Contacts of the helix formed by residues 129 - 137 (chain A) in PDB entry 2PY5
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A PHE* 1.3 92.4 - - + +
130A VAL* 1.3 65.6 + - - +
131A LYS* 4.3 8.1 - - + +
132A LYS* 3.0 22.1 + - + +
133A ILE* 3.0 19.5 + - - +
5J T 3.5 35.9 - - - +
6J T 3.6 22.7 - - - +
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Residues in contact with VAL 130 (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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61A HIS* 3.4 27.1 - - + -
128A PHE 3.7 0.6 + - - -
129A PRO* 1.3 70.5 - - - +
131A LYS* 1.3 66.7 + - + +
133A ILE* 3.2 9.8 + - - +
134A ALA* 2.9 22.0 + - - +
169A ASP* 4.3 23.8 - - + +
172A ILE* 3.7 36.2 - - + +
173A ILE* 4.0 9.0 - - + -
6J T 3.0 21.8 + - - +
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Residues in contact with LYS 131 (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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129A PRO* 3.3 5.5 - - + +
130A VAL* 1.3 80.6 - - + +
132A LYS* 1.3 59.8 + - - +
134A ALA* 3.5 6.6 + - - +
135A LYS* 3.2 22.4 + - - +
141A VAL* 3.7 20.9 - - + +
142A LEU 2.8 28.0 + - - -
143A LYS* 4.2 1.2 - - - +
144A GLY 3.2 29.5 + - - +
145A ASP* 4.0 11.7 - - - +
169A ASP* 5.9 2.7 - - - -
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Residues in contact with LYS 132 (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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128A PHE* 3.8 32.1 - - + -
129A PRO* 3.0 27.3 + - + +
131A LYS* 1.3 76.2 - - - +
133A ILE* 1.3 60.8 + - - +
135A LYS* 3.2 13.9 + - + +
136A ASP* 2.7 61.4 + - - +
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Residues in contact with ILE 133 (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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61A HIS* 3.6 21.8 - - + +
126A LEU* 3.7 17.3 - - + +
128A PHE* 3.5 38.8 - - + +
129A PRO 3.0 13.8 + - - +
130A VAL* 3.5 7.0 - - - +
132A LYS* 1.3 76.1 - - - +
134A ALA* 1.3 57.3 + - - +
136A ASP* 4.9 0.4 - - - -
137A PHE* 2.9 53.0 + - + +
139A LEU* 4.5 0.4 - - + -
172A ILE* 4.1 10.8 - - + -
173A ILE* 3.7 13.7 - - + -
176A ALA* 3.6 29.4 - - + -
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Residues in contact with ALA 134 (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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130A VAL 2.9 16.8 + - - +
131A LYS 3.7 4.5 - - - +
133A ILE* 1.3 75.2 - - - +
135A LYS* 1.3 62.7 + - - +
138A LYS* 3.1 3.3 + - - -
139A LEU* 2.8 44.5 + - - +
141A VAL* 3.7 31.4 - - + -
172A ILE* 3.8 19.9 - - + +
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Residues in contact with LYS 135 (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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131A LYS 3.2 14.2 + - - +
132A LYS* 3.3 22.1 - - + +
134A ALA* 1.3 79.2 - - - +
136A ASP* 1.3 84.8 + - - +
138A LYS* 3.3 21.0 + - - +
141A VAL* 5.3 3.7 - - + +
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Residues in contact with ASP 136 (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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128A PHE* 5.2 4.2 - - - -
132A LYS* 2.7 56.7 + - - +
133A ILE* 4.9 0.4 - - - -
135A LYS* 1.3 97.2 + - - +
137A PHE* 1.3 66.9 + - + +
138A LYS* 3.2 4.5 + - - +
376A GLY* 3.6 14.2 - - - -
380A GLN* 3.6 39.2 + - + +
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Residues in contact with PHE 137 (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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126A LEU* 3.6 30.3 - - + -
128A PHE* 5.0 14.4 - + - -
133A ILE* 2.9 36.6 + - + +
136A ASP* 1.3 81.5 - - + +
138A LYS* 1.3 72.4 + - - +
139A LEU* 3.4 22.6 - - + +
176A ALA* 3.9 24.5 - - + -
179A ILE* 4.7 2.0 - - + +
377A ALA* 3.4 39.7 + - + +
380A GLN* 3.6 25.6 - - + -
381A LEU* 4.1 20.0 - - + -
384A LEU* 5.9 0.7 - - + -
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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