Contacts of the helix formed by residues 160 - 164 (chain A) 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 PRO 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A GLY* 3.7 10.1 - - - -
75A GLY 3.2 38.4 + - - +
76A VAL 4.8 0.2 - - - -
77A PRO* 3.9 29.6 - - + -
81A THR* 4.4 13.2 - - + +
99A GLU* 3.2 33.7 - - - +
158A LYS* 4.1 6.0 - - + -
159A ASP* 1.3 85.1 - - + +
161A PHE* 1.3 62.7 + - + +
162A THR 3.1 4.0 + - - -
163A LEU 3.5 7.1 + - - -
221A MET* 3.9 2.4 - - - +
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Residues in contact with PHE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 5.3 1.3 - - + -
77A PRO* 3.8 23.8 - - + -
104A PRO* 4.8 16.7 - - + +
159A ASP* 2.8 3.8 + - - +
160A PRO* 1.3 81.3 - - + +
162A THR* 1.3 63.6 + - - +
163A LEU 3.2 0.7 - - - -
164A LYS* 2.9 52.6 - - + +
165A SER* 4.4 1.0 + - - -
199A ILE* 3.5 33.4 - - + -
200A ALA* 5.0 9.4 - - + -
202A PHE* 4.5 15.0 - + - -
217A ALA* 4.8 13.9 - - + -
221A MET* 3.6 17.5 - - + -
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Residues in contact with THR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 5.0 6.8 - - + +
73A VAL 3.9 4.5 + - - -
103A ILE* 4.2 24.0 - - + -
104A PRO* 4.6 7.2 - - + +
107A LEU* 4.5 11.2 - - + -
157A ASN* 4.2 8.1 + - - +
159A ASP* 2.7 40.1 + - + +
161A PHE* 1.3 70.2 - - - +
163A LEU* 1.3 71.3 + - - +
164A LYS 2.6 16.6 + - - -
165A SER* 2.6 22.0 + - - -
166A SER 3.5 5.0 + - - -
169A LEU* 3.9 18.1 - - + +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 3.9 12.3 - - + +
73A VAL 3.8 4.9 - - - +
74A GLY* 3.6 28.5 - - - +
75A GLY 4.1 1.3 - - - +
160A PRO 3.5 7.6 + - - +
161A PHE 3.2 0.6 - - - -
162A THR* 1.3 94.0 + - - +
164A LYS* 1.3 58.0 + - - +
165A SER 3.2 0.4 - - - -
166A SER* 3.0 27.2 + - - +
178A PHE* 4.3 24.0 - - + -
179A LEU 3.7 10.5 - - - +
180A LEU* 3.5 45.5 - - + -
221A MET* 3.8 21.6 - - + +
224A GLN* 4.1 0.5 - - - +
225A CYS* 5.7 0.4 - - + -
233A CYS* 5.0 2.7 - - - -
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 2.9 43.2 + - + +
162A THR 2.6 1.4 + - - -
163A LEU* 1.3 80.1 - - - +
165A SER* 1.3 60.6 + - - +
217A ALA* 5.5 9.3 - - - +
220A VAL* 4.5 28.3 - - - +
221A MET* 3.7 24.7 - - + +
224A GLN* 2.8 23.2 + - - +
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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