Contacts of the strand formed by residues 241 - 245 (chain A) in PDB entry 4GSA
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 LEU 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A MET* 3.5 50.0 - - + +
137A TYR* 4.0 31.9 - - + -
138A THR* 3.9 9.9 - - + -
207A ALA 2.9 13.9 + - - +
208A GLY* 3.1 1.7 - - - -
209A VAL 2.8 31.4 + - - +
235A THR* 4.0 5.4 - - - +
239A ASP 5.5 1.1 - - - +
240A ALA* 1.3 79.1 - - - +
242A LEU* 1.3 57.0 + - - +
243A VAL* 3.8 4.2 + - + -
267A ASP* 3.5 20.6 - - + +
268A LEU* 4.2 13.2 - - + -
290A ILE* 4.3 10.3 - - + -
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Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A VAL* 3.9 10.5 - - + +
211A LEU* 4.3 9.6 - - + -
228A LEU 4.8 1.1 - - - +
231A LEU* 4.0 28.7 - - + +
232A ARG* 3.5 60.8 - - + +
235A THR* 3.9 2.0 - - - +
240A ALA 4.0 0.8 + - - -
241A LEU* 1.3 69.2 - - - +
243A VAL* 1.3 61.5 + - - +
244A PHE* 4.0 26.7 - - + -
264A VAL* 4.2 6.3 - - + -
266A PRO* 3.2 15.9 - - + +
267A ASP* 2.8 36.4 + - - -
268A LEU 3.5 3.1 + - - -
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.9 23.8 - - + -
134A MET* 3.3 43.5 - - + -
209A VAL 2.8 12.0 + - - +
210A ILE* 3.2 16.9 - - + +
211A LEU* 3.1 27.7 + - - +
241A LEU* 4.4 5.6 - - + -
242A LEU* 1.3 76.5 - - - +
244A PHE* 1.3 64.8 + - - +
268A LEU* 3.3 33.0 - - + +
269A THR* 4.7 0.9 - - - -
270A THR* 5.0 1.8 - - + -
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Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.7 24.5 - - + -
213A PRO* 4.2 18.2 - - + -
228A LEU* 4.3 24.7 - - + -
231A LEU* 6.0 0.4 - - + -
242A LEU* 4.0 17.2 + - + -
243A VAL* 1.3 77.8 - - - +
245A ASP* 1.3 59.5 + - - +
246A GLU* 3.2 21.2 + - + -
259A GLN* 3.7 19.1 - - + -
264A VAL* 3.4 41.7 - - + -
266A PRO* 3.6 26.0 - - + -
268A LEU 3.1 6.9 + - - -
269A THR* 3.2 7.3 - - - -
270A THR* 3.1 22.3 + - - -
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Residues in contact with ASP 245 (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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127A CYS* 3.4 9.5 - - - -
150A TYR 3.3 0.9 - - - +
151A HIS* 2.9 36.9 - - + -
210A ILE* 4.5 6.2 - - + +
211A LEU 2.8 16.3 + - - +
212A GLU* 3.8 8.5 - - - +
213A PRO* 3.4 13.9 - - - +
243A VAL 3.9 1.6 + - - -
244A PHE* 1.3 69.7 - - - +
246A GLU* 1.3 56.1 + - - +
247A VAL* 3.2 22.3 + - - +
248A MET 5.0 0.5 + - - -
249A THR* 4.3 2.1 + - - +
270A THR* 2.9 20.8 + - - +
434A PLP 2.8 29.9 + - - +
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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