Contacts of the strand formed by residues 233 - 237 (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 ILE 233 (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* 4.1 25.1 - - + -
165F VAL 3.4 9.2 - - - +
166F ALA* 3.8 15.9 - - + -
170F TYR* 4.0 9.4 - - + -
177F PRO* 4.1 9.0 - - + -
183F LEU* 4.1 18.8 - - + -
186F HIS* 3.9 29.8 - - + +
187F PHE 2.9 10.1 + - - +
188F LEU* 3.4 6.3 - - + -
189F LEU 2.8 21.9 + - - -
197F TRP* 3.3 9.6 - - + -
232F GLY* 1.3 75.9 - - - -
234F THR* 1.3 68.7 + - - +
253F ILE* 4.0 22.4 - - + -
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Residues in contact with THR 234 (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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163F ILE 3.7 0.5 - - - +
164F LEU* 3.2 6.9 - - - +
165F VAL* 3.0 44.9 + - + -
189F LEU* 2.7 25.4 + - - -
190F LYS* 4.7 0.5 - - - -
191F GLY 5.1 0.9 + - - -
197F TRP* 3.9 5.4 - - - -
220F LEU* 5.3 0.3 - - - +
223F VAL* 3.0 22.7 - - + +
224F ARG* 5.4 0.9 - - - -
227F CYS* 3.8 17.5 - - + -
232F GLY 4.0 0.8 + - - -
233F ILE* 1.3 73.1 - - - +
235F LEU* 1.3 69.1 + - - +
236F MET* 3.4 27.3 - - + +
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Residues in contact with LEU 235 (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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162F ASP* 3.7 17.3 - - + +
163F ILE* 3.4 32.1 - - - +
164F LEU* 3.7 14.1 - - + +
194F LEU* 3.5 31.0 - - + +
196F LYS 5.1 0.4 - - - +
197F TRP* 3.6 53.6 + - + +
199F LEU* 3.9 12.1 - - + -
220F LEU* 4.1 5.7 - - - +
234F THR* 1.3 78.5 + - - +
236F MET* 1.3 66.7 + - - +
259F ALA* 4.0 18.4 - - + -
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Residues in contact with MET 236 (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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162F ASP* 3.9 4.3 - - - -
163F ILE* 2.7 37.2 + - - +
165F VAL* 4.4 0.7 - - + -
194F LEU* 4.3 0.2 - - - -
220F LEU* 4.0 31.4 - - + +
223F VAL* 4.9 0.9 - - - -
224F ARG* 4.7 15.7 - - + -
234F THR* 3.4 31.0 - - + -
235F LEU* 1.3 74.2 - - - +
237F PRO* 1.3 70.8 - - + +
238F ASP 3.2 0.3 + - - -
240F MET* 3.5 49.1 - - + -
241F ILE* 3.5 31.0 - - + -
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Residues in contact with PRO 237 (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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100F ASN* 5.1 2.0 - - + -
101F LEU* 3.8 25.6 - - + -
160F VAL* 5.5 1.6 - - + -
161F LYS 3.7 1.3 - - - +
162F ASP* 3.1 23.0 - - - +
194F LEU* 4.0 11.0 - - + -
220F LEU* 4.0 11.4 - - + -
236F MET* 1.3 99.9 - - + +
238F ASP* 1.3 67.5 + - - +
239F VAL* 3.2 3.4 - - + +
240F MET* 2.9 34.6 + - + +
241F ILE* 3.8 4.0 + - - +
262F ARG* 4.0 10.5 - - - +
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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