Contacts of the strand formed by residues 158 - 162 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69G ASN* 3.0 29.2 + - - +
70G PHE* 3.7 25.9 - - + -
96G ASP 5.7 0.8 + - - -
97G VAL* 4.7 5.1 - - - +
150G ILE 3.7 1.0 - - - +
151G THR* 3.6 2.1 - - - +
152G VAL* 2.8 37.1 + - - +
154G THR* 3.0 33.1 + - - +
156G PRO 4.1 2.2 - - - +
157G PRO* 1.3 76.3 - - - +
159G VAL* 1.3 61.6 + - - +
160G ALA 4.2 0.2 + - - -
2H PRO* 3.0 35.5 - - + +
3H ARG* 3.6 7.3 + - - +
102H ILE* 3.4 15.7 - - + +
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Residues in contact with VAL 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G SER* 4.0 4.7 + - - -
70G PHE* 5.7 0.4 - - - -
149G THR* 3.6 29.8 - - + -
150G ILE 3.4 4.3 - - - +
151G THR* 4.2 17.0 - - + +
157G PRO* 4.7 2.2 - - + -
158G GLN* 1.3 81.0 - - - +
160G ALA* 1.3 65.6 + - - +
161G THR* 5.0 0.9 - - + -
64H LEU* 3.9 8.3 - - + -
65H SER 5.3 3.4 - - - +
101H MET* 3.3 30.3 - - + -
102H ILE 2.6 13.2 + - - +
103H LEU* 3.5 24.9 - - + -
104H ASN* 2.8 27.5 + - - -
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Residues in contact with ALA 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G THR* 3.5 17.7 - - + +
67G SER* 3.4 23.8 - - - -
70G PHE* 4.3 15.5 - - + -
149G THR* 3.6 0.3 - - - -
150G ILE* 2.7 52.5 + - + +
152G VAL* 6.3 0.2 - - + -
159G VAL* 1.3 76.6 - - - +
161G THR* 1.3 63.8 + - - +
104H ASN* 3.5 4.3 - - - -
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Residues in contact with THR 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G THR* 3.7 3.0 - - - -
66G ASP* 2.6 52.1 + - - +
147G THR* 4.4 4.7 - - + -
148G LEU 3.1 11.0 - - - +
149G THR* 4.1 13.9 - - - +
150G ILE* 5.8 0.2 - - - -
159G VAL* 5.0 1.3 - - + -
160G ALA* 1.3 77.9 - - - +
162G TYR* 1.3 59.5 + - - +
163G HIS* 3.6 11.1 - - - -
17H PHE* 4.0 25.4 - - + -
62H THR* 4.6 6.3 - - + -
103H LEU* 4.5 8.1 - - + -
104H ASN* 2.8 24.5 + - - +
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Residues in contact with TYR 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E ASP 6.2 0.4 - - - -
63G VAL* 3.8 26.8 - - + +
64G ARG 4.7 10.3 - - - -
65G THR* 5.1 3.1 - - - +
66G ASP* 3.9 2.7 - - - +
72G CYS* 3.5 32.8 - - - -
73G SER 4.1 6.1 - - - -
74G VAL* 4.7 2.9 - - - +
75G LEU* 4.5 18.7 + - + -
147G THR* 3.3 3.0 - - - -
148G LEU* 2.7 53.2 + - + -
150G ILE* 5.1 4.9 - - + -
161G THR* 1.3 74.5 - - - +
163G HIS* 1.3 69.1 + - - +
164G ARG 5.1 0.4 - - - -
165G ALA* 3.4 33.6 + - + +
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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