Contacts of the helix formed by residues 365 - 379 (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 ASP 365 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295B GLY* 3.6 10.3 - - - -
296B SER* 2.7 41.7 + - - -
360B ASN* 3.9 11.2 + - - +
361B ARG 4.0 0.6 + - - -
362B GLY 2.9 11.0 + - - +
363B GLY 3.5 0.2 - - - -
364B HIS* 1.3 79.0 - - - +
366B PRO* 1.3 68.3 - - - +
367B LYS* 2.9 25.3 + - - +
368B LYS* 3.0 15.1 + - + -
369B ILE* 2.9 25.6 + - - +
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Residues in contact with PRO 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 3.4 11.9 - - + +
75B LEU* 3.8 27.8 - - + -
78B GLU* 5.1 0.7 - - - +
82B ARG* 4.3 19.1 - - - +
115B THR* 3.9 13.2 - - + -
119B VAL* 3.8 22.2 - - + +
364B HIS 3.4 10.1 - - - +
365B ASP* 1.3 89.2 - - - +
367B LYS* 1.3 56.1 + - + +
369B ILE* 3.7 3.0 - - + +
370B TYR* 2.8 32.1 + - - +
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Residues in contact with LYS 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLN* 4.1 20.0 - - - +
69B PRO 5.5 2.6 - - - +
71B TYR* 4.1 27.8 - - + +
75B LEU* 3.7 29.7 - - + +
296B SER* 4.5 14.7 + - - +
365B ASP* 2.9 13.4 + - - +
366B PRO* 1.3 77.5 - - - +
368B LYS* 1.3 64.6 + - + +
370B TYR* 3.8 1.9 - - - +
371B ALA* 3.2 23.6 + - - +
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Residues in contact with LYS 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASN* 3.5 23.5 - - - +
63B ILE* 5.2 0.8 + - - +
65B VAL* 4.1 4.8 - - - +
68B GLN* 2.8 33.0 + - - +
292B VAL* 3.8 15.9 - - + +
294B TRP 3.5 18.8 - - - +
295B GLY* 3.8 1.1 - - - -
296B SER* 3.7 18.8 + - - +
299B ASP* 2.8 37.3 + - - -
362B GLY 3.8 10.3 - - - +
365B ASP* 3.0 22.8 + - + +
367B LYS* 1.3 73.1 - - - +
369B ILE* 1.3 65.3 + - - +
371B ALA* 3.4 6.4 + - - +
372B ALA* 3.2 21.8 + - - +
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Residues in contact with ILE 369 (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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115B THR* 3.5 36.8 - - + +
116B ILE* 3.8 12.8 - - + +
119B VAL* 3.7 21.3 - - + -
292B VAL* 4.7 6.3 - - + -
362B GLY 4.0 5.8 - - - +
363B GLY* 3.3 31.9 - - - +
365B ASP 2.9 21.1 + - - +
366B PRO* 3.7 4.9 - - + +
368B LYS* 1.3 76.8 - - - +
370B TYR* 1.3 63.0 + - - +
372B ALA* 3.1 6.7 + - - +
373B PHE* 3.1 45.4 + - + -
388B ALA* 6.2 0.7 - - + -
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Residues in contact with TYR 370 (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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69B PRO* 3.7 30.5 - - + -
70B GLU 4.2 4.4 + - - -
71B TYR* 3.6 23.1 - + + -
72B PRO* 3.3 42.8 - - + +
119B VAL* 4.0 8.9 - - + +
123B HIS* 3.9 13.9 - - + -
124B PHE* 3.6 27.6 - + - -
366B PRO 2.8 19.2 + - - +
367B LYS 3.8 3.6 - - - +
369B ILE* 1.3 76.7 - - - +
371B ALA* 1.3 64.9 + - - +
373B PHE 3.3 1.0 + - - -
374B LYS* 2.9 56.8 + - + +
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Residues in contact with ALA 371 (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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63B ILE* 3.3 25.5 - - + +
68B GLN* 3.7 28.7 - - + +
69B PRO* 4.0 15.2 - - + +
367B LYS 3.2 16.6 + - - +
368B LYS* 3.7 7.2 - - - +
369B ILE 3.3 0.2 - - - -
370B TYR* 1.3 79.3 - - - +
372B ALA* 1.3 57.9 + - - +
374B LYS* 3.8 2.1 - - - +
375B LYS* 3.0 24.1 + - - +
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.8 10.2 - - + +
290B ILE* 3.6 21.3 - - + +
292B VAL* 3.5 31.2 - - + -
368B LYS 3.2 3.4 + - - +
369B ILE* 3.1 10.3 + - - +
371B ALA* 1.3 79.4 - - - +
373B PHE* 1.3 58.4 + - + +
375B LYS 3.4 0.7 + - - -
376B ALA* 3.0 28.6 + - - +
386B ILE* 3.9 14.5 - - + +
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Residues in contact with PHE 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 3.9 12.3 - - + -
119B VAL* 5.2 0.2 - - + -
120B CYS* 3.5 29.8 - - - -
124B PHE* 3.5 30.1 - + + -
225B TYR* 3.6 29.8 + + - -
227B PHE* 4.4 1.1 - + - -
254B VAL* 5.0 1.1 - - + -
256B VAL* 3.5 44.0 - - + -
369B ILE* 3.1 44.8 + - + +
372B ALA* 1.3 77.0 - - + +
374B LYS* 1.3 62.6 + - - +
376B ALA* 3.7 3.6 - - + +
377B GLN* 3.0 22.9 + - - +
386B ILE* 3.8 20.6 - - + -
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Residues in contact with LYS 374 (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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69B PRO* 4.5 10.5 - - + -
123B HIS 5.8 1.2 + - - -
124B PHE* 3.5 13.0 - - + -
370B TYR* 2.9 50.3 + - + +
371B ALA* 3.8 5.4 - - - +
373B PHE* 1.3 76.3 - - - +
375B LYS* 1.3 63.6 + - - +
377B GLN* 3.0 46.5 + - - +
378B GLU* 3.3 31.6 + - - +
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Residues in contact with LYS 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B THR* 3.6 26.1 - - - +
63B ILE* 3.9 20.5 - - + +
288B ASN* 4.2 15.8 + - - +
289B VAL 5.0 0.4 + - - -
290B ILE* 3.5 23.4 - - + +
371B ALA 3.0 18.4 + - - +
372B ALA 3.8 3.4 - - - +
374B LYS* 1.3 74.9 - - - +
376B ALA* 1.3 64.8 + - - +
378B GLU* 2.9 26.1 + - + +
379B THR* 3.0 20.0 + - - +
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Residues in contact with ALA 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ASP 5.2 3.1 - - - +
254B VAL* 4.3 18.5 - - + +
290B ILE* 3.9 1.1 - - - +
372B ALA 3.0 17.8 + - - +
373B PHE* 3.7 7.4 - - + +
375B LYS* 1.3 75.4 - - - +
377B GLN* 1.3 62.5 + - - +
379B THR* 3.1 21.8 + - - +
384B THR* 3.6 39.4 + - + -
386B ILE* 4.3 9.2 - - + -
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Residues in contact with GLN 377 (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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123B HIS 5.5 0.5 - - - +
124B PHE* 3.8 21.1 - - + +
223B THR* 5.9 2.7 - - - +
225B TYR* 5.4 3.6 + - - +
373B PHE 3.0 13.3 + - - +
374B LYS* 3.0 51.0 + - - +
375B LYS 3.1 0.2 - - - -
376B ALA* 1.3 78.4 - - - +
378B GLU* 1.3 59.0 + - - +
379B THR 3.9 1.1 + - - +
380B LYS* 4.0 16.3 + - - -
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Residues in contact with GLU 378 (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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374B LYS* 3.3 33.8 - - + +
375B LYS* 2.9 19.8 + - + +
377B GLN* 1.3 84.5 - - + +
379B THR* 1.3 61.3 + - - +
380B LYS* 3.5 16.9 + - - +
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Residues in contact with THR 379 (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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251B ASP* 3.4 19.1 - - - +
288B ASN* 3.3 22.0 + - + +
375B LYS* 3.0 19.7 + - - +
376B ALA 3.1 14.5 + - - +
377B GLN 4.9 0.5 - - - +
378B GLU* 1.3 75.8 - - - +
380B LYS* 1.3 66.7 + - - +
382B LYS* 3.6 32.3 - - + +
384B THR* 3.7 18.2 - - - +
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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