Contacts of the strand formed by residues 273 - 278 (chain C) in PDB entry 1EFP
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 273 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C GLU* 2.7 20.0 + - + +
252C LEU* 3.5 17.2 - - + +
253C TYR* 2.9 26.3 + - - +
271C SER* 4.4 0.5 - - - -
272C LYS* 1.3 82.1 - - + +
274C ILE* 1.3 66.0 + - - +
275C VAL* 4.1 7.0 - - + -
290C ASP* 3.4 7.4 - - + +
291C TYR* 4.0 31.0 - - + -
246D LEU* 6.2 3.6 - - + -
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Residues in contact with ILE 274 (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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253C TYR* 3.4 11.4 - - + +
255C ALA* 5.4 0.2 - - + -
268C MET* 3.3 41.5 - - + +
271C SER* 3.8 15.9 - - - -
273C VAL* 1.3 76.2 - - - +
275C VAL* 1.3 69.4 + - - +
285C ILE* 5.0 3.8 - - + -
288C ILE* 4.2 19.5 - - + +
289C ALA* 3.4 22.3 - - + +
290C ASP* 2.9 34.9 + - - +
291C TYR 3.4 5.5 + - - -
230D ARG* 3.3 31.9 - - - +
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Residues in contact with VAL 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LEU* 3.8 22.2 - - + -
253C TYR 2.8 7.5 + - - +
254C VAL* 4.1 23.6 - - + -
255C ALA* 2.8 27.9 + - - +
273C VAL* 4.3 9.4 - - + -
274C ILE* 1.3 79.4 - - - +
276C ALA* 1.3 69.4 + - - +
277C ILE* 5.2 2.7 - - + -
291C TYR* 3.2 21.8 - - + +
293C LEU* 5.8 0.7 - - + +
304C LEU* 6.2 0.2 - - + -
242D LEU* 3.9 33.7 - - + -
246D LEU* 6.1 5.2 - - + -
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Residues in contact with ALA 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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255C ALA 3.3 7.0 - - - +
275C VAL* 1.3 81.1 - - - +
277C ILE* 1.3 57.8 + - - +
278C ASN 4.1 0.4 - - - -
285C ILE* 3.8 33.2 - - + -
286C PHE* 3.9 10.3 - - + -
289C ALA* 3.7 20.6 - - + -
291C TYR 3.2 4.9 + - - +
292C GLY* 3.2 1.5 - - - -
293C LEU* 2.7 32.4 + - - +
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Residues in contact with ILE 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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254C VAL* 4.5 13.5 - - + -
255C ALA 3.1 5.6 + - - +
256C VAL* 3.5 19.1 - - + +
257C GLY 3.1 24.8 + - - -
258C ILE 5.0 0.2 + - - -
275C VAL* 5.2 4.0 - - + -
276C ALA* 1.3 76.4 - - - +
278C ASN* 1.3 60.3 + - - +
293C LEU* 3.2 18.8 - - + +
295C GLY 4.1 10.1 - - - +
297C LEU* 3.5 25.4 - - + -
300C VAL* 3.4 37.5 - - + -
301C VAL* 3.7 14.8 - - + -
304C LEU* 6.0 5.4 - - + -
399C FAD 4.6 0.9 + - - -
242D LEU* 6.1 2.5 - - + -
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Residues in contact with ASN 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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258C ILE 3.1 30.0 + - - +
277C ILE* 1.3 75.3 - - - +
279C LYS* 1.3 75.3 + - - +
280C ASP* 3.0 6.4 + - - +
283C ALA* 3.5 14.8 - - - +
285C ILE* 4.2 4.4 - - + +
286C PHE* 3.6 22.2 - - + -
293C LEU 3.3 2.4 + - - -
294C VAL* 3.2 10.6 - - - +
295C GLY 2.9 22.4 + - - -
399C FAD 2.8 52.1 + - - -
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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