Contacts of the strand formed by residues 274 - 277 (chain D) in PDB entry 3SZ9
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 274 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272D LYS 3.6 6.0 - - - +
273D SER* 1.3 84.4 - - - +
275D ASN* 1.3 60.1 + - - +
276D ILE* 4.0 4.4 - - + +
307D ARG* 3.4 20.0 - - + +
309D PHE* 4.0 16.6 - - + -
420D ALA* 3.8 33.4 - - + +
428D ALA 3.3 13.9 - - - +
429D ALA* 3.2 18.8 - - + +
430D ALA 2.9 24.7 + - - +
446D LEU* 4.9 2.7 - - + -
456D TYR* 4.8 1.0 - - - -
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Residues in contact with ASN 275 (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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273D SER 3.7 0.2 + - - -
274D PRO* 1.3 74.5 - - - +
276D ILE* 1.3 58.1 + - - +
277D ILE* 3.8 6.0 + - - +
290D ALA* 3.5 32.9 + - - +
293D ALA* 3.8 6.9 - - - +
305D GLY* 4.4 11.8 - - - +
307D ARG 2.8 11.7 + - - +
308D THR* 3.4 10.9 + - - +
309D PHE 2.8 31.8 + - - +
430D ALA* 3.5 10.5 - - - +
432D PHE* 3.3 32.5 - - - -
456D TYR* 4.1 18.6 - - + -
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Residues in contact with ILE 276 (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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274D PRO* 4.7 3.1 - - + -
275D ASN* 1.3 77.3 - - - +
277D ILE* 1.3 60.3 + - - +
278D MET* 3.7 29.0 + - + -
309D PHE* 3.5 10.8 - - + -
410D PHE* 4.1 3.6 - - + -
416D VAL* 3.6 41.1 - - + +
420D ALA* 4.2 7.9 - - + -
430D ALA 2.9 19.4 + - - +
431D VAL* 4.4 2.5 - - + -
432D PHE* 2.8 31.7 + - - +
442D LEU* 4.4 12.3 - - + -
446D LEU* 4.1 32.5 - - + -
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Residues in contact with ILE 277 (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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275D ASN* 3.8 26.0 - - - +
276D ILE* 1.3 80.0 - - - +
278D MET* 1.3 60.8 - - - +
281D ALA* 3.9 13.9 - - + -
283D MET* 6.2 0.4 - - - -
286D ALA* 3.8 30.7 - - + +
308D THR* 4.2 5.2 - - + -
309D PHE 2.8 16.0 + - - +
310D VAL* 3.7 9.3 - - + -
311D GLN 3.1 25.1 + - - -
314D ILE* 3.9 16.8 - - + +
318D PHE* 4.0 28.3 - - + -
410D PHE* 3.8 2.1 - - - -
432D PHE* 3.8 17.0 - - + -
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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