Contacts of the helix formed by residues 165 - 170 (chain B) in PDB entry 1PM9
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 TYR 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ILE* 4.1 7.4 - - - -
160B VAL* 3.4 13.5 - - - -
161B TRP 3.3 21.3 - - - -
162B GLU* 3.0 23.5 + - + +
163B HIS 3.2 1.0 + - - -
164B ALA* 1.3 81.8 - - - +
166B PHE* 1.3 65.3 + + - +
167B LEU 3.4 2.9 - - - -
168B GLN* 3.2 4.4 + - - -
169B TYR* 2.8 36.4 + - + -
170B LYS 3.2 22.4 - - - -
171B ASN* 4.7 4.4 + - - -
173B ARG* 3.0 53.4 + - + +
176B TYR* 3.4 46.0 - + + -
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 6.2 0.4 - - - -
25A LEU* 4.0 17.3 - - + -
163A HIS* 3.5 44.4 - - + -
166A PHE* 5.0 11.7 - + + -
167A LEU* 3.7 41.7 - - + -
162B GLU* 2.7 36.1 + - + +
163B HIS 4.6 0.4 - - - -
165B TYR* 1.3 74.1 - + - +
167B LEU* 1.3 66.1 + - - +
170B LYS* 2.8 66.3 + - + +
171B ASN* 3.6 21.3 - - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 3.5 38.7 - - + +
167A LEU* 3.9 37.9 - - + +
170A LYS* 5.1 4.7 - - - -
19B ASN* 4.5 5.5 + - - +
21B GLN* 3.7 40.8 - - + +
22B ILE* 3.8 24.6 - - + +
25B LEU* 4.0 5.4 - - + -
163B HIS 5.6 0.8 + - - -
165B TYR 3.4 0.8 + - - -
166B PHE* 1.3 78.6 - - - +
168B GLN* 1.3 57.8 + - - +
170B LYS* 3.3 18.5 + - - -
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Residues in contact with GLN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PRO 3.0 27.5 + - - -
17B HIS 3.5 0.4 + - - -
18B ILE* 3.5 5.4 - - - -
19B ASN* 2.7 50.8 + - - +
22B ILE* 3.6 9.5 - - + +
165B TYR 3.2 1.2 + - - -
166B PHE 3.1 0.4 - - - -
167B LEU* 1.3 81.4 - - - +
169B TYR* 1.3 95.6 + - + +
170B LYS* 3.5 8.7 + - - +
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Residues in contact with TYR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B PRO 4.2 0.5 + - - -
17B HIS* 2.6 31.8 + - - -
18B ILE* 5.2 0.7 - - - -
22B ILE* 5.7 0.9 - - + -
165B TYR* 2.8 28.3 + - + +
168B GLN* 1.3 103.5 + - + +
170B LYS* 1.3 70.4 + - - +
172B VAL* 3.0 35.2 + - - +
175B ASP* 3.6 32.5 - - + -
176B TYR* 3.7 32.8 - + + -
179B ALA* 2.9 19.7 - - + +
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Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLN* 2.9 30.7 + - - -
25A LEU* 3.6 30.7 - - + -
167A LEU* 4.2 7.4 - - - -
165B TYR* 3.2 19.9 - - - -
166B PHE* 2.8 48.8 + - + +
167B LEU 3.3 20.2 + - - -
168B GLN 4.2 8.4 + - - +
169B TYR* 1.3 80.2 - - - +
171B ASN* 1.3 66.4 + - - +
172B VAL* 4.5 3.8 - - + +
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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