Contacts of the strand formed by residues 326 - 332 (chain B) in PDB entry 6CIM
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 THR 326 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B THR* 3.9 1.6 + - - -
321B ASN* 3.5 2.1 - - - +
322B MET* 2.9 51.5 + - - +
324B ASN* 3.1 24.1 + - + +
325B GLY* 1.3 80.7 - - - +
327B ILE* 1.3 64.5 + - - +
347B THR* 5.7 2.2 - - - -
348B LEU 3.3 6.7 - - - -
349B ARG* 3.6 33.4 - - + +
350B CYS 4.6 0.4 - - - +
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Residues in contact with ILE 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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262B ILE* 3.8 24.0 - - + -
263B LEU 4.2 1.6 - - - +
264B THR* 3.5 35.9 - - + -
274B VAL* 3.9 20.6 - - + -
320B SER 3.3 7.6 - - - +
321B ASN* 3.7 19.3 - - + -
322B MET* 4.3 2.1 - - - +
325B GLY 5.4 0.2 - - - +
326B THR* 1.3 75.5 - - - +
328B PHE* 1.3 63.4 + - - +
329B LEU* 3.6 29.6 - - + -
347B THR* 3.2 9.4 - - - -
348B LEU* 2.9 44.3 + - + +
350B CYS* 5.6 1.6 - - - -
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Residues in contact with PHE 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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6B VAL* 4.7 6.1 - - + -
15B ILE* 4.3 7.0 - - + -
19B PHE* 3.8 22.4 - + - -
21B LEU* 4.3 5.8 - - + -
48B PHE* 3.7 26.9 - + - -
50B ILE* 4.2 8.3 - - + -
55B LEU* 3.8 24.2 - - + -
319B GLY* 3.0 5.7 - - - -
320B SER 3.0 34.6 + - - +
322B MET* 3.9 17.4 - - + +
327B ILE* 1.3 73.0 - - - +
329B LEU* 1.3 58.6 + - - +
345B PHE* 3.4 52.3 - + + -
346B TYR 3.5 9.0 - - - -
347B THR* 4.0 13.0 - - + -
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Residues in contact with LEU 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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3B LEU* 4.9 5.4 - - + -
262B ILE* 3.7 20.2 - - + -
274B VAL* 5.3 4.5 - - + -
275B GLY* 6.0 3.6 - - - -
307B TRP* 3.9 33.7 - - + -
311B ILE* 5.9 2.9 - - + -
317B TRP* 4.6 18.8 - - + -
318B PHE* 3.6 9.4 - - - +
327B ILE* 3.6 27.1 - - + +
328B PHE* 1.3 74.3 - - - +
330B GLY* 1.3 58.7 + - - +
331B ILE* 6.2 1.6 - - + -
345B PHE* 3.1 12.9 - - - +
346B TYR* 2.8 43.7 + - + +
348B LEU* 4.7 15.0 - - + -
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Residues in contact with GLY 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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317B TRP* 3.3 6.4 - - - +
318B PHE* 2.9 47.7 + - - +
329B LEU* 1.3 77.3 - - - +
331B ILE* 1.3 65.1 + - - +
344B TYR 3.3 9.0 - - - -
345B PHE* 3.5 17.3 - - - -
346B TYR* 5.6 0.4 - - - -
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Residues in contact with ILE 331 (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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310B ASP* 3.4 45.5 - - + +
311B ILE* 3.8 22.7 - - + +
314B SER* 3.6 19.3 - - - +
316B ILE 4.1 0.2 - - - -
317B TRP* 3.7 21.3 - - + -
318B PHE* 4.4 0.2 - - - -
329B LEU* 6.2 1.3 - - + -
330B GLY* 1.3 79.5 - - - +
332B PRO* 1.3 73.4 - - - +
343B PHE* 3.5 5.5 - - - -
344B TYR* 2.9 50.2 + - + +
346B TYR* 4.7 6.5 - - + -
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Residues in contact with PRO 332 (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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314B SER* 3.9 7.0 + - - +
316B ILE* 3.5 46.2 - - + +
318B PHE* 5.1 0.7 - - + -
330B GLY 4.7 0.7 - - - +
331B ILE* 1.3 96.3 - - + +
333B GLY* 1.3 60.0 + - - +
342B ALA 3.5 11.4 - - - +
343B PHE* 3.8 17.5 - - + -
344B TYR* 4.8 1.0 - - - -
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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