Contacts of the strand formed by residues 279 - 282 (chain I) in PDB entry 1DE4
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 279 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255I VAL* 3.2 14.1 - - + +
257I VAL* 4.0 13.0 - - + -
267I LYS* 5.0 1.3 - - + +
268I VAL* 4.1 19.3 - - + +
271I ALA* 3.8 27.4 - - + -
278I GLY* 1.3 80.6 - - - +
280I LEU* 1.3 76.4 + - - +
281I ILE* 3.9 16.6 - - + -
332I ILE* 4.0 10.8 - - + -
333I PRO 3.0 5.0 + - - +
334I VAL* 3.3 14.1 - - + +
335I GLN 2.9 26.0 + - - -
375I LEU* 4.1 2.1 - - - +
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Residues in contact with LEU 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200I VAL* 3.7 26.2 - - + -
232I LEU* 4.1 27.8 - - + -
254I ILE* 4.2 12.8 - - + -
255I VAL 2.8 9.2 + - - +
256I ILE* 3.3 8.0 - - + +
257I VAL* 2.8 29.1 + - - +
279I VAL* 1.3 75.3 - - - +
281I ILE* 1.3 60.3 + - - +
335I GLN* 3.4 8.7 - - + +
337I ILE* 4.3 25.8 - - + -
345I LEU* 4.7 2.2 - - + -
373I VAL* 5.1 4.5 - - + -
375I LEU* 3.6 43.5 - - + -
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Residues in contact with ILE 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220I VAL* 4.7 2.5 - - + -
257I VAL* 3.3 14.1 - - + +
258I ARG 4.4 1.6 - - - +
259I ALA* 4.1 13.9 - - - +
264I PHE* 3.5 59.2 - - + -
267I LYS* 4.4 5.8 - - + -
268I VAL* 4.9 1.3 - - + -
279I VAL* 3.9 13.2 - - + -
280I LEU* 1.3 78.9 - - - +
282I TYR* 1.3 64.8 + - - +
297I PHE* 3.5 15.4 - - + -
334I VAL* 4.0 17.0 - - + -
335I GLN 2.9 14.0 + - - +
336I THR* 3.6 4.2 - - - +
337I ILE* 2.9 27.2 + - - +
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Residues in contact with TYR 282 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234I HIS* 3.1 21.8 + - - -
256I ILE* 3.6 31.4 - - + -
257I VAL 3.0 38.6 + - - -
258I ARG* 3.3 22.6 - - + +
259I ALA 3.0 22.7 + - - -
281I ILE* 1.3 76.2 - - - +
283I MET* 1.3 69.2 + - - +
284I ASP* 3.7 27.0 - - + +
297I PHE* 3.6 5.4 - - - -
337I ILE* 3.5 26.7 - - + +
338I SER 4.3 1.6 - - - +
339I ARG* 4.7 4.3 - - + -
342I ALA* 3.5 22.4 - - + -
346I PHE* 3.5 17.1 - + - -
359I THR* 4.6 0.2 + - - -
360I ASP* 6.1 1.2 - - + +
363I CYS* 4.1 6.9 - - - +
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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