Contacts of the strand formed by residues 326 - 330 (chain B) in PDB entry 6AHU
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 GLN 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B GLU* 3.1 33.5 + - + +
255B LEU 4.1 4.3 - - - +
256B LYS* 3.7 26.9 - - - +
312B TRP* 4.7 1.9 - - - -
313B LYS 4.0 23.9 + - - +
324B SER* 4.2 7.1 + - - +
325B ARG* 1.3 83.8 - - - +
327B LEU* 1.3 65.9 + - - +
328B TRP* 4.8 2.8 + - - +
554B TRP* 3.3 61.0 + - + +
555B ASN* 5.6 1.6 + - - -
556B GLN* 6.0 1.6 - - - +
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Residues in contact with LEU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B LEU 3.0 13.7 - - - +
255B LEU* 3.3 53.7 + - + +
262B ILE* 3.9 25.1 - - + +
266B LEU* 4.8 6.1 - - + -
278B PHE* 5.6 0.7 - - + -
310B PHE* 3.6 33.4 - - + -
311B ILE 3.8 9.2 - - - +
312B TRP* 3.8 33.4 - - + -
325B ARG* 5.4 2.0 - - + +
326B GLN* 1.3 77.2 - - - +
328B TRP* 1.3 66.1 + - - +
329B ILE* 4.5 4.9 - - + -
554B TRP* 5.6 2.2 - - - -
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Residues in contact with TRP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B CYS* 4.4 17.3 - - + -
253B LEU 3.3 1.8 - - - -
254B GLU* 3.5 42.9 - - + +
309B THR 4.4 1.2 - - - +
310B PHE* 3.6 20.3 - - - -
311B ILE* 4.0 22.5 + - + +
326B GLN* 4.8 4.2 + - + +
327B LEU* 1.3 86.3 - - - +
329B ILE* 1.3 63.9 + - - +
330B TRP* 3.8 34.4 + + + +
425B LEU* 5.5 3.1 - - + -
429B MET* 3.6 34.1 - - + -
553B ILE* 4.3 0.7 - - + -
554B TRP* 3.4 54.2 - + + -
598B LEU* 5.8 0.2 - - + -
621B LEU* 3.6 25.6 - - + -
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Residues in contact with ILE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B CYS 3.2 10.9 - - - +
252B CYS* 3.3 8.7 - - - -
253B LEU* 3.2 33.5 + - + +
255B LEU* 4.8 11.9 - - + -
266B LEU* 5.7 4.7 - - + -
269B MET* 5.7 3.4 - - + -
294B LEU* 4.3 13.2 - - + -
308B VAL* 3.8 25.1 - - + -
310B PHE* 3.6 31.4 - - + -
327B LEU* 4.5 4.9 - - + -
328B TRP* 1.3 70.7 - - - +
330B TRP* 1.3 60.8 + - - +
331B LEU* 3.6 24.5 + - + +
339B ILE* 4.1 13.0 - - + -
343B ILE* 5.7 5.8 - - + -
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Residues in contact with TRP 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B TYR* 5.1 8.0 + - + -
251B CYS 3.3 14.1 - - - +
252B CYS* 3.6 20.6 - - + +
289B GLN* 4.2 9.2 - - - -
307B PRO 4.1 1.0 - - - +
308B VAL* 3.3 31.2 - - - +
309B THR* 3.2 41.1 + - - +
311B ILE* 3.6 30.1 - - + -
328B TRP* 3.8 19.6 + + + +
329B ILE* 1.3 70.3 - - - +
331B LEU* 1.3 58.9 + - - +
431B ARG* 3.3 48.5 - - + +
600B ILE* 4.1 14.4 - - + -
602B GLN* 5.2 0.4 - - - -
619B ASP* 4.7 6.7 - - + -
621B LEU* 4.1 31.3 - - + +
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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