Contacts of the strand formed by residues 197 - 201 (chain F) in PDB entry 5FHK
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 TRP 197 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164F LEU* 3.7 21.1 - - + -
183F LEU* 4.3 17.7 - - + -
188F LEU* 3.8 29.4 - - + -
189F LEU 3.5 20.6 - - - -
190F LYS* 3.6 22.6 - - + +
194F LEU 3.0 29.1 + - - -
195F LEU 4.0 4.0 - - - -
196F LYS* 1.3 73.0 - - - +
198F THR* 1.3 61.4 + - - +
199F LEU* 3.6 11.8 + - + +
207F VAL 3.5 2.9 - - - +
208F VAL* 3.3 4.9 - - - +
209F ASN* 2.8 52.1 + - + +
233F ILE* 3.3 24.2 - - + -
234F THR* 3.9 6.1 - - - -
235F LEU* 3.6 39.4 + - + +
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Residues in contact with THR 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F LYS* 3.6 30.0 + - - +
197F TRP* 1.3 70.6 + - - +
199F LEU* 1.3 61.2 + - - +
200F ILE* 4.1 3.5 + - + +
206F THR* 3.9 23.1 - - + -
207F VAL 3.9 2.0 - - - -
208F VAL* 4.4 8.0 - - + +
259F ALA* 3.2 26.6 - - - +
260F ASN 4.7 1.4 + - - -
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Residues in contact with LEU 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164F LEU* 4.1 17.3 - - + -
180F ALA* 4.7 8.1 - - + -
183F LEU* 3.6 31.9 - - + -
197F TRP* 4.2 17.5 - - + +
198F THR* 1.3 73.4 - - - +
200F ILE* 1.3 61.3 + - - +
206F THR* 3.3 4.9 - - - +
207F VAL* 2.8 44.9 + - + +
209F ASN* 5.1 3.6 - - + -
235F LEU* 3.9 31.9 - - + -
254F LEU* 5.4 0.2 - - + -
257F TRP* 3.7 20.2 - - + -
258F SER* 3.6 11.0 - - - +
259F ALA* 4.2 10.1 - - + -
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Residues in contact with ILE 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F THR* 5.1 3.6 - - + +
199F LEU* 1.3 75.1 - - - +
201F ASN* 1.3 68.0 + - - +
204F GLY* 3.7 22.7 - - - +
205F GLU 3.2 10.5 - - - +
206F THR* 3.2 22.7 - - + +
256F ASP 4.0 0.2 - - - +
257F TRP* 3.5 3.7 - - - -
258F SER* 3.0 41.8 + - - +
259F ALA* 5.1 3.6 - - - -
260F ASN 5.5 0.4 - - - +
261F PRO* 5.1 12.6 - - + -
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Residues in contact with ASN 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200F ILE* 1.3 79.2 - - - +
202F SER* 1.3 66.5 + - - +
203F LYS* 3.1 10.9 + - - +
204F GLY* 2.7 43.0 + - - -
205F GLU* 2.8 50.1 + - - +
256F ASP* 3.2 27.0 + - - +
257F TRP* 3.7 25.4 - - + +
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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