Contacts of the helix formed by residues 316 - 328 (chain B) in PDB entry 4O8M
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 ASN 316 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B SER 5.4 5.7 + - - -
314B SER 3.4 0.8 + - - -
315B PRO* 1.3 84.3 + - - +
317B LEU* 1.3 64.9 + - - +
318B TYR 3.3 2.4 + - - -
319B LYS* 3.4 15.5 + - + +
320B ASN* 2.9 24.9 + - + +
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Residues in contact with LEU 317 (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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101B ASP* 3.6 45.8 - - - +
104B VAL* 3.6 27.4 - - + -
125B TRP* 4.2 15.3 - - + +
313B TRP* 3.6 25.3 - - + -
314B SER* 3.2 19.2 + - - +
315B PRO 3.2 4.1 - - - -
316B ASN* 1.3 77.2 - - - +
318B TYR* 1.3 57.4 + - - +
320B ASN* 3.2 12.5 + - - +
321B VAL* 2.9 43.7 + - + +
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Residues in contact with TYR 318 (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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104B VAL* 3.9 12.3 - - + +
107B ALA* 3.6 27.6 - - + -
108B PRO 2.7 28.3 + - - -
109B TYR* 3.2 8.5 + - - +
110B ILE* 3.2 28.1 - - + +
302B VAL* 5.6 0.2 - - - +
306B ILE* 3.5 60.6 + - + +
307B SER* 5.6 0.7 - - - -
313B TRP* 4.5 4.1 - + + -
316B ASN 3.4 0.4 - - - -
317B LEU* 1.3 77.2 - - - +
319B LYS* 1.3 65.3 + - + +
321B VAL* 3.3 0.7 + - - -
322B GLN* 2.8 60.5 + - + +
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Residues in contact with LYS 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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307B SER* 5.8 8.5 - - - -
316B ASN* 3.4 17.1 + - + +
318B TYR* 1.3 82.3 - - + +
320B ASN* 1.3 62.5 + - - +
322B GLN* 3.3 21.9 + - - +
323B GLU* 2.9 22.5 + - - +
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Residues in contact with ASN 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B TRP* 4.7 4.6 - - - +
315B PRO 5.5 0.9 + - - +
316B ASN* 2.9 21.5 + - + +
317B LEU* 3.5 20.3 - - - +
319B LYS* 1.3 75.3 - - - +
321B VAL* 1.3 57.6 + - - +
323B GLU* 3.0 14.1 + - - +
324B LYS* 3.0 53.7 + - - +
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Residues in contact with VAL 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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104B VAL* 3.7 14.1 - - + +
105B ILE* 5.7 0.7 - - - -
110B ILE* 3.8 19.1 - - + -
120B LEU* 3.7 30.3 - - + -
125B TRP* 3.7 33.9 - - + +
317B LEU* 2.9 26.2 + - + +
318B TYR 4.0 2.5 - - - +
320B ASN* 1.3 74.4 - - - +
322B GLN* 1.3 61.4 + - - +
324B LYS* 3.2 11.7 + - + +
325B LEU* 2.8 33.8 + - + +
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Residues in contact with GLN 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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109B TYR 5.1 2.8 + - - -
110B ILE* 3.9 23.3 + - + +
318B TYR* 2.8 41.1 + - + +
319B LYS* 3.3 30.2 + - - +
321B VAL* 1.3 78.2 - - - +
323B GLU* 1.3 61.6 + - - +
325B LEU* 3.2 11.0 + - - +
326B SER* 3.1 23.1 + - - -
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Residues in contact with GLU 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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319B LYS 2.9 13.5 + - - +
320B ASN* 3.0 17.0 + - - +
322B GLN* 1.3 73.5 - - - +
324B LYS* 1.3 78.9 + - - +
326B SER* 2.9 25.5 + - - +
327B GLN* 3.4 22.1 + - - +
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Residues in contact with LYS 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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120B LEU* 4.0 24.9 - - + -
123B SER* 5.3 2.5 - - - +
125B TRP* 3.8 41.1 - - + +
320B ASN* 3.0 39.8 + - - +
321B VAL* 3.5 11.0 - - - +
323B GLU* 1.3 85.6 + - - +
325B LEU* 1.3 64.4 + - - +
326B SER 3.1 1.2 + - - -
327B GLN* 3.1 19.4 + - - +
328B PHE* 3.6 17.2 - - + -
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Residues in contact with LEU 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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110B ILE* 4.1 19.3 - - + +
111B SER* 3.8 27.6 - - - +
116B LYS* 3.4 59.5 - - + +
117B LYS* 3.8 11.2 - - + +
120B LEU* 3.8 20.6 - - + -
321B VAL* 2.8 39.1 + - + +
322B GLN* 3.2 6.3 + - - +
324B LYS* 1.3 75.5 - - - +
326B SER* 1.3 60.2 + - - +
328B PHE* 3.3 15.0 + - + +
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Residues in contact with SER 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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116B LYS* 5.3 6.1 + - - +
322B GLN 3.1 11.4 + - - -
323B GLU* 2.9 18.6 + - - +
324B LYS 3.1 1.0 - - - -
325B LEU* 1.3 73.5 - - - +
327B GLN* 1.3 75.3 + - - +
328B PHE 3.0 14.2 + - - -
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Residues in contact with GLN 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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323B GLU* 3.7 28.4 + - - +
324B LYS* 3.1 11.0 + - - +
326B SER* 1.3 99.8 + - - +
328B PHE* 1.3 66.3 + - + +
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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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116B LYS* 3.5 41.7 - - + +
119B LYS* 3.7 48.3 - - + +
120B LEU* 3.5 27.6 - - + -
123B SER* 5.2 6.5 - - - -
324B LYS* 3.6 19.5 - - + -
325B LEU* 3.3 27.1 + - - +
326B SER 3.0 9.8 - - - -
327B GLN* 1.3 87.9 - - + +
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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