Contacts of the strand formed by residues 355 - 362 (chain D) in PDB entry 3C6M
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 TRP 355 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ALA* 4.0 8.5 - - + -
279D ALA* 6.0 1.8 - - + -
315D GLN* 2.8 36.5 - - + +
317D ASN* 3.4 29.7 + - - +
318D CYS* 3.5 32.1 - - + -
319D VAL* 4.5 0.7 - - - -
344D GLU 3.5 1.0 - - - +
345D ILE* 3.4 1.9 - - - -
346D VAL* 2.7 45.8 + - - +
348D VAL* 4.5 1.8 - - + -
351D TYR* 3.5 31.7 - + + -
353D GLU* 3.6 21.1 - - + +
354D LEU* 1.3 76.8 - - - +
356D VAL* 1.3 81.2 + - - +
357D PHE* 4.0 23.8 - + + -
501D SPM 3.3 34.8 - - + -
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Residues in contact with VAL 356 (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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315D GLN 3.8 0.2 - - - -
316D GLY* 2.7 30.9 + - - -
317D ASN 2.8 17.8 + - - +
319D VAL* 3.6 26.5 - - + -
325D LEU* 4.0 26.2 - - + -
343D LYS* 3.6 36.1 - - + +
344D GLU 3.4 6.7 - - - +
345D ILE* 4.4 8.5 - - + -
355D TRP* 1.3 79.5 - - - +
357D PHE* 1.3 57.5 + - - +
358D TYR* 4.2 16.2 - - + -
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Residues in contact with PHE 357 (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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177D TYR* 3.4 62.6 - + - -
180D ALA* 4.0 12.3 - - + +
181D ILE* 3.7 26.2 - - + -
314D THR 3.5 14.1 - - - +
315D GLN* 4.1 5.8 - - + -
342D SER 3.9 0.2 - - - +
343D LYS* 3.3 5.2 - - - -
344D GLU* 3.0 37.4 + - + +
346D VAL* 3.6 39.5 - - + -
348D VAL* 4.3 2.5 - - + -
355D TRP* 4.0 19.5 - + + -
356D VAL* 1.3 78.0 - - - +
358D TYR* 1.3 65.1 + - - +
359D THR* 5.0 1.2 + - - -
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Residues in contact with TYR 358 (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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312D TYR 4.4 0.4 - - - -
313D PHE* 3.5 7.1 - - - +
314D THR* 2.9 43.1 + - + +
316D GLY* 3.7 28.3 - - - -
325D LEU* 3.2 29.9 + - + +
328D TYR* 3.6 34.9 - + + -
329D GLU* 3.1 24.2 + - + +
332D LEU* 4.6 1.8 - - + -
341D PHE* 3.7 37.5 - + + -
342D SER 3.4 5.2 - - - -
343D LYS* 3.8 19.6 + - + +
356D VAL* 4.2 3.6 - - + -
357D PHE* 1.3 74.5 - - - +
359D THR* 1.3 62.1 + - - +
360D VAL* 4.3 12.1 - - + -
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Residues in contact with THR 359 (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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183D GLY* 5.4 1.2 - - - -
311D LYS* 4.3 16.4 - - + -
312D TYR 3.4 4.5 - - - +
313D PHE* 3.2 37.4 - - + -
341D PHE* 3.1 6.9 - - - +
342D SER* 2.8 49.6 + - - -
357D PHE 5.0 1.4 + - - -
358D TYR* 1.3 73.7 - - - +
360D VAL* 1.3 63.7 + - - +
361D TRP* 3.5 15.3 - - + -
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Residues in contact with VAL 360 (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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299D LEU* 5.4 0.7 - - + -
303D MET* 4.8 7.4 - - + -
306D LEU* 4.5 0.8 - - - +
311D LYS* 3.4 3.8 - - - +
312D TYR* 2.8 66.8 + - + +
328D TYR* 4.7 0.4 - - - +
332D LEU* 4.2 23.8 - - + -
335D LEU* 5.9 0.2 - - + -
339D VAL* 4.0 25.4 - - + -
340D GLU 3.6 10.8 - - - +
341D PHE* 4.1 11.0 - - + -
358D TYR* 4.3 13.5 - - + -
359D THR* 1.3 83.3 - - - +
361D TRP* 1.3 69.5 + - - +
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Residues in contact with TRP 361 (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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303D MET* 5.4 0.4 - - - -
306D LEU* 5.0 4.3 - - - -
308D GLN 5.7 1.1 - - - +
310D GLY 3.7 18.2 - - - +
311D LYS* 4.9 8.3 - - + -
339D VAL* 3.4 7.1 - - - -
340D GLU* 2.8 71.4 + - + +
341D PHE 3.8 17.3 - - - -
342D SER* 3.8 17.9 - - - -
359D THR* 3.5 30.5 - - + -
360D VAL* 1.3 86.1 - - - +
362D LYS* 1.3 72.6 + - - +
363D LYS* 5.2 0.2 - - - -
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Residues in contact with LYS 362 (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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269D GLU* 4.5 4.6 + - - -
303D MET* 3.1 35.8 + - - +
304D LYS 5.0 0.8 + - - -
306D LEU* 2.5 34.4 + - + +
307D LYS 4.0 6.6 + - - +
308D GLN* 3.8 49.9 + - - +
310D GLY 5.1 0.4 + - - -
336D TYR* 3.7 16.1 + - - -
337D CYS* 3.9 22.2 - - + -
338D PRO 3.8 5.4 - - - +
339D VAL* 4.4 2.0 - - - +
361D TRP* 1.3 86.2 - - - +
363D LYS* 1.3 64.9 + - - +
364D ALA* 3.4 1.9 + - - -
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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