - - +
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Residues in contact with ASN 168 (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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164C ARG 5.7 1.3 + - - -
165C GLN* 3.1 36.2 + - - +
167C PRO* 1.3 80.1 - - - +
169C ILE* 1.3 58.7 + - - +
171C ALA* 3.6 9.3 + - - +
172C HIS* 2.9 25.8 + - - -
323C TYR* 3.7 16.3 + - + +
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Residues in contact with ILE 169 (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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152C ALA* 3.9 3.5 - - + +
154C VAL* 3.8 21.1 - - + -
160C LEU* 4.8 2.9 - - + -
165C GLN* 2.8 28.1 + - + +
166C GLY 3.6 3.1 - - - +
168C ASN* 1.3 73.7 - - - +
170C ASP* 1.3 64.9 + - - +
171C ALA 3.2 0.9 + - - -
172C HIS* 3.2 24.5 + - - +
175C VAL* 3.7 14.3 - - + +
177C ARG* 4.0 9.2 - - - +
189C ASP 4.1 0.4 - - - +
190C VAL* 3.6 40.6 - - + +
323C TYR* 3.5 48.2 - - + -
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Residues in contact with ASP 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C GLY 2.8 18.2 + - - +
167C PRO* 4.3 3.1 - - + +
169C ILE* 1.3 74.5 - - - +
171C ALA* 1.3 61.0 + - - +
172C HIS 3.1 1.3 + - - -
177C ARG* 3.9 4.7 + - - -
191C GLY* 3.3 12.0 - - - -
192C THR* 3.1 28.8 + - - +
193C LYS* 3.0 56.5 + - + +
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Residues in contact with ALA 171 (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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167C PRO 3.0 19.1 + - - +
168C ASN* 3.8 9.2 - - - +
169C ILE 3.1 1.4 - - - -
170C ASP* 1.3 76.6 - - - +
172C HIS* 1.3 61.5 + - + +
173C ASP* 3.9 2.8 + - - +
193C LYS* 4.9 0.4 + - - -
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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