Contacts of the strand formed by residues 147 - 151 (chain A) in PDB entry 2HR9
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 ALA 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A MET* 5.7 0.9 - - + -
78A LEU* 5.0 1.1 - - + -
133A GLN 2.8 5.8 - - - +
135A PHE* 2.6 52.1 + - + +
136A ILE* 5.1 0.9 - - - -
146A VAL* 1.3 73.3 - - - +
148A LEU* 1.3 63.7 + - - +
149A LEU 3.7 0.2 - - - -
160A MET* 3.1 34.5 - - + -
161A ILE 3.5 5.6 - - - +
162A PHE* 3.7 15.7 - - + -
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Residues in contact with LEU 148 (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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88A TYR* 3.3 25.6 - - + +
121A GLN* 5.7 1.3 - - + -
125A ILE* 3.5 41.3 - - + -
132A TYR* 3.9 17.5 - - + -
133A GLN 3.2 12.3 - - - +
134A PHE* 4.4 11.0 - - + -
146A VAL* 4.6 5.6 - - + +
147A ALA* 1.3 71.9 - - - +
149A LEU* 1.3 62.1 + - - +
150A ASP* 4.5 0.7 - - - -
159A TYR 3.5 0.7 - - - +
160A MET* 3.2 2.8 - - - -
161A ILE* 2.6 70.3 + - + +
163A PHE* 4.6 13.9 - - + -
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Residues in contact with LEU 149 (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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70A VAL* 4.0 29.6 - - + -
73A VAL* 4.4 6.7 - - + -
131A ASN 3.9 5.4 - - - +
133A GLN* 3.2 20.6 + - + +
135A PHE* 3.5 39.7 - - + -
147A ALA 3.5 1.4 + - - -
148A LEU* 1.3 69.1 - - - +
150A ASP* 1.3 72.0 + - - +
151A TYR* 4.4 22.2 - - + +
158A PRO* 4.2 11.4 - - + -
159A TYR 3.3 9.6 - - - +
160A MET* 3.5 26.7 - - + -
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Residues in contact with ASP 150 (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 ASN* 4.1 11.1 - - - +
132A TYR* 2.7 66.9 + - + -
148A LEU 3.6 1.7 + - - +
149A LEU* 1.3 87.4 - - - +
151A TYR* 1.3 67.4 + - - +
158A PRO* 3.4 4.0 - - - +
159A TYR* 2.6 70.9 + - + +
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Residues in contact with TYR 151 (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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35A MET* 3.8 27.4 - - + +
70A VAL* 4.9 2.6 - - - +
131A ASN 5.9 3.1 - - - -
149A LEU* 4.4 18.9 - - + +
150A ASP* 1.3 80.5 + - - +
152A ARG* 1.3 67.5 + - - +
155A GLY* 3.5 28.5 - - - -
156A VAL 3.1 26.0 - - - -
157A THR 3.4 1.6 - - - -
158A PRO* 3.6 24.1 - - + +
159A TYR* 3.4 11.2 + - - -
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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