Contacts of the strand formed by residues 279 - 284 (chain D) in PDB entry 3IT8
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 PRO 279 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D VAL* 5.9 0.7 - - - +
200D LEU* 3.4 34.7 - - + +
216D TRP* 3.7 32.0 - - + -
217D ILE 3.3 16.6 - - - +
218D GLU* 4.0 1.7 - - - +
237D TRP* 4.3 10.8 - - + +
269D VAL* 4.7 7.4 - - + -
271D THR* 4.8 1.1 - - + -
275D MET* 3.2 29.6 - - + -
278D GLN* 1.3 94.1 - - + +
280D VAL* 1.3 59.8 + - - +
294D THR* 5.8 0.7 - - - -
296D SER* 5.3 0.2 + - - -
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D VAL* 6.3 0.7 - - - -
215D LYS 3.6 0.7 - - - +
216D TRP* 3.6 7.6 - - - -
217D ILE* 2.8 38.4 + - + +
219D SER* 4.6 9.9 - - - +
222D PHE* 3.5 30.3 - - + -
226D TYR* 4.4 1.8 - - + -
279D PRO* 1.3 75.4 - - - +
281D CYS* 1.3 58.3 + - - +
282D VAL* 3.7 1.2 + - + +
292D VAL* 3.2 22.7 - - + -
293D TYR 2.8 24.9 - - - +
294D THR* 3.2 28.5 - - + +
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Residues in contact with CYS 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D VAL* 3.7 16.3 - - + +
202D CYS* 2.0 49.8 - - - -
214D THR* 3.3 20.2 - - - -
215D LYS 3.9 2.5 - - - -
216D TRP* 3.8 19.3 - - + -
280D VAL* 1.3 71.5 - - - +
282D VAL* 1.3 59.2 + - - +
283D VAL* 4.0 5.4 - - - -
292D VAL* 3.5 1.3 - - - -
293D TYR* 2.7 44.3 + - + +
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Residues in contact with VAL 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D THR* 3.4 6.0 + - - -
215D LYS* 2.8 51.4 + - + +
217D ILE* 3.9 23.8 - - + -
222D PHE* 4.0 17.5 - - + -
228D TYR* 3.9 20.6 - - + -
280D VAL* 4.4 3.6 - - + +
281D CYS* 1.3 74.6 - - - +
283D VAL* 1.3 62.3 + - - +
284D PHE* 3.7 27.8 - - + -
290D ALA* 4.7 3.1 - - + -
291D GLN 3.4 12.3 - - - +
292D VAL* 4.2 7.4 - - + -
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Residues in contact with VAL 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D PRO* 5.3 0.7 - - + -
186D VAL* 4.2 4.7 - - + -
202D CYS* 4.0 2.0 - - - -
204D VAL* 4.0 35.2 - - + -
212D VAL* 4.6 5.6 - - + -
213D ILE 3.8 4.5 - - - +
214D THR* 4.1 4.5 - - - +
281D CYS* 4.0 20.0 - - - -
282D VAL* 1.3 74.8 - - - +
284D PHE* 1.3 67.7 + - - +
285D HIS* 4.6 5.6 - - + -
288D LEU* 3.6 19.5 - - + +
290D ALA* 3.4 4.0 - - - -
291D GLN 2.9 29.5 + - - -
293D TYR* 4.0 24.7 - - + -
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Residues in contact with PHE 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D THR* 3.2 19.7 - - - +
102D LEU* 4.2 9.9 - - + -
103D LEU* 3.5 35.9 - - + -
212D VAL* 3.6 3.5 - - - +
213D ILE* 2.8 43.0 + - + +
215D LYS* 3.4 34.8 - - + -
228D TYR* 3.7 34.3 - + - -
282D VAL* 3.7 24.5 - - + -
283D VAL* 1.3 71.4 - - - +
285D HIS* 1.3 62.6 + - - +
289D GLU 3.8 6.5 - - - -
290D ALA* 3.5 24.9 - - + -
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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