Contacts of the strand formed by residues 266 - 273 (chain C) in PDB entry 3MSS
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 LEU 266 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260C VAL* 3.5 3.4 - - - +
261C TRP* 2.8 54.6 + - + +
264C TYR* 3.6 23.8 - - + +
265C SER* 1.3 77.1 - - - +
267C THR* 1.3 74.3 + - - +
268C VAL* 3.6 16.4 + - + +
302C LEU* 4.2 12.8 - - + -
316C GLU* 6.1 1.8 - - + -
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Residues in contact with THR 267 (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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245C LYS* 5.3 1.7 + - - -
258C GLU* 3.4 39.1 + - + +
259C GLY 3.3 6.5 + - - +
260C VAL* 4.6 9.3 - - + +
265C SER 4.1 2.0 + - - -
266C LEU* 1.3 83.2 - - - +
268C VAL* 1.3 64.8 + - - +
316C GLU* 5.0 0.5 - - - -
317C PHE* 3.4 38.0 + - + +
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Residues in contact with VAL 268 (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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242C ILE* 4.4 8.5 - - + -
258C GLU* 3.7 7.4 - - - +
259C GLY 2.8 42.5 + - - +
261C TRP* 4.1 15.0 - - + +
266C LEU* 3.8 19.7 - - + +
267C THR* 1.3 79.0 - - - +
269C ALA* 1.3 60.6 + - - +
270C VAL* 3.7 23.3 - - + -
302C LEU* 3.8 24.7 - - + -
314C ILE* 3.8 13.2 - - + -
315C THR 3.5 8.7 - - - +
316C GLU* 5.1 0.2 - - - -
317C PHE* 4.0 9.7 - - - +
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Residues in contact with ALA 269 (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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1C STI 3.6 37.6 - - + +
248C LEU* 3.8 18.6 - - + -
256C VAL* 4.4 0.4 - - + -
257C TYR 3.6 4.0 - - - -
268C VAL* 1.3 71.5 - - - +
270C VAL* 1.3 64.2 + - - +
314C ILE* 3.3 4.0 - - - +
315C THR* 2.8 46.4 + - - +
316C GLU 4.0 6.7 + - - +
317C PHE* 4.7 0.7 - - + -
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Residues in contact with VAL 270 (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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1C STI 4.0 1.8 - - - +
242C ILE* 4.1 8.5 - - + -
244C MET* 3.7 31.0 - - + -
255C GLU 3.9 0.2 - - - +
256C VAL* 3.3 2.4 - - - +
257C TYR* 2.9 45.0 + - - +
259C GLY* 4.5 2.7 - - - -
268C VAL* 3.7 22.4 - - + -
269C ALA* 1.3 80.2 - - - +
271C LYS* 1.3 61.7 + - - +
272C THR 3.9 1.2 + - - -
312C TYR* 3.5 43.3 - - + -
313C ILE 3.4 3.6 - - - +
314C ILE* 4.2 8.3 - - + -
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Residues in contact with LYS 271 (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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1C STI 3.5 37.2 - - + +
253C TYR 6.0 1.6 - - - -
255C GLU* 3.5 10.3 - - + +
256C VAL* 4.1 14.6 - - + -
270C VAL* 1.3 73.2 - - - +
272C THR* 1.3 65.1 + - - +
283C PHE* 3.6 23.1 - - + -
286C GLU* 3.0 31.0 + - - +
312C TYR* 3.2 6.8 - - - +
313C ILE* 2.7 38.7 + - + +
381C ASP 5.3 0.4 + - - -
382C PHE* 4.4 18.8 + - - +
383C GLY* 5.1 4.9 - - - -
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Residues in contact with THR 272 (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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244C MET* 5.0 4.0 - - + -
255C GLU* 2.9 34.4 + - + +
257C TYR* 3.6 35.0 - - + -
270C VAL 4.8 1.3 - - - -
271C LYS* 1.3 81.5 - - - +
273C LEU* 1.3 76.7 + - - +
283C PHE* 4.0 5.7 - - - -
310C PRO* 4.1 7.3 - - - +
311C PHE 3.1 13.1 + - - -
312C TYR* 3.7 20.6 - - + -
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Residues in contact with LEU 273 (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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255C GLU* 5.5 2.5 - - - -
272C THR* 1.3 89.5 + - - +
280C VAL* 3.8 43.1 - - + +
283C PHE* 3.9 34.5 - - + -
309C PRO* 5.5 1.7 - - - +
310C PRO* 4.0 9.4 - - - +
311C PHE* 3.3 31.9 + - + +
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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