Contacts of the strand formed by residues 236 - 241 (chain C) in PDB entry 3FTN
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 236 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C SER* 3.3 23.3 - - - +
171C VAL* 3.8 34.1 - - + -
195C ILE* 4.1 8.5 - - + -
227C VAL* 4.0 6.1 - - + -
231C THR* 3.9 16.8 - - + -
235C GLY* 1.3 78.0 - - - +
237C ASP* 1.3 62.4 + - - +
238C ARG 3.9 11.0 - - - +
239C VAL* 4.0 13.5 - - + -
255C MET* 3.1 17.9 + - + +
256C VAL* 3.3 5.2 - - - -
257C LYS* 2.9 28.7 + - - +
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Residues in contact with ASP 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ARG* 4.1 14.9 + - - +
165C GLU* 4.4 4.3 - - - +
168C SER* 3.1 23.2 - - - +
169C SER* 2.7 40.9 + - - +
236C VAL* 1.3 73.4 - - - +
238C ARG* 1.3 89.2 + - + +
256C VAL* 4.0 1.0 - - - +
257C LYS* 3.1 32.6 + - - +
260C GLY* 3.3 17.1 - - - -
261C ILE 3.4 0.7 + - - -
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Residues in contact with ARG 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ARG* 5.6 3.0 - - - +
162C ALA* 2.6 35.9 + - + +
163C ASP* 2.7 22.6 + - - +
164C ILE* 4.2 14.1 - - + -
165C GLU* 3.3 34.3 + - - +
168C SER* 4.5 3.6 - - - +
169C SER 3.1 2.5 + - - +
170C VAL* 3.3 22.4 - - + -
171C VAL 2.8 24.7 + - - -
236C VAL* 3.4 3.3 - - - +
237C ASP* 1.3 103.4 + - + +
239C VAL* 1.3 67.4 + - - +
240C ILE 4.3 0.2 - - - -
256C VAL* 4.1 0.4 - - - -
259C GLY 4.5 3.8 + - - -
260C GLY* 3.9 11.5 - - - -
261C ILE* 3.3 33.4 - - - +
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Residues in contact with VAL 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C ALA* 5.5 0.4 - - - +
171C VAL* 3.2 10.3 - - + +
173C ILE* 3.8 23.3 - - + -
236C VAL* 4.0 5.2 - - + -
238C ARG* 1.3 76.8 - - - +
240C ILE* 1.3 63.4 + - - +
241C MET* 4.0 1.7 + - + -
252C ALA* 3.6 38.1 - - + +
255C MET* 3.9 19.5 - - + -
256C VAL* 3.3 25.4 - - + +
261C ILE 3.1 6.7 + - - +
262C ILE* 3.3 5.4 - - + +
263C SER* 2.7 33.8 + - - -
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Residues in contact with ILE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLY* 3.8 30.5 - - - +
159C ALA* 3.9 11.7 - - + +
162C ALA* 4.4 8.3 - - + -
164C ILE* 4.8 0.4 - - + -
170C VAL* 4.2 21.8 - - + -
171C VAL 2.8 11.0 + - - +
172C VAL* 3.5 18.7 - - + -
173C ILE* 2.8 30.3 + - - +
182C GLY* 4.2 19.1 - - - +
186C ALA* 4.5 2.5 - - + -
239C VAL* 1.3 76.5 - - - +
241C MET* 1.3 63.6 + - - +
242C ALA* 3.5 1.3 + - + -
263C SER* 3.2 12.1 - - - +
265C ILE* 3.9 26.7 - - + -
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Residues in contact with MET 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A TRP* 6.3 0.2 - - + -
173C ILE* 4.2 4.7 - - + -
239C VAL* 4.5 2.7 - - + -
240C ILE* 1.3 71.4 - - - +
242C ALA* 1.3 59.3 + - - +
243C GLY 3.7 2.0 - - - +
248C THR* 3.6 22.7 - - + -
249C LEU* 3.8 42.0 - - + +
252C ALA* 4.2 12.3 - - + -
262C ILE* 3.6 25.8 - - + -
263C SER 2.7 12.5 + - - +
264C ASN* 3.5 27.1 - - + +
265C ILE* 3.0 26.2 + - - +
266C ASN* 3.1 9.5 + - + +
268C HIS* 4.0 18.2 - - + +
274C LEU* 5.1 2.2 - - + -
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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