Contacts of the strand formed by residues 158 - 162 (chain R) in PDB entry 1E50
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 GLN 158 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69R ASN* 3.4 29.3 + - - +
70R PHE* 3.6 24.9 - - + -
97R VAL* 4.5 8.8 - - - +
150R ILE 3.6 1.2 - - - +
151R THR* 3.6 2.1 - - - -
152R VAL* 2.9 40.0 + - + +
154R THR* 3.5 21.2 + - - +
156R PRO 4.7 3.6 - - - +
157R PRO* 1.3 77.1 - - - +
159R VAL* 1.3 62.6 + - - +
160R ALA* 5.5 0.2 - - - +
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Residues in contact with VAL 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67R SER* 4.0 12.1 + - - -
70R PHE* 5.4 0.4 - - - -
149R THR* 3.6 29.4 - - + -
150R ILE 3.4 3.1 - - - +
151R THR* 4.4 14.6 - - + +
157R PRO* 5.1 7.4 - - + +
158R GLN* 1.3 79.5 - - - +
160R ALA* 1.3 68.9 + - - +
161R THR* 4.7 6.3 - - - +
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Residues in contact with ALA 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R THR* 3.5 24.2 - - - +
67R SER* 3.7 10.8 - - - -
70R PHE* 4.2 13.2 - - + -
149R THR* 3.3 4.7 - - - -
150R ILE* 2.8 59.5 + - + +
152R VAL* 6.2 0.7 - - + -
158R GLN 5.5 0.2 - - - +
159R VAL* 1.3 77.5 - - - +
161R THR* 1.3 62.4 + - - +
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Residues in contact with THR 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65R THR* 3.3 7.1 - - - -
66R ASP* 2.8 56.4 + - - +
147R THR* 3.4 26.2 - - + -
148R LEU 3.6 6.5 + - - +
149R THR* 4.5 5.8 + - - +
159R VAL* 4.4 8.0 - - - +
160R ALA* 1.3 75.5 + - - +
162R TYR* 1.3 64.9 + - - +
163R HIS* 3.4 15.7 - - + +
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Residues in contact with TYR 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63R VAL* 4.0 33.7 - - + +
64R ARG 4.1 12.8 - - - -
65R THR* 4.5 3.4 - - + -
66R ASP* 4.3 1.3 - - - -
72R CYS* 4.1 28.3 - - - -
73R SER 5.5 0.4 - - - -
74R VAL* 4.1 29.1 - - + +
75R LEU* 5.2 3.6 - - + -
89R PHE* 6.2 0.2 - + - -
147R THR* 3.4 4.8 - - - -
148R LEU* 3.2 39.8 + - + -
150R ILE* 5.9 1.8 - - + -
161R THR* 1.3 79.3 - - - +
163R HIS* 1.3 69.7 + - - +
164R ARG 5.2 0.7 - - - -
165R ALA* 3.2 43.3 - - + +
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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