Contacts of the strand formed by residues 209 - 215 (chain I) 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 THR 209 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211F VAL* 4.6 5.2 - - + -
212F ASP 3.6 5.4 - - - +
213F LYS* 2.8 37.4 + - - -
123I PRO* 3.8 9.2 - - + +
124I PRO* 4.7 10.3 - - + +
203I ALA* 3.8 1.4 - - - +
204I HIS 3.0 30.1 + - - +
205I PRO* 5.0 0.5 - - - +
207I SER* 2.8 20.8 + - - -
208I SER* 1.3 77.1 - - - +
210I LYS* 1.3 68.0 + - - +
211I VAL* 4.0 21.8 - - + -
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Residues in contact with LYS 210 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F LYS 3.9 0.2 - - - +
211F VAL* 3.4 3.6 - - - +
212F ASP* 3.0 52.5 + - + +
201I ASN* 5.9 5.4 - - + -
202I VAL 3.5 14.8 - - - +
203I ALA* 3.6 23.3 - - + -
209I THR* 1.3 74.7 - - - +
211I VAL* 1.3 67.9 + - - +
212I ASP* 5.3 5.8 - - - +
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Residues in contact with VAL 211 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209F THR* 4.5 7.2 - - + -
210F LYS 3.5 7.0 - - - +
211F VAL* 4.1 17.0 - - + -
124I PRO* 5.4 8.1 - - + +
126I VAL* 3.3 33.7 - - + -
200I CYS 3.7 0.2 - - - +
202I VAL* 2.8 48.4 + - + +
209I THR* 4.0 17.0 - - + -
210I LYS* 1.3 80.3 - - - +
212I ASP* 1.3 79.1 + - - +
213I LYS* 4.5 6.1 - - + -
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Residues in contact with ASP 212 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F SER 3.6 1.2 - - - +
209F THR* 3.4 10.2 - - - +
210F LYS* 3.0 48.5 + - + +
212F ASP* 4.4 10.9 - - - +
199I THR* 4.2 8.3 - - - +
200I CYS 3.3 5.4 - - - +
201I ASN* 3.2 34.7 - - - +
210I LYS* 5.3 4.5 - - - +
211I VAL* 1.3 79.6 + - - +
213I LYS* 1.3 63.1 + - - +
214I LYS 4.1 0.2 - - - -
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Residues in contact with LYS 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123F PRO* 4.2 10.4 - - - +
207F SER 3.8 5.5 + - - +
208F SER 3.7 4.7 - - - +
209F THR* 3.0 33.3 + - - +
123H GLU* 3.3 32.0 + - - +
126I VAL* 3.3 40.8 - - + +
128I PRO* 3.9 26.2 - - + -
199I THR* 2.9 14.1 + - - -
200I CYS* 3.0 35.3 + - - -
211I VAL* 4.2 4.5 - - + -
212I ASP* 1.3 74.2 - - - +
214I LYS* 1.3 63.2 + - - +
215I ILE* 3.6 1.9 + - - +
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Residues in contact with LYS 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F SER* 3.1 32.5 + - - +
128I PRO* 4.5 6.8 - - - +
197I THR* 3.6 30.1 + - - +
198I VAL 3.6 12.8 - - - +
199I THR* 3.7 7.8 + - - +
212I ASP 4.1 0.2 - - - -
213I LYS* 1.3 73.1 - - - +
215I ILE* 1.3 67.2 + - - +
216I VAL* 3.2 35.4 + - + +
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Residues in contact with ILE 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I PRO* 3.2 32.8 - - + -
129I LEU 3.6 12.8 - - - +
130I ALA* 3.8 23.1 - - + -
143I LEU* 3.8 34.5 - - + -
144I GLY 3.8 7.9 - - - +
145I CYS* 4.2 7.4 - - + -
159I TRP* 3.7 26.9 - - + -
193I TRP* 3.2 21.1 + - + -
198I VAL* 3.0 17.0 + - + +
200I CYS* 5.1 0.2 - - - -
213I LYS* 4.4 5.6 - - + +
214I LYS* 1.3 74.0 - - - +
216I VAL* 1.3 63.7 + - - +
217I PRO* 4.4 0.2 - - - +
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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