Contacts of the helix formed by residues 308 - 317 (chain B) in PDB entry 1L8A
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 GLY 308 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B ASP* 3.4 13.8 + - - -
306B THR 3.4 3.0 - - - -
307B SER* 1.3 79.5 + - - +
309B LYS* 1.3 61.7 + - - +
310B LEU 3.4 2.5 - - - -
311B ILE* 3.7 16.1 + - - +
312B GLN* 3.3 20.1 + - - +
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Residues in contact with LYS 309 (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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305B ASP* 3.1 1.6 + - - +
307B SER* 3.2 11.0 - - - +
308B GLY* 1.3 77.5 - - - +
310B LEU* 1.3 61.1 + - - +
311B ILE 3.2 0.2 - - - -
312B GLN* 3.3 33.5 + - - +
313B LEU* 2.9 27.9 + - - +
341B TYR* 3.5 38.0 - - + -
343B GLU* 3.2 46.4 + - + -
344B THR* 3.5 9.4 - - + -
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B TRP* 4.3 4.7 - - + -
301B LEU* 4.0 25.1 - - + +
302B LEU* 3.8 27.8 - - + -
305B ASP* 2.8 22.1 + - + +
309B LYS* 1.3 73.3 - - - +
311B ILE* 1.3 57.4 + - - +
313B LEU* 3.3 7.6 + - + +
314B MET* 2.8 50.3 + - + +
337B PHE* 4.3 13.0 - - + -
338B PHE* 4.1 22.2 - - + -
344B THR* 3.5 9.7 - - + +
347B LEU* 3.9 21.3 - - + -
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Residues in contact with ILE 311 (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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58B ASN* 3.5 26.2 - - + +
60B ILE* 4.0 36.3 - - + -
302B LEU* 4.0 14.1 - - + +
305B ASP* 4.3 0.9 + - - +
308B GLY* 3.7 15.6 + - - +
309B LYS 3.2 0.4 - - - -
310B LEU* 1.3 74.9 - - - +
312B GLN* 1.3 54.9 + - - +
314B MET* 3.1 7.5 + - + +
315B ASN* 2.7 60.4 + - - +
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Residues in contact with GLN 312 (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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308B GLY 3.3 11.9 + - - +
309B LYS* 3.3 30.7 + - - +
311B ILE* 1.3 77.1 - - - +
313B LEU* 1.3 58.0 + - - +
315B ASN* 3.2 10.8 + - + +
316B GLU* 2.8 38.4 + - - +
341B TYR* 2.7 40.0 + - - -
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Residues in contact with LEU 313 (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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309B LYS 2.9 17.5 + - - +
310B LEU* 3.5 6.3 - - + +
312B GLN* 1.3 76.4 - - - +
314B MET* 1.3 59.6 + - - +
316B GLU* 3.3 18.2 - - + +
317B THR* 2.6 41.4 + - - +
337B PHE* 3.1 62.4 - - + +
338B PHE* 4.2 2.9 - - - +
340B LYS* 3.6 24.7 - - + -
341B TYR* 3.9 6.4 - - + -
344B THR* 4.2 19.1 - - + +
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Residues in contact with MET 314 (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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59B TYR* 3.4 19.9 - - + +
60B ILE* 3.9 13.9 - - - -
273B LYS* 3.1 13.7 + - - -
294B TRP* 3.3 39.3 - - + +
298B TRP* 3.3 40.4 - - + -
302B LEU* 4.1 13.2 - - + -
310B LEU* 2.8 28.9 + - + +
311B ILE* 3.5 5.2 - - - +
313B LEU* 1.3 77.7 - - - +
315B ASN* 1.3 62.3 + - - +
317B THR 3.7 0.9 + - - -
322B TYR* 2.6 29.8 + - - +
337B PHE* 4.1 11.4 - - + -
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Residues in contact with ASN 315 (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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56B ILE* 6.5 0.9 - - - -
58B ASN* 2.9 29.3 - - - +
59B TYR* 2.6 38.0 + - - +
273B LYS* 3.1 28.7 - - - +
276B ASN* 5.0 3.1 + - - +
311B ILE* 2.7 34.8 + - - +
312B GLN* 3.5 7.9 - - - +
314B MET* 1.3 75.1 - - - +
316B GLU* 1.3 59.0 + - - +
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Residues in contact with GLU 316 (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 LYS* 5.1 1.1 - - - +
312B GLN* 2.8 37.5 + - + +
313B LEU* 3.3 16.8 - - + +
315B ASN* 1.3 72.2 - - - +
317B THR* 1.3 69.7 + - - +
318B VAL* 3.4 11.3 + - - +
340B LYS* 5.1 4.0 - - - +
341B TYR* 2.6 41.1 + - - -
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Residues in contact with THR 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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273B LYS* 2.8 29.6 + - - +
313B LEU* 2.6 31.9 + - - +
315B ASN 3.4 0.4 - - - -
316B GLU* 1.3 78.6 - - - +
318B VAL* 1.3 68.7 + - - +
321B ASP* 3.8 21.3 - - + +
322B TYR* 3.3 33.7 - - + -
325B PHE* 4.2 12.1 - - + -
337B PHE* 3.7 10.6 - - - -
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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