Contacts of the helix formed by residues 352 - 359 (chain B) in PDB entry 4V1M
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 ALA 352 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B LEU* 3.3 39.7 - - + +
334B ILE* 3.5 28.9 - - + -
335B GLY 4.2 1.8 - - - +
348B ARG 2.8 26.1 + - - -
349B ILE 2.8 13.1 + - - -
351B TYR* 2.9 29.6 - - - +
353B LYS* 1.4 66.6 + - - +
355B ILE* 2.9 19.0 + - - +
356B LEU* 3.3 12.5 + - + +
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Residues in contact with LYS 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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327B ARG* 5.7 5.2 - - - +
331B LEU* 4.0 26.1 - - + +
349B ILE* 3.5 13.9 + - - +
350B GLN* 3.4 20.2 - - + +
352B ALA* 1.4 75.9 - - - +
354B ASP* 1.3 64.3 + - - +
356B LEU* 3.4 5.8 + - - +
357B GLN* 3.2 26.3 + - - +
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Residues in contact with ASP 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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350B GLN* 3.0 43.5 + - - +
351B TYR* 3.2 12.9 + - + -
352B ALA 3.1 0.2 + - - -
353B LYS* 1.3 77.3 - - - +
355B ILE* 1.4 52.6 + - - +
357B GLN* 3.1 10.8 + - - +
358B LYS* 2.7 52.9 + - + +
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Residues in contact with ILE 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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273B LEU* 4.7 13.5 - - + -
274B PRO 3.3 28.3 - - - +
275B TYR* 3.5 16.2 - - + -
276B ILE* 3.5 34.5 - - + -
334B ILE* 5.4 0.9 - - + -
351B TYR* 3.2 42.7 + - + +
352B ALA* 2.9 14.5 + - - +
354B ASP* 1.4 69.7 - - + +
356B LEU* 1.3 59.8 + - + +
359B GLU* 2.8 20.5 + - + +
360B PHE 2.7 31.2 + - - +
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Residues in contact with LEU 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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273B LEU* 4.4 20.9 - - + -
285B ILE* 4.7 9.9 - - + -
288B ALA* 3.9 23.6 - - + +
289B LEU* 4.9 11.6 - - + +
331B LEU* 3.8 28.0 - - + -
334B ILE* 4.7 8.5 - - + -
352B ALA* 3.3 11.3 + - + +
353B LYS* 3.8 7.4 - - - +
355B ILE* 1.3 78.8 - - + +
357B GLN* 1.3 56.6 + - - +
360B PHE* 3.4 41.5 - - + +
374B LYS* 2.9 21.5 + - - +
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Residues in contact with GLN 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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353B LYS* 3.2 18.5 + - - +
354B ASP* 3.1 12.0 + - - +
356B LEU* 1.3 77.7 - - - +
358B LYS* 1.3 71.1 + - + +
366B GLN* 2.8 45.1 - - - +
367B LEU* 3.0 22.0 - - - +
368B GLU* 2.8 44.4 + - + +
374B LYS* 3.3 17.4 + - - +
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Residues in contact with LYS 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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250B PHE* 4.8 5.9 - - + -
354B ASP* 2.7 32.0 + - + +
357B GLN* 1.3 88.4 - - + +
359B GLU* 1.3 67.1 + - + +
360B PHE 3.9 0.7 - - - -
362B PRO* 4.0 4.1 - - - +
366B GLN* 2.8 41.1 + - + +
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Residues in contact with GLU 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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250B PHE* 3.2 40.1 - - + -
252B SER* 3.4 27.0 + - - -
274B PRO* 3.1 38.0 - - + +
275B TYR* 3.2 46.7 + - + -
354B ASP 4.1 0.2 + - - -
355B ILE* 2.8 21.7 + - + +
358B LYS* 1.3 78.4 - - + +
360B PHE* 1.4 56.4 + - - +
361B LEU 3.7 0.3 + - - -
362B PRO* 3.3 17.6 - - - +
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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