Contacts of the helix formed by residues 355 - 367 (chain B) in PDB entry 6FY5
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 ASP 355 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313B PRO* 6.1 0.3 - - - +
323B LYS* 2.8 27.4 + - - -
354B PHE* 1.3 82.0 + - + +
356B SER* 1.4 62.9 + - - +
357B GLU* 3.4 6.3 + - - +
358B SER* 2.7 35.2 + - - -
359B ILE* 3.1 25.4 + - - +
1002B EDO 4.0 4.7 + - - -
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Residues in contact with SER 356 (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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354B PHE 4.1 1.0 + - - -
355B ASP* 1.4 69.7 - - - +
357B GLU* 1.3 61.1 + - - +
359B ILE* 3.2 12.1 + - - +
360B GLY* 2.9 26.5 + - - -
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Residues in contact with GLU 357 (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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323B LYS* 2.8 30.2 + - - +
355B ASP* 3.4 7.0 + - - +
356B SER* 1.3 76.3 - - - +
358B SER* 1.4 58.5 + - - +
360B GLY* 3.2 2.5 + - - -
361B ILE* 2.9 48.1 + - + +
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Residues in contact with SER 358 (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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323B LYS* 3.3 19.6 - - - +
353B LEU* 4.0 10.8 - - - -
354B PHE 5.4 0.4 - - - -
355B ASP* 2.7 37.6 + - - -
356B SER 3.3 0.2 - - - -
357B GLU* 1.4 73.9 - - - +
359B ILE* 1.4 62.6 + - - +
361B ILE* 3.2 4.7 + - - +
362B TYR* 3.0 33.3 + - - -
1002B EDO 2.8 31.0 + - - -
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Residues in contact with ILE 359 (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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186B LEU* 3.7 30.7 - - + -
199B LEU* 4.5 2.6 - - + +
201B GLN* 3.4 26.0 - - - +
353B LEU* 3.8 28.3 - - + +
354B PHE 4.2 4.5 - - - +
355B ASP 3.1 22.5 + - - +
356B SER* 3.2 12.1 + - - +
358B SER* 1.4 76.6 - - - +
360B GLY* 1.3 57.1 + - - +
362B TYR* 3.4 1.4 + - - +
363B VAL* 2.9 46.8 + - + +
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Residues in contact with GLY 360 (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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356B SER 2.9 14.4 + - - -
357B GLU* 3.7 3.1 - - - -
359B ILE* 1.3 77.4 - - - +
361B ILE* 1.3 55.9 + - - +
363B VAL* 3.3 7.1 + - - +
364B GLN* 2.9 40.1 + - - +
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Residues in contact with ILE 361 (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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323B LYS* 3.6 28.0 - - + +
324B GLN* 3.6 39.7 - - + +
327B ALA* 3.8 15.3 - - + -
357B GLU* 2.9 44.1 + - + +
358B SER* 3.7 4.3 - - - +
360B GLY* 1.3 76.0 - - - +
362B TYR* 1.3 57.6 + - + +
364B GLN* 3.4 14.3 + - - +
365B GLU* 2.9 29.4 + - + +
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Residues in contact with TYR 362 (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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199B LEU* 3.9 19.5 - - + -
314B PHE* 4.7 0.9 - - - -
323B LYS* 4.6 3.8 - - + -
326B ALA* 4.0 4.7 + - - +
327B ALA* 3.6 43.5 + - + -
330B THR* 4.8 4.4 + - - -
331B LEU* 4.1 14.3 - - + +
351B PHE* 4.5 11.7 - + - -
353B LEU* 3.7 28.7 - - + -
358B SER* 3.0 29.3 + - - +
359B ILE 4.0 1.1 - - - +
361B ILE* 1.3 74.1 - - + +
363B VAL* 1.4 54.8 + - - +
365B GLU* 3.2 4.6 + - - +
366B MET* 2.8 39.0 + - - +
1001B EDO 3.1 23.3 + - - -
1002B EDO 2.7 40.5 + - - -
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Residues in contact with VAL 363 (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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186B LEU* 6.2 0.4 - - + -
187B SER* 4.4 15.7 - - - +
199B LEU* 3.4 23.6 - - + -
359B ILE* 2.9 32.6 + - + +
360B GLY* 3.7 7.2 - - - +
362B TYR* 1.4 73.4 - - - +
364B GLN* 1.4 65.7 + - + +
366B MET* 3.4 4.6 + - - +
367B ALA* 3.1 24.6 + - + +
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Residues in contact with GLN 364 (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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360B GLY* 2.9 28.2 + - - +
361B ILE* 3.6 14.6 - - - +
363B VAL* 1.4 79.4 - - + +
365B GLU* 1.3 65.9 + - + +
367B ALA* 3.6 15.6 + - - +
368B LYS* 3.8 17.2 - - - +
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Residues in contact with GLU 365 (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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324B GLN* 2.8 38.6 + - - +
327B ALA* 4.0 20.4 - - + -
328B GLN* 4.0 19.4 - - - +
331B LEU* 3.6 22.2 - - + +
361B ILE* 2.9 22.5 + - + +
362B TYR 3.2 0.6 + - - +
364B GLN* 1.3 75.5 - - - +
366B MET* 1.3 66.2 + - - +
368B LYS* 3.2 49.9 + - - +
369B LEU* 4.2 6.2 + - - +
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Residues in contact with MET 366 (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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187B SER* 5.1 3.1 - - - +
188B SER* 4.3 5.2 - - - +
189B LYS* 3.6 44.0 - - + +
197B LEU* 3.7 32.1 - - + +
199B LEU* 3.5 44.9 - - + -
331B LEU* 3.7 25.4 - - + -
362B TYR 2.8 18.0 + - - +
363B VAL* 3.9 4.3 - - - +
365B GLU* 1.3 72.9 - - - +
367B ALA* 1.4 57.6 + - - +
368B LYS 3.1 5.3 + - - -
369B LEU* 3.2 30.5 + - + +
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Residues in contact with ALA 367 (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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342A SER 5.0 7.0 - - - +
343A ALA* 5.8 2.0 - - - +
189B LYS* 4.8 11.4 + - - +
363B VAL* 3.1 17.0 + - + +
364B GLN* 3.7 11.7 - - - +
365B GLU 3.3 0.6 - - - -
366B MET* 1.4 74.5 - - - +
368B LYS* 1.4 59.3 + - + +
369B LEU 3.5 3.4 - - - +
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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