Contacts of the strand formed by residues 343 - 349 (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 PHE 343 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A PRO* 5.4 5.8 - - + -
12B ILE* 4.1 17.9 - - + +
15B ILE 4.2 21.3 - - - -
16B GLN* 5.7 0.2 - - + -
17B PRO* 4.2 17.3 - - + -
316B ILE* 5.2 3.4 - - + -
318B PHE* 3.3 35.9 - + - -
331B ILE 3.5 13.9 - - - +
332B PRO* 3.8 21.3 - - + -
333B GLY 4.9 0.2 - - - +
341B GLU* 3.3 15.9 + - - +
342B ALA* 1.3 93.2 - - + +
344B TYR* 1.3 64.4 + - - +
345B PHE* 3.6 24.8 + + + -
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Residues in contact with TYR 344 (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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5B MET* 4.8 16.2 - - + -
310B ASP* 6.1 4.5 - - + -
330B GLY* 3.3 1.7 - - - -
331B ILE* 2.9 53.1 + - + +
332B PRO 4.8 1.1 - - - -
333B GLY* 4.0 26.2 - - - -
340B SER* 3.2 25.0 + - - -
341B GLU* 3.7 26.3 + - + -
343B PHE* 1.3 77.2 - - - +
345B PHE* 1.3 62.0 + - - +
346B TYR* 4.0 16.7 - - + +
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Residues in contact with PHE 345 (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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5B MET* 3.8 4.8 - - - +
6B VAL* 2.9 38.0 + - + +
8B VAL* 3.7 20.2 - - + -
12B ILE* 3.9 19.1 - - + -
15B ILE* 3.4 46.2 - - + -
318B PHE* 3.8 20.6 - + - -
328B PHE* 3.4 30.3 - + + -
329B LEU 3.1 17.7 - - - +
330B GLY* 3.5 7.6 - - - -
343B PHE* 3.6 28.9 - + + -
344B TYR* 1.3 72.5 - - - +
346B TYR* 1.3 69.0 + - - +
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Residues in contact with TYR 346 (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* 3.5 34.5 - - + -
4B GLN 3.1 9.4 - - - +
5B MET* 3.3 46.3 - - + +
6B VAL* 4.0 1.1 - - - -
308B THR* 3.8 15.2 + - + +
310B ASP* 3.7 21.7 + - - +
311B ILE* 3.5 32.1 - - + +
328B PHE* 3.5 6.2 - - - -
329B LEU* 2.8 43.6 + - + +
330B GLY* 5.6 0.2 - - - -
331B ILE* 4.7 6.7 - - + -
344B TYR* 4.0 26.4 - - + +
345B PHE* 1.3 78.6 - - - +
347B THR* 1.3 64.8 + - - +
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Residues in contact with THR 347 (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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2B SER 3.4 5.4 - - - +
3B LEU* 4.4 2.0 - - - -
4B GLN* 2.8 46.4 + - - +
6B VAL* 3.5 21.3 - - + +
50B ILE* 3.6 26.9 - - + +
53B ASN* 5.2 1.6 + - - -
322B MET* 4.4 7.6 - - - -
326B THR* 5.7 2.5 - - - -
327B ILE 3.2 9.2 - - - +
328B PHE* 4.0 8.3 - - + -
346B TYR* 1.3 75.6 - - - +
348B LEU* 1.3 60.7 + - - +
349B ARG* 4.0 15.2 + - - +
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Residues in contact with LEU 348 (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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1B MET* 3.8 27.1 - - + -
2B SER 3.7 13.5 - - - +
3B LEU* 4.3 16.2 - - + +
274B VAL* 4.1 31.4 - - + -
305B PRO* 4.2 17.7 - - + -
307B TRP* 4.0 24.9 - - + -
325B GLY 4.0 0.9 - - - +
326B THR* 3.3 3.3 - - - -
327B ILE* 2.9 43.6 + - + +
329B LEU* 4.7 8.5 - - + +
346B TYR 4.2 0.4 - - - -
347B THR* 1.3 71.7 - - - +
349B ARG* 1.3 63.0 + - - +
350B CYS* 4.5 5.5 - - - -
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Residues in contact with ARG 349 (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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1B MET* 3.0 30.4 - - - +
2B SER* 3.2 28.5 + - - +
4B GLN* 5.5 6.9 - - - +
53B ASN* 4.5 14.5 + - - -
326B THR* 3.6 25.0 - - + +
347B THR* 4.7 16.0 + - - +
348B LEU* 1.3 74.1 - - - +
350B CYS* 1.3 63.5 + - - +
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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