Contacts of the strand formed by residues 238 - 241 (chain F) in PDB entry 3SRF
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 MET 238 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70F VAL* 4.2 10.8 - - + -
108F ALA* 3.8 26.9 - - + -
109F VAL 3.6 1.0 + - - +
110F ALA* 3.5 23.2 - - + -
111F LEU* 3.1 23.6 + - - +
236F VAL* 3.6 4.3 - - - +
237F ASP* 1.3 94.9 - - + +
239F VAL* 1.3 68.3 + - - +
240F PHE* 3.6 15.9 - - + -
264F ILE* 3.8 2.7 - - - +
265F LYS* 3.2 20.2 - - + +
267F ILE* 4.5 7.2 - - + -
460F ARG 4.4 0.4 - - - +
461F GLN* 4.4 9.0 - - - -
464F LEU* 3.6 41.1 - - + +
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Residues in contact with VAL 239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F LEU* 3.3 16.2 - - + +
113F THR* 4.3 10.1 - - + -
228F LEU* 3.6 33.9 - - + -
236F VAL* 4.4 8.7 - - + -
238F MET* 1.3 79.6 - - - +
240F PHE* 1.3 70.7 + - - +
241F ALA* 3.3 4.1 + - - +
253F VAL* 4.4 9.6 - - + -
257F LEU* 4.2 9.6 - - + -
264F ILE* 3.7 18.2 - - + -
265F LYS 2.8 12.6 + - - +
266F ILE* 3.7 10.5 - - + +
267F ILE 2.9 27.4 + - - +
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Residues in contact with PHE 240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F ILE* 4.0 14.6 - - + -
70F VAL* 4.8 0.2 - - + -
72F ARG* 3.8 26.5 - - + -
110F ALA* 3.6 20.9 - - + -
111F LEU 2.7 10.8 + - - +
112F ASP* 3.4 28.6 - - + +
113F THR* 3.1 25.1 + - - -
238F MET* 3.6 22.2 - - + -
239F VAL* 1.3 70.5 - - - +
241F ALA* 1.3 60.1 + - - +
242F SER 3.4 1.0 + - - -
267F ILE* 3.4 37.2 - - + -
269F LYS* 3.6 13.8 - - + +
290F MET* 4.3 10.5 - - - -
324F ILE* 3.9 17.5 - - + -
359F MET* 4.0 11.2 - - - -
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Residues in contact with ALA 241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F THR* 3.4 7.6 - - + +
239F VAL* 3.3 7.8 + - + +
240F PHE* 1.3 68.7 - - - +
242F SER* 1.3 65.3 + - - +
244F ILE* 3.3 27.2 - - + +
253F VAL* 4.3 16.6 - - + -
266F ILE* 4.3 13.2 - - + -
267F ILE 2.7 16.4 + - - +
268F SER* 4.6 0.2 - - - -
269F LYS* 2.9 26.5 + - - +
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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