Contacts of the helix formed by residues 442 - 457 (chain A) in PDB entry 1L2L
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 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A GLU* 4.2 8.1 - - - -
295A ASN* 5.7 2.9 - - - -
345A HIS* 3.5 31.1 + - - -
440A GLY 2.3 19.3 + - - +
441A ILE* 1.3 65.3 - - - +
443A ASP* 1.3 56.5 + - - -
445A ILE* 3.4 9.2 + - - +
446A SER* 3.0 29.8 + - - -
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Residues in contact with ASP 443 (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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116A GLN* 2.8 51.7 + - - +
120A MET* 4.3 1.6 - - - -
269A GLU* 3.6 24.8 - - - +
441A ILE* 2.5 32.0 + - + +
442A GLY* 1.3 71.0 - - - +
444A THR* 1.3 64.3 + - - +
446A SER* 4.3 4.5 - - - -
447A SER* 3.0 33.3 + - - +
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Residues in contact with THR 444 (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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119A ILE* 5.8 0.5 - - - +
120A MET* 4.5 1.6 - - - -
123A LEU* 3.9 29.2 - - + +
371A ALA* 4.5 10.0 - - + +
372A ALA 5.2 0.4 - - - +
375A LYS* 3.6 17.2 + - + -
381A ILE* 4.1 23.6 - - + -
440A GLY* 3.0 18.4 + - - -
441A ILE* 3.2 20.1 - - - +
443A ASP* 1.3 78.7 - - - +
445A ILE* 1.3 59.1 + - - +
448A SER* 2.6 38.2 + - - +
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Residues in contact with ILE 445 (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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343A HIS* 3.6 19.1 - - - +
345A HIS* 4.0 24.9 - - + +
350A TYR* 3.4 41.5 - - + +
368A SER* 3.2 18.6 - - - +
372A ALA* 3.9 20.4 - - + -
440A GLY* 3.8 20.4 - - - +
442A GLY* 3.5 10.3 - - - +
443A ASP 3.1 0.4 - - - -
444A THR* 1.3 75.6 - - - +
446A SER* 1.3 66.2 + - - +
449A ALA* 3.1 20.4 + - - +
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Residues in contact with SER 446 (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 HIS* 3.1 28.0 + - - -
269A GLU* 2.7 35.9 + - - +
293A GLY* 4.3 3.1 - - - -
341A ARG* 4.9 0.2 + - - -
343A HIS* 3.8 19.3 - - - -
345A HIS* 4.3 4.5 - - - -
442A GLY 3.0 9.5 + - - -
443A ASP 3.9 2.1 + - - -
445A ILE* 1.3 77.9 - - - +
447A SER* 1.3 59.3 + - - +
449A ALA* 4.2 0.5 - - - +
450A PHE* 3.0 30.0 + - - +
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Residues in contact with SER 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN* 5.0 0.3 + - - -
120A MET* 3.3 34.5 - - - +
124A LEU* 4.6 2.4 - - - +
233A ILE* 3.4 30.4 - - - +
267A HIS* 4.8 2.0 - - - -
443A ASP* 3.0 23.4 + - - +
444A THR 4.4 0.2 - - - -
446A SER* 1.3 76.9 + - - +
448A SER* 1.3 66.4 + - - +
450A PHE* 4.5 1.8 - - - -
451A VAL* 3.1 30.3 + - - +
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Residues in contact with SER 448 (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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22A ILE* 5.1 0.7 - - - +
123A LEU* 4.1 2.9 - - - +
128A TYR* 2.8 38.4 + - - -
367A PHE* 3.9 13.5 - - - -
368A SER* 4.1 11.9 - - - -
371A ALA* 4.3 3.0 - - - +
444A THR* 2.6 29.7 + - - +
445A ILE 3.4 2.9 + - - -
447A SER* 1.3 76.0 - - - +
449A ALA* 1.3 51.5 + - - +
451A VAL* 4.4 1.5 - - - +
452A SER* 2.7 39.6 + - - -
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Residues in contact with ALA 449 (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* 3.7 7.1 + - - +
343A HIS* 3.5 25.4 - - + +
364A ALA* 3.2 18.9 - - + +
365A LEU* 4.4 2.5 - - + -
368A SER* 3.6 12.5 - - - +
445A ILE 3.1 16.5 + - - +
448A SER* 1.3 75.2 - - - +
450A PHE* 1.3 66.3 + - - +
452A SER* 3.5 5.6 - - - -
453A GLU* 2.9 27.2 + - - +
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Residues in contact with PHE 450 (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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231A LEU* 3.8 23.8 - - + -
232A ALA 3.7 11.2 - - - -
233A ILE* 4.2 8.5 - - + -
265A ARG* 3.5 33.0 - - + -
267A HIS* 3.6 35.4 - + + -
290A TYR* 4.7 0.4 - + - -
291A SER* 4.0 11.4 - - - -
341A ARG* 3.7 25.2 - - - +
446A SER 3.0 20.8 + - - +
447A SER* 3.9 2.7 - - - +
449A ALA* 1.3 78.4 - - - +
451A VAL* 1.3 73.8 + - + +
453A GLU* 3.4 3.3 + - - +
454A PHE* 3.0 55.7 - + - -
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Residues in contact with VAL 451 (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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22A ILE* 4.4 5.4 - - + -
25A VAL* 3.6 20.3 - - + +
28A VAL* 4.2 20.0 - - + -
124A LEU* 4.2 19.5 - - + -
130A ILE* 3.3 33.2 - - + -
231A LEU* 4.0 10.4 - - + +
233A ILE* 4.3 4.3 - - + -
447A SER 3.1 17.9 + - - +
448A SER* 4.4 1.6 - - - +
450A PHE* 1.3 88.9 - - + +
452A SER* 1.3 62.2 + - - +
454A PHE* 3.5 2.1 + - - -
455A SER* 3.2 16.3 + - - -
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Residues in contact with SER 452 (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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18A VAL* 3.7 32.1 - - - -
22A ILE* 4.4 6.5 - - - +
364A ALA* 3.3 17.5 - - - +
367A PHE* 3.8 9.0 - - - -
448A SER 2.7 24.3 + - - -
449A ALA* 3.3 5.7 + - - -
451A VAL* 1.3 74.0 - - - +
453A GLU* 1.3 68.3 + - - +
455A SER* 2.6 25.4 + - - -
456A LEU* 3.4 11.7 - - - +
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Residues in contact with GLU 453 (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 30.4 + - - -
356A GLU* 2.6 39.7 - - - +
360A HIS* 4.1 13.0 - - - +
361A VAL* 3.6 23.6 - - - +
364A ALA* 3.4 13.0 - - + +
449A ALA 2.9 19.0 + - - +
450A PHE 3.7 4.0 - - - +
451A VAL 3.3 0.2 - - - -
452A SER* 1.3 79.7 + - - +
454A PHE* 1.3 60.6 + - + +
456A LEU* 3.4 12.3 + - - +
457A HIS* 2.7 38.0 + - + -
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Residues in contact with PHE 454 (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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25A VAL* 4.6 2.5 - - - -
230A GLU* 3.9 14.4 - - - +
231A LEU* 4.1 23.3 - - + -
265A ARG* 3.0 39.3 - - - +
290A TYR* 3.6 29.8 - + - -
341A ARG* 4.1 2.9 - - - -
356A GLU* 3.9 4.0 - - + -
450A PHE* 3.0 56.1 + + - -
451A VAL 3.9 0.4 - - - -
452A SER 3.3 0.4 - - - -
453A GLU* 1.3 92.3 - - - +
455A SER* 1.3 61.8 + - - +
456A LEU 3.1 2.5 - - - -
457A HIS* 3.4 44.0 + + + +
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Residues in contact with SER 455 (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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18A VAL* 5.2 0.9 - - - +
21A SER* 3.4 20.4 + - - +
22A ILE* 3.6 21.6 + - - +
24A LYS* 2.8 37.0 + - - +
25A VAL* 3.6 17.0 - - - +
451A VAL 3.2 13.0 + - - -
452A SER* 2.6 22.8 + - - -
454A PHE* 1.3 78.2 - - - +
456A LEU* 1.3 63.0 + - - +
457A HIS 3.4 0.8 - - - -
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Residues in contact with LEU 456 (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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17A LYS* 4.4 24.5 - - + +
18A VAL* 4.6 8.1 - - + +
21A SER* 3.6 28.7 - - - +
24A LYS* 3.8 7.9 + - - +
360A HIS* 3.5 45.5 - - + +
363A ASP* 3.8 35.4 - - + +
364A ALA 4.8 0.7 - - - +
452A SER 3.4 17.3 - - - +
453A GLU* 3.6 6.3 - - - +
454A PHE 3.1 0.2 - - - -
455A SER* 1.3 80.1 - - - +
457A HIS* 1.3 69.0 + - - +
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Residues in contact with HIS 457 (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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24A LYS* 4.1 8.2 + - - -
265A ARG* 4.7 10.3 - - - +
356A GLU* 4.1 14.9 - - + +
357A LYS 5.6 3.8 + - - -
360A HIS* 4.1 20.7 + - + -
361A VAL* 5.7 1.3 - - + -
453A GLU* 2.7 52.4 + - + -
454A PHE* 3.6 42.7 - + + +
455A SER 3.4 2.8 - - - -
456A LEU* 1.3 86.8 - - - +
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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