Contacts of the helix formed by residues 318 - 327 (chain A) 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 VAL 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A GLY 3.3 18.2 - - - +
271A ASN* 3.7 22.2 - - - +
272A GLY* 3.3 14.8 - - - +
273A LYS* 4.1 6.1 - - + -
316A GLU 3.5 8.3 + - - +
317A THR* 1.3 77.3 - - - +
319A ASP* 1.3 66.0 + - - +
320A GLY* 4.6 0.2 - - - -
321A ASP* 3.2 27.5 + - - +
322A TYR* 3.1 24.2 + - - -
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Residues in contact with ASP 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TYR* 4.0 7.8 + - - -
261A LEU* 3.5 40.3 - - + +
267A PRO* 5.2 2.2 - - + -
269A THR 3.3 18.4 + - - +
270A GLY* 4.2 2.2 - - - -
272A GLY 2.7 18.8 + - - +
273A LYS* 3.3 15.0 - - - +
274A ILE* 2.9 35.8 + - - +
275A ILE 5.2 0.2 + - - -
318A VAL* 1.3 71.6 - - - +
320A GLY* 1.3 58.2 + - - +
322A TYR* 3.3 4.9 + - - +
323A GLN* 2.8 32.0 + - - +
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PRO* 5.4 4.7 - - - -
270A GLY* 2.8 30.5 + - - -
318A VAL* 4.6 0.2 - - - -
319A ASP* 1.3 73.2 - - - +
321A ASP* 1.3 61.5 + - - +
323A GLN* 3.2 9.1 + - - +
324A THR* 3.1 24.7 + - - -
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Residues in contact with ASP 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLU 5.5 0.2 - - - +
317A THR* 3.3 22.6 - - + +
318A VAL* 3.2 27.0 + - - +
320A GLY* 1.3 73.0 - - - +
322A TYR* 1.3 59.3 - - - +
324A THR* 2.8 29.1 + - - -
325A PHE* 3.1 26.5 + - + -
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Residues in contact with TYR 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.5 30.7 - + - -
261A LEU* 4.3 7.0 - - + -
294A TRP* 3.7 22.3 - + - -
314A MET* 2.7 41.0 + - - +
317A THR* 3.2 31.4 - - + -
318A VAL 3.1 20.8 + - - -
319A ASP* 3.6 9.2 - - - +
321A ASP* 1.3 79.7 - - - +
323A GLN* 1.3 61.8 + - - +
325A PHE* 3.4 19.4 + + - +
326A LYS 3.2 15.8 + - - -
337A PHE* 3.8 18.1 - + - -
361A ARG* 3.7 21.8 + - - +
389A HIS* 5.4 3.4 - + - -
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Residues in contact with GLN 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ASN 3.0 0.8 + - - -
261A LEU* 3.0 36.3 + - - +
262A GLN* 2.6 41.2 + - + +
267A PRO* 5.0 7.0 - - + +
319A ASP 2.8 14.0 + - - +
320A GLY* 3.4 10.8 - - - +
321A ASP 3.0 0.2 - - - -
322A TYR* 1.3 78.2 - - - +
324A THR* 1.3 56.6 + - - +
326A LYS* 2.8 41.9 + - + +
327A SER* 3.7 5.0 + - - -
361A ARG* 3.0 13.5 + - - -
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Residues in contact with THR 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A GLY 3.1 12.2 + - - -
321A ASP* 2.8 13.5 + - - -
323A GLN* 1.3 73.4 - - - +
325A PHE* 1.3 68.2 + - + +
326A LYS 2.9 1.3 - - - -
327A SER* 2.9 23.4 + - - +
328A LYS* 3.3 18.2 - - + +
332A TYR* 3.7 31.9 - - + +
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Residues in contact with PHE 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A THR* 3.8 13.5 - - + -
321A ASP* 3.1 34.5 + - + -
322A TYR* 3.4 20.4 - + - +
324A THR* 1.3 80.1 - - + +
326A LYS* 1.3 62.7 + - - +
328A LYS* 3.0 11.3 + - - +
332A TYR* 3.8 19.5 - + - -
333A VAL* 4.3 14.6 - - + -
336A HIS* 3.8 25.8 - - + -
337A PHE* 3.7 41.3 - + + -
357A TRP* 2.9 26.8 - - - -
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Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ASN 3.3 4.6 + - - -
262A GLN* 2.5 31.9 + - - +
322A TYR 3.2 3.2 + - - +
323A GLN* 2.8 33.3 + - + +
325A PHE* 1.3 79.7 - - - +
327A SER* 1.3 54.7 + - - +
357A TRP* 3.5 17.4 - - - -
361A ARG* 2.9 46.1 - - - +
391A ILE* 3.4 31.0 - - + +
392A LYS 3.2 20.3 + - - +
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Residues in contact with SER 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A GLN 3.7 3.7 + - - -
324A THR* 2.9 19.0 + - - +
326A LYS* 1.3 76.6 - - - +
328A LYS* 1.3 78.8 + - - +
357A TRP* 4.8 0.2 - - - -
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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