Contacts of the strand formed by residues 286 - 290 (chain C) in PDB entry 3ELP
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 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304B LYS* 5.1 0.9 + - - -
280C LEU* 2.9 49.6 - - + +
281C GLU* 4.8 4.4 - - - +
283C ASN* 3.3 21.3 + - + +
284C PRO 3.4 0.7 - - - +
285C TRP* 1.3 85.2 - - - +
287C GLU* 1.3 65.3 + - - +
288C LYS* 3.6 23.6 - - - +
289C VAL* 3.8 14.1 - - + -
316C PHE* 4.2 11.7 - - + -
317C TYR 3.7 7.4 - - - +
319C LYS* 3.9 11.1 + - - +
394C LEU* 4.4 5.2 - - + -
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Residues in contact with GLU 287 (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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301B GLU* 3.2 23.2 - - - +
304B LYS* 3.4 18.7 + - - -
286C VAL* 1.3 74.9 - - - +
288C LYS* 1.3 66.2 + - + +
317C TYR* 2.8 27.8 + - + +
318C ILE 4.7 1.1 - - - +
319C LYS* 3.3 38.9 + - + +
320C GLY 5.6 0.9 - - - +
372C THR* 5.9 0.2 - - - +
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Residues in contact with LYS 288 (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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301B GLU* 4.7 22.4 - - + +
281C GLU* 6.2 0.9 - - - +
286C VAL* 3.4 6.0 - - - +
287C GLU* 1.3 84.7 - - + +
289C VAL* 1.3 66.1 + - - +
290C ILE* 4.1 17.5 - - + +
316C PHE* 3.5 1.4 - - - -
317C TYR* 2.9 60.7 + - + +
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Residues in contact with VAL 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ALA* 3.9 6.5 - - - +
280C LEU* 3.9 6.1 - - + -
281C GLU* 3.5 56.9 + - + +
286C VAL* 3.8 11.7 - - + -
288C LYS* 1.3 79.8 - - - +
290C ILE* 1.3 81.7 + - - +
291C TYR* 3.9 2.3 + - + -
294C LEU* 3.9 18.4 - - + -
296C SER* 4.6 9.5 + - - +
297C HIS* 5.7 1.0 - - - -
314C VAL* 4.1 17.3 - - + -
315C THR 3.5 11.0 - - - +
316C PHE* 4.2 3.4 - - + -
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Residues in contact with ILE 290 (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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163C THR* 3.3 26.7 - - + +
164C GLN* 3.4 11.3 + - + -
288C LYS* 4.1 24.2 - - + +
289C VAL* 1.3 84.2 - - - +
291C TYR* 1.3 59.9 + - - +
296C SER 6.1 0.4 - - - +
297C HIS* 3.9 22.2 - - + +
298C PRO* 5.0 14.6 - - + -
315C THR* 2.6 43.8 + - + +
317C TYR* 3.8 24.0 - - + +
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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