Contacts of the helix formed by residues 335 - 348 (chain A) in PDB entry 1LI5
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 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333A ALA 3.4 1.4 + - - -
334A GLY* 1.3 74.5 - - - +
336A GLU* 1.3 57.8 - - - +
337A ALA 3.2 2.7 - - - -
338A PHE* 2.8 28.1 + - - +
339A GLU* 2.9 12.0 + - - +
362A MET* 5.1 0.7 - - - -
380A MET* 3.1 20.8 - - - +
383A HIS* 3.0 29.1 + - - -
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Residues in contact with GLU 336 (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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332A PRO 5.4 0.2 - - - +
333A ALA* 4.5 3.8 - - - -
334A GLY* 3.1 29.1 + - - +
335A GLY* 1.3 70.7 - - - +
337A ALA* 1.3 63.1 + - - +
339A GLU* 3.3 7.5 + - - +
340A ALA* 3.0 23.2 + - - +
383A HIS* 3.5 17.7 + - - +
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Residues in contact with ALA 337 (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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334A GLY 4.8 1.5 + - - +
335A GLY 3.2 1.0 - - - -
336A GLU* 1.3 77.9 - - - +
338A PHE* 1.3 70.3 + - + +
340A ALA* 3.4 8.6 + - - +
341A ARG* 3.3 26.3 + - - +
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Residues in contact with PHE 338 (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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334A GLY 5.1 0.2 - - - -
335A GLY* 2.8 10.6 + - - +
337A ALA* 1.3 81.6 - - + +
339A GLU* 1.3 64.0 + - - +
341A ARG* 3.1 23.8 + - - +
342A PHE* 2.9 23.0 + - - +
358A VAL* 3.6 12.1 - - + +
361A ASP* 3.7 14.1 - - + -
362A MET* 3.5 61.0 - - + -
365A GLU* 4.0 22.0 - - + -
380A MET* 3.9 28.9 - - + -
387A LEU* 4.2 2.2 - - - -
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Residues in contact with GLU 339 (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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56A PHE* 4.2 9.8 - - + -
335A GLY 2.9 11.5 + - - +
336A GLU* 3.3 9.9 + - - +
338A PHE* 1.3 76.0 - - - +
340A ALA* 1.3 63.3 + - - +
342A PHE* 3.2 1.1 + - - +
343A ILE* 2.9 42.0 + - + +
383A HIS* 2.9 30.4 + - + -
386A LYS* 3.0 23.8 + - - -
387A LEU* 3.7 25.9 - - + +
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Residues in contact with ALA 340 (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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336A GLU 3.0 12.7 + - - +
337A ALA* 3.5 12.6 - - - +
339A GLU* 1.3 77.3 - - - +
341A ARG* 1.3 57.7 + - + +
343A ILE* 3.4 8.4 + - - +
344A GLU* 2.9 26.9 + - - +
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Residues in contact with ARG 341 (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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337A ALA 3.3 13.4 + - - +
338A PHE* 3.1 26.4 + - - +
340A ALA* 1.3 79.0 - - + +
342A PHE* 1.3 65.8 + - - +
344A GLU* 3.1 15.0 + - - +
345A ALA* 2.8 24.8 + - - +
354A GLU* 4.7 1.7 - - - +
357A SER* 5.0 3.6 + - - -
358A VAL* 3.6 32.5 - - + +
361A ASP* 2.8 42.6 + - - +
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Residues in contact with PHE 342 (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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53A TYR* 4.6 1.6 - + - -
56A PHE* 4.3 11.9 - + - -
338A PHE 2.9 12.5 + - - +
339A GLU* 3.5 7.4 - - - +
341A ARG* 1.3 74.4 - - - +
343A ILE* 1.3 61.0 - - + +
345A ALA* 3.1 4.7 + - - +
346A MET* 2.9 50.0 + - + +
355A ALA* 3.8 33.4 - - + +
358A VAL* 4.1 11.1 - - + +
359A LEU* 4.5 8.5 - - + -
387A LEU* 3.3 59.9 - - + -
390A VAL* 3.9 26.0 - - + -
391A LEU* 4.0 18.8 - - + -
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Residues in contact with ILE 343 (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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53A TYR* 3.4 19.8 + - + +
56A PHE* 3.6 31.0 - - + -
57A LEU* 4.2 12.8 - - + -
339A GLU* 2.9 29.9 + - + +
340A ALA* 3.4 11.2 - - - +
342A PHE* 1.3 79.1 - - + +
344A GLU* 1.3 58.4 + - - +
347A ASP* 2.8 51.8 + - - +
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Residues in contact with GLU 344 (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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340A ALA 2.9 15.2 + - - +
341A ARG* 3.1 18.9 + - - +
343A ILE* 1.3 78.0 - - - +
345A ALA* 1.3 64.0 + - - +
347A ASP* 3.7 7.0 - - - +
348A ASP* 3.4 20.7 + - + +
354A GLU* 4.4 10.8 - - - +
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Residues in contact with ALA 345 (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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341A ARG 2.8 11.9 + - - +
342A PHE* 3.5 7.4 - - - +
344A GLU* 1.3 78.0 - - - +
346A MET* 1.3 61.6 + - - +
348A ASP* 3.2 12.1 + - - +
351A ASN* 3.2 23.6 - - - +
354A GLU* 3.5 29.6 - - + +
355A ALA* 3.7 32.1 - - - +
358A VAL* 5.1 1.1 - - + -
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Residues in contact with MET 346 (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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2A LEU* 3.9 4.5 - - - +
49A VAL* 3.6 20.0 - - + -
53A TYR* 3.4 42.4 - - + -
342A PHE* 2.9 43.3 + - + +
345A ALA* 1.3 73.0 - - - +
347A ASP* 1.3 58.5 + - - +
348A ASP 3.1 0.2 - - - -
350A PHE* 3.1 31.0 + - + -
351A ASN 4.1 3.1 - - - +
352A THR* 4.1 17.9 - - + -
355A ALA* 3.7 24.0 - - + -
390A VAL* 5.0 0.9 - - + -
391A LEU* 3.6 27.4 - - + -
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Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.4 25.4 + - - +
2A LEU* 3.3 28.2 + - - +
3A LYS* 2.7 31.7 + - - +
53A TYR* 2.9 17.8 + - - -
57A LEU* 4.2 5.9 - - - +
343A ILE* 2.8 33.7 + - - +
344A GLU* 3.7 8.3 - - - +
345A ALA 3.2 0.2 - - - -
346A MET* 1.3 77.2 - - - +
348A ASP* 1.3 57.8 + - - +
349A ASP 3.2 2.7 + - - -
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Residues in contact with ASP 348 (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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3A LYS* 4.5 3.7 - - - +
12A LYS* 2.5 38.5 + - - +
297A HIS* 4.7 1.2 - - - -
344A GLU* 3.4 9.8 + - + +
345A ALA* 3.2 10.7 + - - +
346A MET 3.1 1.0 - - - -
347A ASP* 1.3 75.5 - - - +
349A ASP* 1.3 68.6 + - - +
350A PHE 3.3 1.2 + - - -
351A ASN* 3.4 29.2 + - + +
354A GLU* 4.8 3.9 - - - +
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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