Contacts of the strand formed by residues 156 - 161 (chain G) in PDB entry 1SGF
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 TYR 156 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ILE* 4.0 22.1 - - + +
19G GLY* 3.9 30.3 - - - -
20G PHE* 3.5 4.9 - - - -
21G LYS* 3.8 37.9 - - + +
22G CYS* 3.2 9.3 - - - -
139G SER* 3.1 5.5 - - - -
140G GLY 3.0 32.9 + - - +
144G ILE* 3.7 33.7 - - + +
152G THR* 4.4 10.9 - - + +
154G ASP* 3.4 28.6 + - + -
155G LEU* 1.3 71.7 - - - +
157G CYS* 1.3 59.8 + - - +
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Residues in contact with CYS 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ILE* 4.5 0.9 - - - -
19G GLY* 3.4 0.9 - - - -
20G PHE* 2.8 54.1 + - + +
22G CYS* 2.0 46.2 - - + -
23G GLU 5.1 0.2 - - - -
26G SER* 4.8 1.1 - - - -
27G GLN* 3.9 26.2 - - - -
137G LEU* 3.9 13.2 - - + -
138G ALA 3.5 5.4 - - - -
139G SER* 4.0 5.4 - - - -
156G TYR* 1.3 73.1 - - - +
158G VAL* 1.3 62.9 + - - +
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Residues in contact with VAL 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ILE* 3.5 27.6 - - + -
17G VAL 4.4 1.1 - - - +
18G GLY 3.4 27.4 - - - +
19G GLY* 3.8 2.2 - - - -
20G PHE* 4.6 4.0 - - + -
136G CYS 3.6 1.0 - - - +
137G LEU* 3.2 9.6 - - - +
138G ALA* 2.9 45.8 + - + +
157G CYS* 1.3 76.1 - - - +
159G ASN* 1.3 67.1 + - - +
160G LEU* 3.8 19.6 + - + -
188G LYS* 3.8 22.0 - - + -
190G THR* 5.2 4.0 - - + +
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Residues in contact with ASN 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G PHE* 4.7 15.8 - - + -
135G THR* 4.0 20.4 - - + +
136G CYS 3.3 5.4 - - - +
137G LEU* 4.6 7.0 - - + +
158G VAL* 1.3 73.7 - - - +
160G LEU* 1.3 62.9 + - - +
185G GLU* 4.8 1.6 - - - +
188G LYS* 2.7 39.5 + - - +
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Residues in contact with LEU 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135G THR* 3.4 8.5 - - - +
136G CYS* 2.7 37.1 + - + +
138G ALA* 4.1 19.5 - - + -
158G VAL* 4.0 20.2 - - + -
159G ASN* 1.3 76.6 - - - +
161G LYS* 1.3 63.2 + - - +
183G ALA* 4.5 3.8 - - + +
184G GLY* 3.8 22.2 - - - +
185G GLU* 5.1 0.4 - - - -
188G LYS* 3.8 38.4 - - + +
189G ASP* 4.2 3.4 - - - +
190G THR* 4.9 0.9 - - + -
199G LEU* 4.1 8.3 - - + -
228G TYR* 3.3 34.1 - - + +
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Residues in contact with LYS 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G GLY* 5.1 13.2 - - - +
134G SER 3.7 5.6 - - - +
135G THR* 5.2 7.4 - - + +
136G CYS* 5.0 0.2 - - - -
160G LEU* 1.3 76.9 - - - +
162G LEU* 1.3 60.5 + - - +
163G LEU* 3.1 21.1 + - + +
183G ALA* 3.3 2.8 - - - -
184G GLY 3.0 36.1 + - - +
185G GLU* 2.8 44.4 + - - +
186G ASP* 5.4 2.0 - - - +
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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