Contacts of the strand formed by residues 238 - 241 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A VAL* 4.4 14.4 - - + -
108A ALA* 3.7 27.1 - - + -
109A VAL 3.6 1.4 + - - +
110A ALA* 3.5 19.2 - - + -
111A LEU 3.2 21.8 + - - -
236A VAL* 3.6 4.8 - - - +
237A ASP* 1.3 94.9 - - + +
239A VAL* 1.3 67.5 + - - +
240A PHE* 3.8 19.3 - - + -
264A ILE* 3.8 4.0 - - - +
265A LYS* 3.2 22.0 - - + +
267A ILE* 4.7 2.7 - - + -
460A ARG 4.5 0.4 - - - +
461A GLN* 4.1 18.2 - - + -
464A LEU* 3.8 33.0 - - + -
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Residues in contact with VAL 239 (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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111A LEU* 3.3 16.4 - - + +
113A THR* 4.1 11.0 - - + -
228A LEU* 3.8 33.4 - - + +
231A GLY* 6.1 0.4 - - - -
236A VAL* 4.4 10.3 - - + -
238A MET* 1.3 78.8 - - - +
240A PHE* 1.3 68.1 + - - +
241A ALA* 3.8 17.5 - - + +
253A VAL* 4.7 4.3 - - + -
257A LEU* 4.6 5.6 - - + -
264A ILE* 3.8 17.0 - - + -
265A LYS 2.7 12.9 + - - +
266A ILE* 3.8 6.9 - - + -
267A ILE* 2.8 30.3 + - - +
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Residues in contact with PHE 240 (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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47A ILE* 4.2 22.0 - - + -
70A VAL* 4.6 0.9 - - + -
72A ARG* 4.2 19.5 - - + -
110A ALA* 3.5 27.8 - - + -
111A LEU 2.6 10.9 + - - +
112A ASP* 3.0 44.6 - - + +
113A THR 3.5 5.6 + - - -
238A MET* 3.8 18.4 - - + -
239A VAL* 1.3 74.3 - - - +
241A ALA* 1.3 63.9 + - - +
242A SER 3.4 1.0 + - - -
267A ILE* 3.5 39.3 - - + -
269A LYS* 3.6 10.7 - - + +
290A MET* 4.8 7.9 - - - -
324A ILE* 3.9 20.0 - - + -
359A MET* 4.5 4.7 - - - -
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Residues in contact with ALA 241 (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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113A THR* 3.6 10.1 - - + +
239A VAL* 3.5 14.2 - - + +
240A PHE* 1.3 71.3 - - - +
242A SER* 1.3 61.7 + - - +
244A ILE* 3.7 22.8 - - + +
253A VAL* 4.2 18.4 - - + -
266A ILE* 4.6 9.6 - - + -
267A ILE 3.0 11.9 + - - +
268A SER* 5.0 0.2 - - - -
269A LYS* 2.9 30.8 + - - +
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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