Contacts of the strand formed by residues 198 - 201 (chain Z) 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 PRO 198 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29Z TRP* 3.8 20.6 - - + +
30Z HIS* 3.6 24.0 - - + +
44Z GLY 4.9 1.1 - - - +
45Z VAL* 3.4 29.1 - - + -
137Z LEU 3.9 0.2 - - - -
138Z ALA* 3.4 25.8 - - - +
139Z SER* 3.8 9.8 + - - +
197Z GLY* 1.3 87.4 - - - +
199Z LEU* 1.3 60.5 + - - +
200Z ILE* 3.7 16.4 - - + -
209Z LEU* 3.8 11.2 - - + -
211Z GLY 3.5 6.1 - - - +
213Z THR* 4.2 2.5 + - - -
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Residues in contact with LEU 199 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Z CYS* 3.7 20.0 - - + -
137Z LEU 3.3 5.8 - - - +
138Z ALA* 4.5 2.2 - - + -
160Z LEU* 4.3 12.6 - - + -
162Z LEU* 4.6 0.9 - - + -
181Z LEU* 4.5 15.0 - - + -
183Z ALA* 4.3 10.8 - - + -
198Z PRO* 1.3 72.7 - - - +
200Z ILE* 1.3 58.8 + - - +
201Z CYS* 3.4 20.2 + - - -
209Z LEU* 4.4 0.4 - - - +
210Z GLN* 3.2 23.3 + - - -
211Z GLY* 2.8 28.2 + - - +
228Z TYR* 3.7 54.1 - - + -
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Residues in contact with ILE 200 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Z GLN* 3.8 7.6 - - - +
29Z TRP* 3.1 46.0 - - + +
121Z ILE* 4.0 13.2 - - + -
135Z THR 4.1 1.0 - - - +
136Z CYS* 3.5 1.2 - - - -
137Z LEU* 2.8 48.2 + - + +
198Z PRO* 3.9 17.7 - - + -
199Z LEU* 1.3 71.8 - - - +
201Z CYS* 1.3 59.1 + - - +
202Z ASP 3.8 1.2 + - - -
207Z GLY* 3.6 36.8 + - - +
208Z VAL 3.5 7.0 - - - +
209Z LEU* 4.4 4.7 - - - -
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Residues in contact with CYS 201 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Z PRO* 5.0 5.6 - - + -
134Z SER* 4.5 10.1 - - - -
135Z THR 3.9 0.9 - - - -
136Z CYS* 2.0 49.1 - - - -
162Z LEU* 4.5 9.4 - - - -
181Z LEU* 5.9 0.2 - - - -
199Z LEU* 3.4 23.5 + - - -
200Z ILE* 1.3 69.4 - - - +
202Z ASP* 1.3 72.5 + - - +
207Z GLY 3.2 1.3 - - - -
208Z VAL* 3.0 25.1 + - - +
210Z GLN* 4.4 18.0 - - + +
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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