Contacts of the strand formed by residues 275 - 280 (chain A) in PDB entry 4D85
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 ILE 275 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A VAL* 4.7 6.7 - - + -
199A GLU 3.7 6.7 - - - +
200A ILE* 4.9 13.9 - - + -
226A LEU* 5.3 7.0 - - + -
236A ALA* 6.3 1.6 - - + -
240A ILE* 4.0 14.6 - - + -
273A PRO 4.1 2.5 - - - +
274A VAL* 1.3 77.7 - - - +
276A SER* 1.3 70.8 - - - +
277A LEU* 4.7 12.1 - - + -
290A ILE 3.7 0.5 - - - +
291A THR* 3.2 4.5 - - - +
292A ILE* 2.9 49.1 + - + +
297A TYR* 3.6 24.2 - - + +
311A ILE* 3.4 33.2 - - + -
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Residues in contact with SER 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A VAL* 3.3 11.8 - - - +
199A GLU* 2.9 50.2 + - - -
274A VAL* 5.2 2.1 + - - +
275A ILE* 1.3 75.0 + - - +
277A LEU* 1.3 63.8 + - - +
278A TYR* 4.5 1.3 - - - -
289A ARG* 3.5 26.5 + - - -
290A ILE 3.2 3.6 - - - -
291A THR* 2.9 27.4 + - - +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ILE* 4.4 24.5 - - + -
197A ARG 3.6 2.5 - - - -
198A VAL* 4.0 23.6 - - + -
226A LEU* 5.4 9.0 - - + -
228A LEU* 5.6 6.5 - - + -
275A ILE* 4.7 9.9 - - + -
276A SER* 1.3 81.4 - - - +
278A TYR* 1.3 63.6 + - - +
279A LEU* 3.8 4.4 + - + +
289A ARG* 3.4 1.0 - - - -
290A ILE* 2.9 55.3 + - + +
292A ILE* 6.5 0.2 - - + -
318A THR* 5.1 3.4 - - + -
320A MET* 4.3 26.7 - - + -
324A ILE* 4.6 13.5 - - + -
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Residues in contact with TYR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ILE* 3.4 7.8 - - - +
196A VAL* 2.8 45.9 + - + -
197A ARG* 2.8 44.9 + - + +
199A GLU* 2.9 39.4 + - + -
276A SER* 4.5 2.2 - - - -
277A LEU* 1.3 74.1 - - - +
279A LEU* 1.3 57.2 + - - +
287A SER* 4.0 14.1 - - - +
288A PHE 3.1 9.9 - - - +
289A ARG* 2.8 50.4 + - + -
361A PHE* 3.6 35.7 - + + -
363A THR* 5.3 2.0 - - - -
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A THR* 3.8 17.9 - - + +
193A VAL* 4.4 13.9 - - + -
194A ILE 3.5 15.7 - - - +
195A ILE* 3.8 22.9 - - + -
196A VAL* 4.4 1.6 - - - -
277A LEU* 4.7 9.6 - - + +
278A TYR* 1.3 75.2 - - - +
280A MET* 1.3 64.9 + - - +
287A SER* 3.2 7.3 - - - -
288A PHE* 2.8 50.0 + - + +
290A ILE* 4.5 13.2 - - + -
320A MET* 4.6 7.2 - - + -
341A PHE* 3.7 35.4 - - + -
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Residues in contact with MET 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A THR* 2.7 33.0 + - - +
184A PRO* 3.2 24.3 - - + +
194A ILE* 3.1 42.2 + - + +
196A VAL* 4.0 3.9 - - + +
279A LEU* 1.3 71.4 - - - +
281A GLY* 1.3 72.4 + - - +
288A PHE* 3.8 1.4 - - - -
366A MET* 3.6 61.0 - - + +
367A GLU* 4.1 9.9 - - + +
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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