Contacts of the strand formed by residues 249 - 254 (chain C) in PDB entry 3THT
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 249 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240C ASP* 3.2 31.2 - - + +
245C PHE* 4.6 3.1 - - + -
247C ASP 2.5 23.3 + - - +
248C GLU* 1.3 73.4 - - - +
250C VAL* 1.3 73.9 + - - +
251C SER* 5.1 0.2 - - - +
282C MET* 2.7 66.0 + - + +
287C ARG* 3.7 25.4 - - + +
332C THR* 4.0 7.9 - - + -
333C PHE 3.9 3.4 - - - -
334C ARG* 3.6 35.2 - - + +
335C LYS 5.7 0.7 - - - +
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Residues in contact with VAL 250 (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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208C LEU* 6.2 0.4 - - + -
211C TRP* 5.4 6.5 - - + -
217C ILE* 3.8 28.3 - - + -
221C PRO* 6.1 0.9 - - + -
248C GLU* 4.5 0.4 - - + +
249C ILE* 1.3 84.2 - - - +
251C SER* 1.3 66.9 + - - +
279C LEU* 3.7 23.3 - - + -
280C LEU* 2.9 12.3 - - - +
281C VAL* 4.0 20.0 - - + -
282C MET* 6.0 0.9 - - - -
332C THR* 3.2 6.1 - - - +
333C PHE* 3.1 54.2 + - + +
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Residues in contact with SER 251 (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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249C ILE* 5.1 1.6 - - - +
250C VAL* 1.3 79.4 + - - +
252C LEU* 1.3 61.9 + - - +
253C SER* 3.7 3.1 + - - -
260C MET* 5.8 0.2 - - - +
274C LEU* 6.1 0.4 - - - -
278C SER 3.5 2.3 - - - +
279C LEU* 3.4 6.6 - - - -
280C LEU* 2.8 54.6 + - - +
282C MET* 5.4 4.2 - - - +
328C ARG* 5.2 4.0 - - - -
330C SER* 5.2 0.9 - - - -
331C PHE 3.5 5.2 - - - -
332C THR* 3.2 21.0 + - - +
403C AKG 3.7 23.8 + - - +
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Residues in contact with LEU 252 (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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143C ILE* 3.8 29.4 - - + -
144C ILE* 4.4 8.1 - - + -
152C LEU* 3.6 32.1 - - + -
204C CYS* 6.4 0.7 - - + -
207C PHE* 6.2 0.7 - - + -
211C TRP* 4.1 18.2 - - + +
251C SER* 1.3 69.8 - - - +
253C SER* 1.3 62.5 + - - +
254C LEU* 3.5 23.5 + - + +
277C ARG 5.2 1.1 - - - -
278C SER 3.6 5.8 - - - +
279C LEU* 4.1 9.1 - - + +
329C THR 3.8 0.2 - - - +
330C SER* 3.2 7.8 - - - -
331C PHE* 2.9 51.6 + - + +
333C PHE* 4.5 10.5 - - + -
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Residues in contact with SER 253 (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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251C SER* 3.7 5.2 + - - -
252C LEU* 1.3 69.6 - - - +
254C LEU* 1.3 57.7 + - - +
256C SER 5.2 2.5 - - - -
274C LEU* 3.7 22.8 - - - +
275C PRO 3.7 19.3 - - - -
276C ARG* 4.2 2.2 - - - -
277C ARG* 2.6 36.2 + - - -
278C SER* 3.1 13.3 + - - -
280C LEU* 5.7 0.2 - - - +
328C ARG* 3.1 33.2 + - - +
329C THR 4.1 1.6 - - - -
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Residues in contact with LEU 254 (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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144C ILE* 3.5 32.3 - - + -
149C GLU* 3.7 18.8 - - + +
152C LEU* 3.8 27.4 - - + -
153C LEU* 4.2 16.8 - - + +
252C LEU* 3.9 23.8 - - + +
253C SER* 1.3 84.4 - - - +
255C GLY* 1.3 60.1 + - - +
256C SER 3.4 4.0 + - - -
276C ARG* 4.7 1.1 - - - -
277C ARG* 4.5 1.8 - - - +
328C ARG* 3.6 2.9 - - - +
329C THR 2.7 43.5 + - - +
331C PHE* 4.1 24.9 - - + -
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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