Contacts of the helix formed by residues 347 - 355 (chain B) in PDB entry 6S1M
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 347 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297B GLY* 3.6 8.7 + - - -
298B GLU* 3.4 54.1 - - + +
306B LEU* 3.7 18.8 - - + +
308B GLN* 3.9 4.0 + - - +
330B ASN* 2.6 37.3 + - - +
344B THR* 4.4 2.3 + - - -
345B SER* 4.4 4.0 - - - +
346B GLY* 1.3 75.4 - - - +
348B ASN* 1.3 66.4 + - - +
349B VAL 3.5 0.4 - - - -
350B SER* 4.3 2.6 - - - +
351B ASP* 3.3 21.0 + - - +
382B LEU* 3.8 17.6 - - + +
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Residues in contact with ASN 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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306B LEU* 5.7 2.2 - - + +
344B THR* 3.5 27.2 + - - +
346B GLY* 4.3 0.3 - - - -
347B GLN* 1.3 75.3 + - - +
349B VAL* 1.3 87.4 + - - +
351B ASP* 3.2 5.1 + - - +
352B ILE* 3.0 36.2 + - + +
365B LEU* 5.9 0.6 - - - +
368B THR* 4.8 2.3 - - - +
374B ILE* 3.1 41.2 + - - +
375B SER* 3.6 26.9 - - - +
377B THR* 5.0 0.5 + - - -
382B LEU* 4.4 2.4 - - + +
402B TYR* 4.3 7.9 + - - -
404B CYS* 4.8 0.2 - - - -
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Residues in contact with VAL 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B GLY* 5.0 1.1 - - - -
347B GLN 3.5 1.2 - - - +
348B ASN* 1.3 93.8 + - - +
350B SER* 1.3 59.0 + - - +
352B ILE* 3.5 4.2 + - - +
353B PHE* 3.0 25.5 + - - +
361B HIS* 3.4 36.8 - - + +
364B ILE* 4.0 26.4 - - + +
365B LEU* 3.9 24.2 - - + -
368B THR* 5.2 4.5 - - - +
404B CYS* 3.7 28.7 - - - -
407B THR* 5.4 0.2 - - + -
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Residues in contact with SER 350 (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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346B GLY 4.1 17.2 + - - -
347B GLN* 4.2 3.7 + - - -
348B ASN 3.4 0.2 - - - -
349B VAL* 1.3 77.4 - - - +
351B ASP* 1.3 59.6 + - - +
353B PHE* 3.3 12.7 + - - +
354B ARG* 3.0 35.3 + - - +
361B HIS* 5.1 8.6 - - - -
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Residues in contact with ASP 351 (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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347B GLN 3.3 20.2 + - - +
348B ASN* 3.2 7.5 + - - +
350B SER* 1.3 76.8 - - - +
352B ILE* 1.3 65.6 + - - +
354B ARG* 3.2 25.0 + - - +
355B TYR* 3.5 20.1 - - - +
377B THR* 2.6 32.9 + - - +
381B THR* 3.4 23.3 + - - +
382B LEU* 3.5 25.7 - - + +
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Residues in contact with ILE 352 (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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154B VAL* 4.6 9.4 - - + -
348B ASN* 3.0 20.8 + - + +
349B VAL 3.8 4.3 - - - +
351B ASP* 1.3 74.9 - - - +
353B PHE* 1.3 61.5 + - - +
354B ARG 3.3 0.7 + - - -
355B TYR 3.4 2.0 + - - +
356B SER* 3.3 26.1 + - - -
358B MET* 4.2 21.3 - - + -
364B ILE* 3.8 20.6 - - + -
367B TRP* 4.2 16.6 - - + -
368B THR* 3.3 25.8 - - - +
374B ILE 5.2 1.1 - - - +
375B SER* 5.6 0.4 - - - +
376B PRO* 4.2 19.1 - - + -
377B THR* 4.3 20.4 - - + +
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Residues in contact with PHE 353 (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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124B SER 5.7 4.9 - - - -
125B LYS* 2.8 43.1 + - + +
349B VAL 3.0 15.4 + - - +
350B SER* 3.4 17.5 - - - +
351B ASP 3.2 0.4 - - - -
352B ILE* 1.3 77.7 - - - +
354B ARG* 1.3 59.6 + - + +
358B MET 3.6 13.2 - - - -
359B GLU* 3.3 52.5 - - + -
361B HIS* 3.9 21.3 - + + -
364B ILE* 3.9 13.0 - - + +
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Residues in contact with ARG 354 (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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124B SER* 4.0 26.0 + - - +
125B LYS* 3.8 5.0 - - - +
126B TYR* 3.3 55.5 + - + -
127B ILE 4.6 0.7 + - - -
350B SER* 3.0 24.1 + - - +
351B ASP* 3.5 16.2 - - - +
352B ILE 3.2 0.8 - - - -
353B PHE* 1.3 82.7 - - + +
355B TYR* 1.3 83.2 + - + +
356B SER 3.5 2.8 + - - +
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Residues in contact with TYR 355 (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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99B LYS* 4.1 12.1 + - - +
101B MET* 3.9 28.2 - - + +
104B GLN* 4.8 10.3 - - + +
105B PRO* 4.9 9.7 - - + +
126B TYR* 3.9 38.9 - + + -
127B ILE* 4.0 9.4 - - - -
153B LEU 4.4 0.2 - - - +
154B VAL* 3.3 23.5 - - + +
155B THR* 6.4 1.8 - - + -
351B ASP* 3.5 22.0 - - - +
352B ILE 3.4 4.8 + - - +
354B ARG* 1.3 93.7 + - + +
356B SER* 1.3 58.5 + - - +
377B THR* 5.8 4.3 - - + -
381B THR* 3.6 46.7 + - + +
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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