Contacts of the strand formed by residues 135 - 140 (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 THR 135 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G GLY 3.2 6.5 + - - -
134G SER* 1.3 73.3 - - - +
136G CYS* 1.3 62.3 + - - +
159G ASN* 4.0 24.2 - - + +
160G LEU 3.4 12.3 - - - +
161G LYS* 4.8 7.5 - - + +
200G ILE 4.0 0.3 - - - +
201G CYS* 3.6 0.3 - - - -
202G ASP* 3.2 34.9 + - - +
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Residues in contact with CYS 136 (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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134G SER 3.8 9.9 - - - -
135G THR* 1.3 76.6 - - - +
137G LEU* 1.3 60.7 + - - +
158G VAL 3.6 0.3 - - - +
159G ASN* 3.3 4.6 - - - -
160G LEU* 2.7 43.3 + - + +
162G LEU* 3.9 22.4 - - - -
183G ALA* 5.2 1.1 - - + -
199G LEU* 3.8 20.4 - - + -
200G ILE 3.3 4.9 - - - +
201G CYS* 2.0 47.8 - - - -
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Residues in contact with LEU 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G PHE* 5.0 7.2 - - + -
27G GLN* 3.1 37.5 - - - +
29G TRP* 6.0 0.2 - - + -
136G CYS* 1.3 73.9 - - - +
138G ALA* 1.3 64.4 + - - +
157G CYS* 3.9 15.0 - - + -
158G VAL* 3.2 32.8 - - - +
159G ASN* 4.3 6.3 - - + +
198G PRO 3.3 1.6 - - - +
199G LEU* 3.2 7.0 - - - -
200G ILE* 2.9 48.0 + - + +
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Residues in contact with ALA 138 (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* 3.7 2.5 - - - +
137G LEU* 1.3 78.3 - - - +
139G SER* 1.3 59.8 - - - +
157G CYS* 3.5 0.7 - - - -
158G VAL* 2.9 36.9 + - + +
160G LEU* 4.1 17.3 - - + -
190G THR* 3.7 28.5 - - + -
198G PRO 3.2 13.9 - - - +
199G LEU* 4.1 6.7 - - + -
213G THR* 4.7 1.1 - - - +
228G TYR* 4.6 0.9 - - + -
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Residues in contact with SER 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ILE* 4.0 7.9 - - - +
22G CYS* 4.2 3.6 - - - -
27G GLN* 4.1 16.7 + - - +
30G HIS* 3.0 33.4 + - - -
137G LEU* 5.5 0.6 - - - +
138G ALA* 1.3 76.1 - - - +
140G GLY* 1.3 61.2 + - - +
155G LEU* 4.4 1.8 - - - -
156G TYR 3.1 13.2 - - - -
157G CYS* 4.0 16.2 - - - -
190G THR* 5.6 0.3 - - - +
194G ASP* 4.3 10.4 - - - +
197G GLY* 4.5 0.5 - - - -
198G PRO* 3.6 17.0 + - - +
200G ILE* 5.9 0.3 - - - +
213G THR* 5.3 1.4 + - - -
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Residues in contact with GLY 140 (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* 3.9 7.2 - - - +
30G HIS* 3.7 15.1 - - - -
40G TYR* 5.4 0.2 - - - -
139G SER* 1.3 76.2 - - - +
141G TRP* 1.3 57.7 + - - -
142G GLY 3.1 9.2 + - - +
152G THR* 3.9 3.6 + - - -
155G LEU* 3.8 8.7 - - - +
156G TYR* 3.0 25.0 + - - +
194G ASP* 3.3 16.6 - - - +
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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