Contacts of the helix formed by residues 165 - 173 (chain C) in PDB entry 3AP3
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 165 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU* 4.3 34.3 - - - +
161C PHE 4.6 1.9 + - - -
162C THR 2.5 17.4 + - - -
164C LYS* 1.3 78.6 - - - +
166C SER* 1.3 58.0 + - - +
167C VAL 3.3 2.5 - - - -
168C TYR* 3.1 13.2 + - - +
169C LEU* 2.8 26.6 + - - +
224C GLN* 3.3 2.2 - - - -
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Residues in contact with SER 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162C THR 3.7 1.8 + - - -
163C LEU* 3.3 18.1 + - - +
165C SER* 1.3 73.5 - - - +
167C VAL* 1.3 65.7 + - - +
169C LEU* 2.7 11.0 + - - -
170C SER* 2.7 26.9 + - - -
178C PHE* 3.6 30.7 - - - -
221C MET 5.0 0.2 + - - -
224C GLN* 3.0 29.6 + - - +
225C CYS* 4.3 2.9 + - - -
228C VAL* 4.3 9.6 - - - +
233C CYS* 6.0 0.4 - - - -
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Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C SER* 1.3 73.3 - - - +
168C TYR* 1.3 61.9 + - + +
170C SER* 3.6 4.4 + - - -
171C ARG* 3.3 55.5 + - - +
224C GLN* 2.7 46.7 + - - +
227C GLU* 3.8 38.6 - - + +
228C VAL* 4.1 10.7 - - + +
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Residues in contact with TYR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C LEU* 4.2 23.8 - - + -
110C ARG* 2.6 46.8 + - + -
134C ASP* 2.9 32.0 + - - -
137C MET* 3.4 17.0 - - + +
165C SER* 3.1 13.5 + - - +
167C VAL* 1.3 80.3 - - + +
169C LEU* 1.3 66.8 + - + +
171C ARG* 2.9 29.1 + - + +
172C LEU* 3.0 38.7 + - + +
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Residues in contact with LEU 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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72C PHE* 4.2 19.7 - - + -
103C ILE* 6.0 1.6 - - + -
107C LEU* 4.1 27.4 - - + -
141C ILE* 4.9 5.8 - - + -
162C THR* 3.7 38.8 - - - +
165C SER* 2.8 15.1 + - - +
166C SER 2.7 7.6 + - - +
168C TYR* 1.3 72.7 - - + +
170C SER* 1.3 55.5 + - - +
172C LEU* 2.9 35.1 + - + +
173C PHE* 2.9 23.6 + - + +
176C SER* 4.6 0.2 - - - -
178C PHE* 3.3 31.2 - - + -
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Residues in contact with SER 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C SER 2.7 18.9 + - - -
167C VAL 3.8 5.2 - - - -
169C LEU* 1.3 72.6 - - - +
171C ARG* 1.3 60.4 - - - +
173C PHE 3.2 17.7 - - - -
174C PRO* 3.4 8.5 - - - +
176C SER* 3.9 5.4 - - - -
178C PHE* 3.6 18.8 - - - -
228C VAL* 4.7 7.9 - - - -
232C LYS* 2.8 42.3 + - - +
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Residues in contact with ARG 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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134C ASP* 5.8 3.1 - - - +
138C GLN* 4.8 3.3 + - - -
167C VAL* 3.3 47.3 + - - +
168C TYR* 2.9 22.2 + - + +
170C SER* 1.3 76.4 - - - +
172C LEU* 1.3 64.1 + - + +
174C PRO* 4.7 7.4 - - - +
227C GLU* 4.8 6.1 + - - -
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Residues in contact with LEU 172 (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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66C LYS* 3.9 4.7 - - - +
134C ASP* 3.4 47.8 - - + +
137C MET* 3.8 17.7 - - + -
138C GLN* 3.2 27.4 + - + +
141C ILE* 4.2 11.2 - - + -
168C TYR* 3.0 41.0 + - + +
169C LEU* 2.9 13.3 + - + +
171C ARG* 1.3 82.0 - - + +
173C PHE* 1.3 90.1 + - + +
174C PRO* 4.1 2.5 - - - +
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Residues in contact with PHE 173 (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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66C LYS* 3.0 26.2 - - - +
68C MET 5.0 0.2 - - - +
70C LEU* 3.9 14.4 - - + -
72C PHE* 4.3 23.6 - + - -
138C GLN* 3.9 28.9 - - + -
141C ILE* 4.5 19.5 - - + -
142C LEU* 3.8 26.5 - - + -
145C ILE* 5.9 0.2 - - + -
169C LEU* 2.9 19.2 + - + -
170C SER* 3.2 5.3 - - - +
172C LEU* 1.3 106.1 - - + +
174C PRO* 1.3 59.6 - - - +
175C ASN 3.0 3.6 - - - -
176C SER* 2.6 50.4 + - - +
232C LYS* 4.1 0.2 + - - -
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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