Contacts of the strand formed by residues 205 - 210 (chain E) in PDB entry 1FSK
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 ILE 205 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112E ALA* 4.8 10.1 - - + -
113E PRO* 4.4 28.0 - - + +
115E VAL* 3.6 31.7 - - + +
194E CYS 3.8 0.9 - - - +
196E ALA* 2.9 43.3 + - + +
198E HIS* 5.0 7.0 - - + +
200E THR* 5.4 0.4 - - - +
201E SER* 3.9 19.5 - - - +
203E SER 4.4 0.9 - - - +
204E PRO* 1.3 73.0 - - + +
206E VAL* 1.3 68.6 + - - +
207E LYS* 5.1 7.2 - - + -
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Residues in contact with VAL 206 (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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115E VAL* 5.5 0.4 - - - -
193E THR* 3.4 24.2 - - - +
194E CYS 3.4 7.6 - - - +
195E GLU* 2.8 31.9 - - - +
204E PRO* 3.6 12.5 + - + +
205E ILE* 1.3 77.1 - - - +
207E LYS* 1.3 87.0 + - - +
208E SER* 5.2 2.2 - - - +
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Residues in contact with LYS 207 (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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115E VAL* 3.7 48.3 + - + +
116E SER* 4.8 1.5 - - - +
117E ILE* 3.9 18.6 - - + +
194E CYS* 2.6 41.2 + - - +
205E ILE* 5.1 7.9 - - + -
206E VAL* 1.3 93.5 - - - +
208E SER* 1.3 58.7 + - - +
138F ASN* 5.2 10.3 + - - +
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Residues in contact with SER 208 (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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117E ILE* 3.8 12.8 - - - +
191E SER* 5.7 3.0 - - - -
192E TYR 2.7 22.7 - - - -
193E THR* 3.0 26.3 + - - -
206E VAL* 5.2 2.3 - - - +
207E LYS* 1.3 71.8 - - - +
209E PHE* 1.3 60.7 + - - +
134F ALA 5.2 3.5 - - - +
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Residues in contact with PHE 209 (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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117E ILE* 3.9 19.1 - - + -
119E PRO* 3.3 40.4 - - + -
120E PRO* 4.5 1.8 - - + -
132E VAL* 3.7 20.6 - - + -
186E TYR* 3.3 22.0 - + - -
191E SER* 3.4 4.7 - - - -
192E TYR* 2.9 71.1 + + + +
208E SER* 1.3 77.0 - - - +
210E ASN* 1.3 63.9 + - - +
211E ARG* 3.9 11.9 - - - -
214E CYS* 5.7 4.7 - - - -
132F GLY* 6.4 2.0 - - - -
134F ALA* 5.0 18.6 - - + +
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Residues in contact with ASN 210 (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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190E ASN* 3.7 4.4 - - - +
191E SER* 3.6 22.3 - - - +
209E PHE* 1.3 77.6 - - - +
211E ARG* 1.3 66.8 + - - +
212E ASN* 2.8 43.6 + - - +
213E GLU* 2.8 41.2 + - + +
214E CYS* 3.4 8.3 + - - -
134F ALA* 5.1 5.0 - - - +
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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