Contacts of the strand formed by residues 236 - 243 (chain E) in PDB entry 1FYT
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 GLN 236 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125E PRO* 3.4 33.8 - - + +
215E VAL 3.8 0.2 - - - +
216E GLN* 3.5 4.0 - - - +
217E PHE* 2.6 50.9 + - + +
232E LYS 4.4 3.6 + - - -
234E VAL* 2.9 33.3 + - + +
235E THR* 1.3 77.7 - - - +
237E ILE* 1.3 65.5 + - - +
238E VAL* 4.0 17.3 + - + +
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Residues in contact with ILE 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214E GLN* 3.7 41.7 - - + +
215E VAL 3.4 3.4 - - - +
216E GLN* 3.5 36.8 - - + +
236E GLN* 1.3 76.1 - - - +
238E VAL* 1.3 69.7 + - - +
239E SER* 4.4 3.8 + - - +
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Residues in contact with VAL 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E PRO* 5.1 0.2 - - + -
126E PRO* 3.8 35.9 - - + +
127E GLU* 4.6 1.3 - - - -
128E VAL* 3.5 33.4 - - + +
214E GLN 3.6 0.2 - - - -
215E VAL* 2.7 45.7 + - + +
236E GLN* 4.0 23.3 - - + +
237E ILE* 1.3 79.9 - - - +
239E SER* 1.3 62.8 + - - +
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Residues in contact with SER 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E VAL* 4.3 6.2 - - - +
212E ARG* 3.4 26.8 + - - +
213E CYS 3.1 13.7 - - - -
214E GLN* 4.0 10.6 + - - -
237E ILE* 4.2 3.4 - - - +
238E VAL* 1.3 81.3 - - - +
240E ALA* 1.3 63.0 + - - +
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Residues in contact with ALA 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D SER* 5.8 2.0 - - - +
128E VAL* 3.6 24.7 - - + +
129E ALA* 3.9 2.5 - - - -
130E VAL* 3.6 29.7 - - + +
212E ARG* 3.3 5.0 - - - +
213E CYS 2.9 28.8 + - - -
239E SER* 1.3 75.9 - - - +
241E GLU* 1.3 61.0 + - - +
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Residues in contact with GLU 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E VAL* 4.6 7.5 - - - +
210E HIS* 2.6 37.3 + - - +
211E PHE 3.2 12.1 - - - +
212E ARG* 4.0 9.7 + - + +
240E ALA* 1.3 76.8 - - - +
242E ALA* 1.3 64.9 + - - +
243E TRP* 4.2 13.8 + - + +
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Residues in contact with ALA 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E VAL* 4.3 16.4 - - + +
132E GLU* 3.8 32.5 - - + +
146E LEU* 4.6 4.0 - - + -
204E TRP* 4.6 7.2 - - + -
210E HIS* 3.9 2.6 - - - -
211E PHE* 2.9 35.0 + - - +
241E GLU* 1.3 76.2 - - - +
243E TRP* 1.3 69.2 + - - +
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Residues in contact with TRP 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E GLU* 4.6 1.9 + - - +
204E TRP* 3.4 18.4 - - - -
207E PRO 3.6 20.4 - - - +
208E ARG* 3.9 11.7 - - - -
209E ASN 3.6 11.4 - - - -
210E HIS* 3.3 40.6 - + + -
211E PHE* 4.6 0.2 - - - -
241E GLU* 4.2 14.5 + - + -
242E ALA* 1.3 82.8 - - - +
244E GLY* 1.3 71.9 + - - +
245E ARG* 4.1 8.0 + - - +
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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