Contacts of the helix formed by residues 321 - 331 (chain B) in PDB entry 4U7Y
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 PHE 321 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 4.3 12.6 - - + -
45A VAL* 3.6 47.3 - - + -
46A LYS* 4.9 11.9 - - + -
55A LYS* 3.8 16.2 - - + -
58A ILE* 4.9 1.1 - - + -
59A ARG* 3.4 51.1 - - + -
62A CYS* 5.6 0.9 - - + -
320B ASP* 1.3 87.3 + - - +
322B ASP* 1.3 61.2 + - - +
323B ASP 3.4 2.2 - - - -
324B LEU* 3.5 23.6 + - + +
325B SER* 3.0 30.4 + - - +
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Residues in contact with ASP 322 (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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320B ASP* 3.1 23.5 + - - +
321B PHE* 1.3 76.3 + - - +
323B ASP* 1.3 56.0 + - - +
325B SER* 3.1 7.1 + - - -
326B ARG* 2.7 38.2 + - - +
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Residues in contact with ASP 323 (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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321B PHE 3.4 0.6 - - - -
322B ASP* 1.3 76.5 - - - +
324B LEU* 1.3 62.5 + - + +
326B ARG* 3.3 27.6 + - - +
327B ARG* 2.9 38.0 + - - +
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.0 13.5 - - + -
59A ARG* 3.9 23.3 - - + +
62A CYS* 4.0 15.7 - - + -
63A THR* 3.8 29.2 - - + +
66A LEU* 3.6 20.5 - - + +
321B PHE* 3.5 35.1 + - + +
322B ASP 3.3 0.4 - - - -
323B ASP* 1.3 77.7 - - + +
325B SER* 1.3 61.4 + - - +
327B ARG* 4.4 14.1 - - - +
328B PHE* 2.8 31.7 + - - +
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Residues in contact with SER 325 (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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42A LEU* 4.0 17.0 - - - +
46A LYS* 3.2 29.6 + - - +
321B PHE 3.0 19.9 + - - -
322B ASP* 3.1 8.9 + - - -
324B LEU* 1.3 75.7 - - - +
326B ARG* 1.3 64.1 + - - +
328B PHE* 3.4 2.4 + - - +
329B GLU* 3.0 31.8 + - - +
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Residues in contact with ARG 326 (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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322B ASP 2.7 19.7 + - - +
323B ASP* 3.5 31.5 + - - +
325B SER* 1.3 75.5 - - - +
327B ARG* 1.3 88.9 - - - +
329B GLU* 3.4 5.3 + - - +
330B GLU* 3.2 24.0 + - - +
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Residues in contact with ARG 327 (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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63A THR* 4.4 8.9 + - - +
66A LEU* 3.7 16.5 - - + +
67A ASP* 2.9 38.0 + - - +
70A GLU* 2.8 44.2 + - - +
323B ASP* 2.9 24.3 + - - +
324B LEU* 3.9 19.2 - - - +
326B ARG* 1.3 100.7 - - - +
328B PHE* 1.3 63.5 + - - +
330B GLU* 3.5 8.2 + - - +
331B LEU* 3.1 22.5 + - - +
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Residues in contact with PHE 328 (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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35A GLN* 3.2 40.6 - - + -
36A HIS* 6.1 0.4 - + - -
38A VAL* 3.7 20.4 - - + -
39A GLN* 3.4 35.7 - - + -
42A LEU* 3.8 24.2 - - + -
66A LEU* 3.9 8.6 - - + +
324B LEU 2.8 21.0 + - - +
325B SER* 3.8 4.5 - - - +
326B ARG 3.3 0.2 - - - -
327B ARG* 1.3 74.5 - - - +
329B GLU* 1.3 70.9 + - + +
331B LEU* 3.1 18.1 + - + +
332B LYS* 3.6 32.6 - - + +
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Residues in contact with GLU 329 (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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325B SER* 3.0 20.6 + - - +
326B ARG* 3.8 5.8 - - - +
327B ARG 3.4 0.2 - - - -
328B PHE* 1.3 83.5 - - + +
330B GLU* 1.3 63.9 + - - +
332B LYS* 3.1 33.1 + - - +
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Residues in contact with GLU 330 (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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70A GLU* 5.9 0.7 - - - +
326B ARG* 3.2 15.7 + - - +
327B ARG* 3.8 8.5 - - - +
329B GLU* 1.3 73.2 - - - +
331B LEU* 1.3 53.6 + - - +
332B LYS* 2.7 23.7 + - - +
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Residues in contact with LEU 331 (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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31A LEU* 4.5 7.6 - - + -
35A GLN* 3.1 59.6 - - + +
66A LEU* 4.1 17.0 - - + -
69A ALA* 3.8 26.5 - - + +
70A GLU* 3.6 33.7 - - + +
73A LYS* 5.2 5.8 - - + -
327B ARG 3.1 13.2 + - - +
328B PHE* 3.1 13.6 + - + +
330B GLU* 1.3 74.0 - - - +
332B LYS* 1.3 60.6 + - - +
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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