Contacts of the strand formed by residues 274 - 279 (chain C) in PDB entry 3MDY
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 GLN 274 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLN* 5.4 9.5 + - - +
206C MET* 6.0 1.0 - - - +
232C VAL* 3.2 28.2 - - + +
233C PHE 3.5 2.0 - - - +
234C PHE* 3.8 25.7 - - + -
266C ILE* 3.4 6.2 - - - +
267C LYS* 2.8 66.9 + - - +
272C TRP* 3.4 10.0 + - - +
273C THR* 1.3 78.2 - - - +
275C LEU* 1.3 63.6 + - - +
276C TYR* 4.0 19.6 + - + -
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Residues in contact with LEU 275 (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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231C LYS 3.5 3.8 - - - +
232C VAL* 3.5 2.1 - - - -
233C PHE* 2.8 42.3 + - + +
234C PHE 4.1 15.3 - - - +
235C THR* 4.2 6.5 - - - +
238C GLU* 3.7 46.4 - - + +
241C TRP* 3.7 34.1 - - + -
265C ASP 3.8 2.2 - - - -
266C ILE* 3.5 39.3 - - + -
273C THR* 4.4 8.3 - - + -
274C GLN* 1.3 74.8 - - - +
276C TYR* 1.3 62.0 + - - +
86D THR* 5.3 0.7 - - + -
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Residues in contact with TYR 276 (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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201C ALA* 4.0 37.0 + - + -
204C ILE* 4.8 7.1 + - + -
206C MET* 3.6 31.7 - - + +
230C VAL* 3.5 23.6 - - + -
231C LYS 3.5 2.5 - - - -
232C VAL* 4.2 17.0 - - + -
241C TRP* 2.9 16.2 + - - -
264C ALA* 3.1 3.3 - - - -
265C ASP 2.8 32.4 + - - +
267C LYS* 3.1 27.5 - - + +
274C GLN* 4.0 28.3 + - + -
275C LEU* 1.3 81.4 - - - +
277C LEU* 1.3 59.0 + - - +
278C ILE* 4.0 16.2 - - + -
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Residues in contact with LEU 277 (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 LDN 5.9 1.1 - - + +
229C ALA 4.0 0.5 - - - +
230C VAL* 3.6 0.9 - - - -
231C LYS* 2.9 45.2 + - + +
233C PHE* 4.0 15.0 - - + -
241C TRP* 4.2 5.2 - - + +
244C GLU* 3.5 45.1 - - + +
245C THR* 4.1 13.2 - - - +
248C TYR* 4.0 13.9 - - + -
261C PHE* 3.5 37.9 - - + -
263C ALA 3.8 1.1 - - - -
264C ALA* 4.5 0.7 - - + +
276C TYR* 1.3 73.0 - - - +
278C ILE* 1.3 60.2 + - - +
279C THR* 4.0 13.1 + - + +
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Residues in contact with ILE 278 (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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200C ILE* 3.4 35.4 - - + -
204C ILE* 4.2 7.2 - - + -
228C VAL* 3.8 26.9 - - + -
229C ALA 3.4 10.5 - - - +
230C VAL* 4.2 9.6 - - + -
261C PHE* 4.0 2.3 - - - -
262C ILE* 2.8 37.2 + - + -
263C ALA* 2.6 34.1 + - + +
265C ASP* 4.8 6.3 - - + -
276C TYR* 4.1 24.5 - - + -
277C LEU* 1.3 74.0 - - - +
279C THR* 1.3 67.0 + - - +
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Residues in contact with THR 279 (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 LDN 3.3 28.3 - - + -
228C VAL* 3.6 1.9 - - - +
229C ALA* 2.9 27.0 + - - +
248C TYR* 4.7 9.2 - - + -
259C LEU* 3.7 20.0 - - + -
260C GLY 3.2 15.0 - - - +
261C PHE* 4.5 4.7 - - - -
262C ILE* 3.5 14.7 - - - +
277C LEU* 4.4 19.7 - - + +
278C ILE* 1.3 80.5 - - - +
280C ASP* 1.3 76.2 + - - +
281C TYR 3.5 0.2 + - - -
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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