Contacts of the strand formed by residues 199 - 203 (chain A) in PDB entry 1FS6
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 VAL 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A PHE 3.4 2.9 - - - +
193A LEU* 3.5 45.1 - - + +
196A ALA* 4.0 2.5 - - + -
198A GLU* 1.3 81.0 - - - +
200A MET* 1.3 62.2 + - - +
201A ILE* 3.6 26.0 - - + -
229A LEU* 3.8 24.9 - - + +
232A HIS* 3.7 22.2 - - + +
234A LYS 2.9 9.5 + - - +
235A ALA* 3.3 3.7 - - - +
236A ILE* 2.9 26.7 + - - +
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Residues in contact with MET 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 3.2 38.8 - - + -
16A ALA* 3.9 26.2 - - - +
19A HIS* 3.3 30.5 - - + -
20A ILE* 4.9 5.8 - - - -
133A LEU* 4.0 15.5 - - + -
134A PHE 2.9 9.6 + - - +
135A MET* 3.2 14.7 - - - +
136A GLY 2.9 24.4 + - - +
199A VAL* 1.3 75.2 - - - +
201A ILE* 1.3 61.1 + - - +
202A LEU* 4.4 6.5 - - + -
236A ILE* 3.4 14.1 - - + +
238A VAL* 3.9 16.8 - - + -
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Residues in contact with ILE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A MET 5.1 0.2 - - - -
136A GLY* 3.2 17.9 - - - +
137A GLY 3.7 27.1 - - - +
138A VAL* 4.0 9.6 - - + -
144A ILE* 5.6 3.4 - - + -
193A LEU* 5.2 7.4 - - + -
199A VAL* 3.6 17.5 - - + -
200A MET* 1.3 80.4 - - - +
202A LEU* 1.3 70.3 + - - +
203A VAL* 3.7 13.8 + - + +
226A ILE* 3.9 11.2 - - + -
229A LEU* 3.6 26.2 - - + -
236A ILE 2.9 6.2 + - - +
237A MET* 3.5 13.7 - - + -
238A VAL* 2.9 26.5 + - - +
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.2 15.9 - - + -
16A ALA* 3.8 24.9 - - + -
40A PRO* 5.1 1.1 - - + -
44A THR* 3.3 29.4 - - + +
45A PRO* 3.8 25.4 - - + -
48A THR* 3.7 14.8 - - - +
135A MET* 3.6 35.4 - - + -
136A GLY 2.8 12.6 + - - +
137A GLY* 3.6 13.3 - - - -
138A VAL* 4.2 3.1 + - - +
200A MET* 4.4 7.9 - - + -
201A ILE* 1.3 77.6 - - - +
203A VAL* 1.3 61.1 + - - +
204A LEU* 5.2 0.2 - - + -
238A VAL* 3.6 6.5 - - + +
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A VAL* 4.3 8.7 - - + -
201A ILE* 4.0 13.0 - - + +
202A LEU* 1.3 76.9 - - - +
204A LEU* 1.3 62.3 + - - +
208A LYS* 3.5 31.4 - - + +
212A LEU* 4.0 20.0 - - + -
237A MET* 3.9 29.8 - - + -
238A VAL 2.8 11.4 + - - +
239A CYS* 3.1 30.6 - - + +
240A ASP 3.2 6.8 + - - -
243A SER* 3.6 15.2 + - - +
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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