Contacts of the helix formed by residues 345 - 356 (chain B) in PDB entry 5M64
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 SER 345 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335B ARG* 3.8 10.8 - - - +
342B PRO 5.0 1.3 - - - -
343B ASP 2.9 9.2 + - - -
344B GLN* 1.3 73.1 - - - +
346B ASP* 1.3 66.6 + - - +
347B LEU* 3.5 17.2 - - - +
348B GLU* 2.2 35.8 + - - -
349B VAL* 2.9 26.5 + - - +
108M LEU* 4.4 13.7 - - - -
109M ARG 5.4 1.3 - - - -
110M GLY 5.9 1.8 - - - -
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Residues in contact with ASP 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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327B LEU* 3.2 10.4 - - - +
328B GLN* 2.9 61.1 + - - +
331B GLY* 3.9 6.5 - - - -
332B ASP* 4.1 3.2 - - - +
335B ARG* 3.1 22.4 + - - +
345B SER* 1.3 72.5 - - - +
347B LEU* 1.3 64.2 + - - -
349B VAL* 3.7 9.0 - - - -
350B GLY* 2.9 24.3 + - - -
108M LEU* 3.4 15.0 - - - +
109M ARG* 3.9 19.0 + - - +
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Residues in contact with LEU 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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327B LEU* 3.6 17.6 - - + +
328B GLN* 3.4 15.9 - - - +
345B SER* 3.1 14.5 - - - +
346B ASP* 1.3 82.5 + - - +
348B GLU* 1.3 85.7 + - + +
351B GLN* 3.9 9.5 - - - +
108M LEU* 3.7 20.4 - - + -
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Residues in contact with GLU 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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343B ASP 4.9 2.4 - - - +
344B GLN* 4.2 20.0 - - + +
345B SER* 2.2 41.8 + - - +
347B LEU* 1.3 100.2 - - + +
349B VAL* 1.3 60.3 + - - +
350B GLY 3.2 1.1 - - - -
351B GLN* 3.5 3.6 + - - +
352B GLU* 2.9 30.5 + - - +
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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
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331B GLY* 3.7 10.8 - - - +
334B PHE 3.8 14.6 - - - +
335B ARG* 3.7 21.5 - - - +
338B PHE* 5.7 0.7 - - + -
340B ALA* 3.6 31.2 - - + +
344B GLN* 4.1 11.1 + - + +
345B SER 2.9 22.0 + - - +
346B ASP* 3.7 11.7 - - - -
348B GLU* 1.3 73.7 - - - +
350B GLY* 1.3 60.2 + - - +
352B GLU* 4.0 5.8 - - + -
353B VAL* 2.9 44.6 + - + +
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Residues in contact with GLY 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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327B LEU* 3.5 16.6 - - - +
330B LEU* 4.7 3.0 - - - +
331B GLY* 3.8 16.6 - - - -
346B ASP 2.9 21.7 + - - -
349B VAL* 1.3 79.5 - - - +
351B GLN* 1.3 56.0 + - - +
353B VAL* 3.5 5.7 - - - +
354B LEU* 3.0 30.3 + - - +
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Residues in contact with GLN 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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279B ALA 4.4 5.5 + - - -
280B LEU* 3.2 36.3 + - - +
327B LEU* 3.5 17.3 - - + +
347B LEU 3.9 14.4 - - - +
348B GLU* 3.5 3.9 + - - +
350B GLY* 1.3 72.7 - - - +
352B GLU* 1.3 64.6 + - - +
354B LEU* 4.1 4.3 - - - +
355B ASP* 2.9 59.4 + - - +
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Residues in contact with GLU 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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69B GLY* 4.8 3.5 - - - -
338B PHE* 6.1 0.7 - - + -
344B GLN* 5.2 8.7 - - - +
348B GLU 2.9 19.9 + - - +
349B VAL* 3.7 8.7 - - + +
351B GLN* 1.3 78.5 - - - +
353B VAL* 1.3 66.8 + - + +
355B ASP* 3.6 2.0 + - - +
356B ARG* 2.5 70.6 + - - +
364B LYS* 5.9 2.2 + - - -
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Residues in contact with VAL 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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330B LEU* 5.4 4.0 - - + +
331B GLY* 5.8 0.2 - - - -
334B PHE* 4.4 27.6 - - + +
337B VAL* 5.1 1.3 - - + -
338B PHE* 3.5 44.7 - - + -
340B ALA* 5.7 0.2 - - + -
349B VAL* 2.9 40.6 + - + +
350B GLY* 3.5 9.9 - - - +
352B GLU* 1.3 74.9 - - + +
354B LEU* 1.3 64.2 + - + +
356B ARG* 3.5 2.7 + - - +
357B ILE* 3.0 32.9 + - + +
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Residues in contact with LEU 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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276B ILE* 4.4 18.8 - - + -
279B ALA* 3.5 32.8 - - + +
280B LEU* 3.6 31.2 - - + -
327B LEU* 4.0 11.0 - - + -
330B LEU* 4.2 15.9 - - + -
350B GLY 3.0 20.0 + - - +
351B GLN* 3.8 7.0 - - - +
352B GLU 3.2 0.2 - - - -
353B VAL* 1.3 74.2 - - + +
355B ASP* 1.3 59.3 + - - +
356B ARG 3.0 3.8 - - - -
357B ILE* 2.9 26.5 + - + -
358B VAL* 3.1 35.3 + - + +
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Residues in contact with ASP 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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280B LEU* 3.3 15.8 - - - +
351B GLN* 2.9 46.5 + - - +
352B GLU* 4.3 2.9 - - - +
354B LEU* 1.3 77.9 - - - +
356B ARG* 1.3 58.8 + - + +
358B VAL* 4.6 2.6 - - - +
360B VAL* 3.3 27.4 - - - +
363B GLY 5.7 5.4 - - - +
364B LYS* 5.3 25.7 + - + +
365B ASP 5.9 0.6 + - - -
370B LYS* 3.9 15.5 + - - +
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Residues in contact with ARG 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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67B ASP 4.9 6.0 + - - -
68B ILE* 3.3 31.1 + - - +
69B GLY* 3.5 13.9 - - - +
240B ARG* 3.1 28.4 + - - +
246B GLN* 2.5 30.9 + - - +
338B PHE* 4.9 16.5 - - + -
352B GLU* 2.5 50.3 + - - +
353B VAL* 3.9 7.2 - - - +
354B LEU 3.0 1.2 - - - -
355B ASP* 1.3 79.9 - - + +
357B ILE* 1.3 51.8 + - - +
360B VAL* 4.3 1.8 - - + -
364B LYS* 5.4 15.5 - - - +
414B LYS* 5.8 3.6 - - - +
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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