Contacts of the helix formed by residues 127 - 136 (chain B) in PDB entry 2YPR
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 ASP 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B ASN* 3.0 33.1 - - - +
113B ILE 2.8 20.3 + - - +
114B MET* 4.5 2.2 - - - +
115B SER* 4.8 12.4 - - - +
125B ARG* 3.8 1.4 + - - -
126B PHE* 1.3 71.1 - - - +
128B PHE* 1.3 56.6 + - - +
129B GLN* 3.4 13.9 + - - +
130B GLY* 3.2 18.6 + - - -
131B LEU* 2.9 24.7 + - - +
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Residues in contact with PHE 128 (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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50A TRP* 4.6 1.6 - + - -
51A GLN* 3.3 23.3 - - + +
54A LEU* 3.7 43.7 - - + -
55A GLU* 3.7 33.8 + - + -
58A ALA* 3.6 22.4 - - + -
54B LEU* 3.9 19.7 - - + -
68B TRP* 3.6 26.5 - + - -
73B GLY* 4.3 4.3 - - - -
126B PHE* 3.7 26.2 + + + -
127B ASP* 1.3 69.6 + - - +
129B GLN* 1.4 59.9 + - - +
131B LEU* 3.7 14.6 - - + +
132B ALA* 3.0 22.7 + - - +
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Residues in contact with GLN 129 (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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47A ILE* 6.1 2.2 - - - +
51A GLN* 3.3 22.3 - - - +
55A GLU* 4.1 4.3 + - - +
90A ARG* 4.8 13.3 - - - +
127B ASP* 3.2 11.1 + - - +
128B PHE* 1.4 75.8 - - - +
130B GLY* 1.3 58.6 + - - +
132B ALA* 3.4 4.9 + - - +
133B GLN* 3.0 28.2 + - + +
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Residues in contact with GLY 130 (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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111B LYS 4.4 5.9 - - - +
112B ASN* 3.2 31.8 - - - +
113B ILE* 4.4 0.4 - - - +
127B ASP* 3.2 11.6 + - - -
129B GLN* 1.3 79.0 - - - +
131B LEU* 1.4 61.4 + - - +
133B GLN* 3.6 7.9 + - - +
134B ALA* 3.2 21.8 + - - +
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Residues in contact with LEU 131 (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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50A TRP* 4.2 21.3 - - + -
54A LEU* 5.0 0.2 - - + -
131A LEU* 4.8 2.7 - - + -
50B TRP* 3.8 49.1 - - + -
54B LEU* 4.4 8.3 - - + -
112B ASN 4.1 0.2 + - - -
113B ILE* 4.1 29.4 - - + +
126B PHE* 4.5 4.5 - - + -
127B ASP 2.9 17.5 + - - +
128B PHE* 3.7 21.5 - - + +
129B GLN 3.3 0.2 - - - -
130B GLY* 1.4 75.3 - - - +
132B ALA* 1.4 57.0 + - - +
134B ALA* 3.0 21.7 + - + +
135B CYS* 3.0 26.2 + - - -
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Residues in contact with ALA 132 (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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42A LYS* 5.3 1.0 - - - +
50A TRP* 3.6 29.7 - - + +
51A GLN* 3.4 26.0 - - + +
128B PHE 3.0 14.1 + - - +
129B GLN 3.6 4.3 - - - +
131B LEU* 1.4 75.7 - - - +
133B GLN* 1.4 59.8 + - - +
135B CYS* 3.3 4.7 + - - +
136B GLN* 3.3 25.5 + - - +
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Residues in contact with GLN 133 (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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129B GLN* 3.0 17.1 + - + +
130B GLY* 3.7 10.3 - - - +
132B ALA* 1.4 74.2 - - - +
134B ALA* 1.3 61.2 + - - +
135B CYS 3.4 0.5 + - - -
136B GLN* 3.4 22.8 + - - +
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Residues in contact with ALA 134 (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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135A CYS* 4.0 9.3 - - - +
111B LYS 4.9 4.7 - - - +
113B ILE* 4.3 20.9 - - + -
130B GLY 3.2 13.0 + - - +
131B LEU* 3.0 13.1 + - + +
133B GLN* 1.3 73.9 - - - +
135B CYS* 1.4 59.3 + - - +
136B GLN 3.5 5.5 - - - +
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Residues in contact with CYS 135 (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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42A LYS* 3.4 36.3 + - + +
50A TRP* 4.2 11.7 - - - -
134A ALA 4.0 2.9 - - - +
135A CYS* 3.0 50.4 - - + +
131B LEU* 3.0 37.1 + - - -
132B ALA* 3.4 12.1 - - - +
133B GLN 3.2 0.4 - - - -
134B ALA* 1.4 76.7 - - - +
136B GLN* 1.4 64.6 + - - +
137B PRO* 3.9 0.7 - - - +
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Residues in contact with GLN 136 (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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42A LYS* 5.0 1.6 - - + -
43A GLY* 3.8 27.6 - - - +
44A SER* 4.1 11.9 - - - +
45A GLY 5.0 2.7 - - - +
132B ALA 3.3 15.9 + - - +
133B GLN* 3.4 20.3 + - - +
134B ALA 4.0 5.2 - - - +
135B CYS* 1.4 78.9 - - - +
137B PRO* 1.4 71.1 - - + +
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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