Contacts of the strand formed by residues 276 - 281 (chain E) in PDB entry 1TYE
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 ARG 276 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230E TYR* 3.4 19.1 + - - -
268E GLU* 3.7 20.6 + - + +
269E ILE 3.9 0.2 - - - -
270E LEU* 3.5 22.2 - - + +
274E TYR 3.8 4.8 + - - -
275E GLN* 1.3 72.4 + - - +
277E LEU* 1.3 64.5 + - - +
278E HIS 4.9 5.6 - - - +
279E ARG* 3.2 33.7 - - - +
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Residues in contact with LEU 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E PHE 4.8 5.4 - - - +
245E ASP* 4.2 18.2 - - + +
252E GLU* 4.2 15.7 - - + +
269E ILE* 2.7 34.5 + - + +
270E LEU 4.4 2.5 - - - -
271E ASP* 4.0 33.0 - - + +
275E GLN* 3.2 16.5 + - + +
276E ARG* 1.3 78.8 - - - +
278E HIS* 1.3 81.0 + - + +
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Residues in contact with HIS 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E PHE* 4.6 13.0 + - + -
268E GLU* 3.4 5.5 - - - +
269E ILE* 3.0 51.0 + - + +
276E ARG* 4.9 3.8 - - - +
277E LEU* 1.3 102.2 + - + +
279E ARG* 1.3 62.9 + - - +
280E LEU* 4.3 12.3 - - + -
339E ALA* 2.8 38.1 - - + +
340E LEU* 3.9 30.6 + - + +
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Residues in contact with ARG 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227E ASN* 5.5 0.8 + - - -
229E GLU* 4.8 5.3 + - - -
230E TYR* 2.9 28.3 + - - -
260E TRP* 3.4 43.1 - - - -
266E ALA* 4.5 5.2 - - + -
267E VAL 3.6 5.2 - - - +
268E GLU* 2.9 27.5 + - + +
276E ARG* 3.2 24.7 - - - +
278E HIS* 1.3 76.4 - - - +
280E LEU* 1.3 73.1 + - - +
281E ARG* 3.7 15.8 + - - +
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Residues in contact with LEU 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E ALA* 3.4 1.7 - - - -
267E VAL* 2.9 48.7 + - + +
269E ILE* 4.6 9.0 - - + -
278E HIS* 4.7 4.0 - - + -
279E ARG* 1.3 83.8 - - - +
281E ARG* 1.3 60.4 + - - +
289E PHE* 3.3 15.5 - - + -
306E LEU* 3.7 24.5 - - + -
308E VAL* 5.7 0.2 - - + -
331E PHE* 4.0 42.0 - - + -
340E LEU* 4.2 19.3 - - + +
341E GLY 4.1 11.2 - - - +
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Residues in contact with ARG 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E GLU* 3.7 21.6 + - - -
260E TRP* 3.8 19.9 - - + -
261E SER* 4.5 5.3 + - - -
264E LEU* 3.5 26.7 - - + +
265E GLY 4.1 5.2 - - - -
266E ALA* 4.6 2.9 - - - +
279E ARG* 3.7 20.0 + - - +
280E LEU* 1.3 76.4 - - - +
282E ALA* 1.3 67.3 + - - +
289E PHE* 3.9 8.9 - - - -
331E PHE* 5.6 1.9 - - - -
2I NAG 3.0 36.2 + - - -
3I MAN 6.4 1.8 - - - -
4I BMA 4.2 23.3 + - - +
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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