Contacts of the helix formed by residues 320 - 329 (chain B) in PDB entry 4E1O
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 320 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B GLN* 3.6 17.7 - - - +
269B TRP* 5.1 4.7 - - + -
297B ASP 4.8 0.2 + - - -
318B VAL* 4.3 8.4 - - - +
319B LYS* 1.3 82.2 - - + +
321B LYS* 1.3 62.0 + - - +
322B TYR* 3.2 19.9 + - - +
323B LYS* 3.2 56.9 + - + +
324B LEU* 3.7 3.1 + - - +
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Residues in contact with LYS 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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135B HIS* 5.9 1.1 - - - +
140B SER 5.1 2.4 + - - -
141B GLN* 2.8 43.2 + - - +
142B GLY* 4.4 7.6 - - - +
318B VAL* 4.0 12.4 - - + +
319B LYS 4.0 0.2 - - - -
320B ASP* 1.3 73.5 - - - +
322B TYR* 1.3 67.7 + - + +
324B LEU* 3.2 8.3 + - - +
325B GLN* 3.1 19.6 + - - +
349B TRP* 3.7 45.9 + - + -
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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
----------------------------------------------------------
320B ASP* 3.2 9.8 + - - +
321B LYS* 1.3 83.1 - - + +
323B LYS* 1.3 59.1 + - - +
325B GLN* 3.1 35.5 + - + +
326B GLN* 2.9 61.5 + - + +
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Residues in contact with LYS 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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160B ALA* 4.2 7.6 - - + +
163B LYS* 5.4 0.7 - - - +
164B ASN* 3.8 36.6 + - + +
269B TRP* 3.8 31.8 - - + -
297B ASP* 4.4 14.3 + - - -
320B ASP* 3.2 41.6 + - + +
322B TYR* 1.3 78.7 - - - +
324B LEU* 1.3 59.4 + - - +
326B GLN* 3.5 14.4 + - - +
327B THR* 2.9 24.1 + - - -
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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
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156B ILE* 3.4 29.6 - - + -
160B ALA* 3.9 16.6 - - + -
269B TRP* 5.0 2.9 - - + -
316B PHE* 4.2 11.9 - - + -
318B VAL* 4.0 25.1 - - + -
320B ASP 3.7 3.1 + - - +
321B LYS* 3.2 13.8 + - - +
322B TYR 3.1 0.4 - - - -
323B LYS* 1.3 78.7 - - - +
325B GLN* 1.3 57.0 + - - +
327B THR* 3.0 27.4 + - - -
328B PHE* 3.4 12.4 - - + -
348B HIS 3.7 3.1 - - - +
349B TRP* 3.8 54.1 - - + +
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Residues in contact with GLN 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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321B LYS 3.1 8.1 + - - +
322B TYR* 3.1 35.8 + - + +
324B LEU* 1.3 78.7 - - - +
326B GLN* 1.3 58.3 + - - +
328B PHE 3.2 0.2 + - - -
329B SER* 2.9 47.0 + - - -
348B HIS* 3.5 44.1 + - + +
349B TRP* 6.1 2.0 - - + +
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Residues in contact with GLN 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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163B LYS* 4.1 21.6 + - + +
164B ASN* 4.9 9.7 + - - -
167B LEU* 3.8 25.6 - - + +
322B TYR* 2.9 49.5 + - + +
323B LYS* 3.7 15.5 - - - +
324B LEU 3.2 0.2 - - - -
325B GLN* 1.3 76.3 - - - +
327B THR* 1.3 61.4 + - - +
328B PHE 3.3 0.2 - - - -
329B SER* 4.5 5.9 + - - -
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Residues in contact with THR 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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202A LEU* 4.3 23.2 - - - +
203A ILE* 4.7 4.2 - - + +
159B LEU* 3.7 39.7 - - + +
160B ALA* 3.2 17.9 - - - +
163B LYS* 4.1 18.0 - - + +
323B LYS 2.9 17.2 + - - -
324B LEU 3.0 11.1 + - - -
326B GLN* 1.3 77.5 - - - +
328B PHE* 1.3 76.5 + - + +
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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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199A LYS* 3.5 42.0 + - - +
202A LEU* 4.7 3.8 - - - -
203A ILE* 3.8 25.8 - - + -
156B ILE* 3.7 42.4 - - + -
159B LEU* 4.3 7.2 - - + -
324B LEU* 3.4 19.5 - - + +
325B GLN 3.2 2.1 + - - +
327B THR* 1.3 99.8 - - + +
329B SER* 1.3 66.2 + - - +
330B VAL* 3.3 3.3 + - - +
348B HIS* 3.5 26.5 + - - +
349B TRP 4.1 1.1 - - - -
350B GLN 3.6 30.7 - - - -
351B ILE* 4.2 7.2 - - + -
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Residues in contact with SER 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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198A GLU* 5.1 1.0 - - - +
202A LEU* 3.4 13.0 - - - +
325B GLN* 2.9 35.3 + - - -
326B GLN* 4.5 5.4 + - - -
327B THR 3.9 0.6 - - - -
328B PHE* 1.3 75.7 - - - +
330B VAL* 1.3 73.3 + - - +
331B ASN* 5.5 1.9 - - - +
348B HIS* 3.9 14.2 + - - -
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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