Contacts of the helix formed by residues 318 - 327 (chain B) in PDB entry 4U7B
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 318 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B ALA 3.3 11.8 - - - +
317B LYS* 1.3 77.0 - - - +
319B ASP* 1.3 66.8 + - - +
320B GLU* 4.1 18.5 - - + +
321B PHE* 3.1 21.9 + - + +
322B TYR* 3.5 6.3 - - - -
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Residues in contact with ASP 319 (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 GLN 3.6 7.4 - - - +
200B SER* 3.1 28.3 - - - +
201B GLY* 4.7 2.4 - - - -
317B LYS 3.9 1.3 + - - +
318B ASP* 1.3 71.9 - - - +
320B GLU* 1.3 63.9 + - - +
322B TYR* 3.1 20.8 + - - +
323B TRP* 3.1 8.9 + - - -
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Residues in contact with GLU 320 (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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318B ASP* 3.1 13.5 - - + +
319B ASP* 1.3 76.3 - - - +
321B PHE* 1.3 63.6 + - - +
323B TRP* 3.3 17.9 - - + +
324B ARG* 2.8 68.4 + - - +
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Residues in contact with PHE 321 (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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286B HIS* 2.8 74.4 + + - -
287B LEU* 4.4 10.3 - - + -
290B SER* 3.8 5.2 - - - -
317B LYS* 3.2 52.5 - - + -
318B ASP* 3.1 19.6 + - + +
320B GLU* 1.3 88.4 - - - +
322B TYR* 1.3 81.1 + + - +
324B ARG* 3.2 17.5 + - - +
325B GLY 3.2 7.1 + - - -
4C G 4.1 4.9 - - - -
5C G 3.8 12.1 - - - -
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Residues in contact with TYR 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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197B TRP* 3.4 34.3 - + + -
198B ASP 3.7 16.4 - - - +
199B GLN* 3.8 3.6 - - - +
201B GLY* 3.9 20.2 - - - -
202B VAL* 4.4 17.0 - - + +
286B HIS* 4.3 1.1 - - - -
287B LEU* 4.2 20.9 - - + -
313B TRP* 5.1 0.3 - - - -
314B PHE* 3.1 39.0 + + - +
317B LYS* 3.5 32.0 - - + +
318B ASP 3.5 13.5 - - - -
319B ASP* 3.1 10.5 + - - +
321B PHE* 1.3 86.0 - + - +
323B TRP* 1.3 66.9 + - - +
325B GLY 3.1 2.1 + - - -
326B ILE* 3.1 20.1 + - - +
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Residues in contact with TRP 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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199B GLN* 3.1 54.4 + - + +
319B ASP 3.1 1.8 + - - -
320B GLU* 3.3 25.8 - - + +
322B TYR* 1.3 74.4 - - - +
324B ARG* 1.3 77.5 + - + +
326B ILE* 3.2 3.1 + - - +
327B HIS* 3.0 77.0 + + + -
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Residues in contact with ARG 324 (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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286B HIS* 4.2 1.3 - - - -
320B GLU* 2.8 46.9 + - - +
321B PHE* 3.4 27.9 - - - +
323B TRP* 1.3 89.0 - - + +
325B GLY* 1.3 64.6 + - - +
327B HIS* 3.2 3.0 + - - -
328B LYS* 3.1 41.6 + - + +
4C G 3.5 37.4 + - - -
5C G 4.9 4.4 + - - -
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Residues in contact with GLY 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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197B TRP* 4.4 6.1 - - - -
282B PRO* 4.4 1.2 - - - +
285B TYR* 2.9 27.9 + - - -
286B HIS* 3.2 38.4 - - - -
321B PHE 3.2 4.8 + - - -
322B TYR 3.1 5.6 + - - -
324B ARG* 1.3 79.7 - - - +
326B ILE* 1.3 59.1 + - - +
328B LYS* 3.6 6.6 + - - +
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Residues in contact with ILE 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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149B LEU* 3.9 26.3 - - + +
152B ILE* 3.5 33.9 - - + -
154B THR* 4.3 7.4 - - + -
197B TRP* 3.6 30.3 - - + -
198B ASP* 4.6 2.2 - - - -
199B GLN* 3.8 25.8 - - + +
282B PRO* 4.2 13.5 - - + -
322B TYR 3.1 14.3 + - - +
323B TRP 3.7 5.6 - - - +
325B GLY* 1.3 71.5 - - - +
327B HIS* 1.3 59.8 + - + +
328B LYS 3.1 4.0 - - - -
329B LEU* 3.1 37.5 + - + +
330B PRO* 4.2 0.5 - - - +
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Residues in contact with HIS 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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143B TYR* 5.2 4.2 + - - -
147B SER* 4.9 6.3 - - - -
149B LEU* 3.9 26.5 - - + +
150B HIS* 5.3 1.1 - - + -
199B GLN* 3.1 26.8 + - + -
323B TRP* 3.0 80.4 + + + +
324B ARG* 3.2 4.0 + - - +
326B ILE* 1.3 76.3 - - + +
328B LYS* 1.3 58.2 + - - +
329B LEU 3.3 0.9 - - - -
330B PRO* 3.3 18.0 - - - +
331B GLU* 4.5 4.9 + - - +
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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