Contacts of the strand formed by residues 158 - 164 (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 VAL 158 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E TYR* 4.5 4.3 + - - -
126E PRO* 4.1 7.2 - - + -
150E ALA* 6.2 0.4 - - + -
153E PHE* 3.8 49.1 - - + -
156E ASP* 3.7 10.3 + - - +
157E HIS* 1.3 80.8 - - - +
159E GLU* 1.3 69.7 + - - +
160E LEU* 5.9 0.2 - - + -
179E PRO* 5.4 0.9 - - + -
193E LEU* 4.1 21.5 - - + -
215E VAL* 4.0 23.8 - - + -
216E GLN 3.3 6.1 - - - +
217E PHE* 4.2 3.6 - - + -
218E TYR* 4.9 0.2 - - - -
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Residues in contact with GLU 159 (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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9E ARG* 4.4 5.2 + - - -
10E TYR* 2.6 39.1 + - - +
158E VAL* 1.3 77.2 - - - +
160E LEU* 1.3 62.3 + - - +
161E SER* 4.9 2.1 + - - -
214E GLN 3.7 1.2 - - - +
215E VAL* 3.5 2.1 - - - -
216E GLN* 3.0 36.1 + - + +
218E TYR* 3.0 25.6 + - + -
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Residues in contact with LEU 160 (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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148E CYS* 4.3 7.0 - - + +
150E ALA* 4.7 6.1 - - + -
158E VAL* 4.1 1.8 - - + +
159E GLU* 1.3 72.6 - - - +
161E SER* 1.3 78.0 + - - +
162E TRP* 4.2 6.1 - - + -
175E THR* 4.3 14.4 + - + +
193E LEU* 4.2 29.9 - - + +
194E SER 4.8 0.7 - - - -
195E SER* 3.8 38.8 - - - +
213E CYS* 4.0 20.2 - - - -
214E GLN 3.3 3.8 - - - -
215E VAL* 3.8 23.8 - - + -
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Residues in contact with SER 161 (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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159E GLU 4.9 2.2 + - - -
160E LEU* 1.3 80.6 - - - +
162E TRP* 1.3 63.9 + - - +
163E TRP* 3.0 22.3 + - - -
168E GLU* 3.6 24.9 - - - -
212E ARG 3.8 0.3 - - - +
213E CYS* 3.6 2.9 - - - -
214E GLN* 2.8 47.5 + - - +
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Residues in contact with TRP 162 (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 7.4 - - + -
146E LEU* 3.7 37.5 - - + -
147E VAL 4.1 2.2 - - - -
148E CYS* 3.5 36.8 - - + -
160E LEU* 4.2 8.4 - - + +
161E SER* 1.3 73.0 - - - +
163E TRP* 1.3 67.7 + - - +
164E VAL 4.3 0.2 - - - -
168E GLU* 3.5 3.3 - - - +
169E VAL* 2.9 33.3 + - + +
173E VAL* 3.6 37.7 - - + +
195E SER* 2.9 27.6 + - - -
196E ARG 3.5 4.8 + - - -
197E LEU* 3.4 40.8 - - + -
211E PHE* 4.7 2.7 - - + -
212E ARG 3.4 21.8 - - - -
213E CYS* 4.2 14.8 - - + -
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Residues in contact with TRP 163 (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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161E SER* 3.0 31.8 + - - -
162E TRP* 1.3 80.2 - - - +
164E VAL* 1.3 63.4 + - - +
166E GLY* 3.4 32.4 + - - +
167E LYS* 3.4 6.5 - - - +
168E GLU* 3.5 39.3 - - + -
210E HIS* 3.6 2.4 + - - +
211E PHE* 3.5 3.1 - - - -
212E ARG* 2.8 67.9 + - + +
214E GLN* 3.7 23.2 - - + +
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Residues in contact with VAL 164 (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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163E TRP* 1.3 73.5 - - - +
165E ASN* 1.3 82.3 + - - +
166E GLY 3.2 0.2 - - - -
167E LYS* 3.0 22.5 + - - +
169E VAL* 3.9 25.1 - - + +
197E LEU* 4.0 17.3 - - + -
199E VAL* 5.4 2.2 - - + -
203E PHE* 3.4 37.2 - - + -
209E ASN* 5.1 0.2 - - + -
210E HIS 3.3 7.4 - - - +
211E PHE* 3.9 23.6 - - + -
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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