Contacts of the helix formed by residues 366 - 378 (chain B) in PDB entry 1T4L
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 LEU 366 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A A 5.2 12.6 - - - +
16A G 5.7 0.4 - - - +
364B GLY* 3.1 10.0 - - - +
365B SER* 1.3 79.7 - - - +
367B ASP* 1.3 74.9 + - - +
368B MET* 3.4 35.2 - - + +
369B ASN* 3.2 32.9 + - - +
370B ALA* 3.1 13.9 + - - +
425B ILE* 4.6 0.9 - - - -
429B GLU* 2.8 13.8 + - - +
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Residues in contact with ASP 367 (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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14A C 3.3 23.1 + - - -
365B SER 4.2 1.4 - - - +
366B LEU* 1.3 75.9 - - - +
368B MET* 1.3 62.1 + - - +
370B ALA* 2.4 30.1 + - - -
371B LYS* 2.9 36.6 + - + -
425B ILE* 3.8 38.3 - - + +
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Residues in contact with MET 368 (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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14A C 4.6 9.4 - - - +
15A A 2.8 61.9 - - - +
16A G 3.7 9.4 - - - +
17A A 4.5 9.2 - - + +
18A A 4.0 15.0 - - + +
366B LEU* 3.4 22.0 - - + +
367B ASP* 1.3 82.0 + - - +
369B ASN* 1.3 107.5 + - - +
371B LYS* 3.7 3.3 - - - +
372B ARG* 3.1 42.0 + - - +
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Residues in contact with ASN 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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17A A 4.3 14.9 + - - +
364B GLY* 5.4 6.1 - - - -
366B LEU* 3.2 35.5 + - + +
367B ASP 2.8 3.6 + - - -
368B MET* 1.3 103.2 - - - +
370B ALA* 1.3 65.4 + - - +
372B ARG* 3.3 5.2 - - - +
373B GLN* 2.9 21.0 + - - +
429B GLU* 5.9 1.1 - - - +
432B LEU* 4.7 5.6 - - + -
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Residues in contact with ALA 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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366B LEU 3.1 7.6 + - - +
367B ASP* 2.4 22.6 + - - +
369B ASN* 1.3 71.0 - - - +
371B LYS* 1.3 70.2 + - + +
373B GLN* 2.6 20.1 + - - +
374B LEU* 3.1 9.1 + - - +
425B ILE 4.5 0.9 - - - +
428B ALA* 3.3 26.5 - - + -
429B GLU* 3.7 20.4 - - + +
432B LEU* 3.4 17.8 - - + +
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Residues in contact with LYS 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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14A C 4.2 6.1 + - - -
20A A 2.8 62.8 + - - +
21A A 3.0 32.5 + - - +
367B ASP* 2.9 51.5 + - + +
368B MET* 3.7 3.6 - - - +
370B ALA* 1.3 75.5 - - + +
372B ARG* 1.3 87.6 + - - +
374B LEU* 3.1 28.3 - - + +
375B TYR* 3.2 6.9 + - - +
428B ALA* 4.3 5.3 - - + +
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Residues in contact with ARG 372 (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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17A A 5.3 9.2 - - + +
18A A 2.7 65.9 + - + +
19A G 2.8 60.5 + - - +
20A A 3.6 0.6 + - - -
368B MET* 3.1 33.0 + - - +
369B ASN* 3.3 7.0 - - - +
370B ALA 2.6 4.6 + - - -
371B LYS* 1.3 89.3 + - - +
373B GLN* 1.3 64.4 + - - +
374B LEU 2.6 4.4 + - - -
376B SER* 2.4 46.9 + - - +
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Residues in contact with GLN 373 (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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369B ASN 2.9 11.3 + - - +
370B ALA 2.6 12.8 + - - +
372B ARG* 1.3 72.9 - - - +
374B LEU* 1.3 63.4 + - - +
376B SER* 3.4 4.9 + - - -
377B LEU* 2.8 46.8 - - + +
378B ILE* 3.2 4.7 + - - +
432B LEU* 3.2 38.2 - - + +
438B LEU* 3.1 41.6 - - + +
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Residues in contact with LEU 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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20A A 6.1 1.6 - - - -
370B ALA 3.3 9.0 - - - +
371B LYS* 3.1 13.7 - - + +
372B ARG 2.6 4.6 + - - -
373B GLN* 1.3 77.3 - - - +
375B TYR* 1.3 68.1 + - + +
376B SER 3.1 5.3 + - - -
378B ILE* 3.1 2.3 + - - +
379B GLY* 2.4 34.0 + - - -
385B LEU* 4.9 11.7 - - + -
387B TYR* 2.9 35.4 - - + +
428B ALA* 3.8 13.7 - - + +
431B ALA* 3.8 16.6 - - + -
432B LEU* 3.1 31.9 - - + +
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Residues in contact with TYR 375 (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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19A G 3.3 37.8 - - - +
20A A 3.1 43.5 - - - -
371B LYS 3.2 4.7 + - - +
372B ARG* 3.5 0.7 - - - -
374B LEU* 1.3 87.6 - - + +
376B SER* 1.3 58.0 + - - +
379B GLY* 4.0 25.8 - - - +
384B ARG 5.6 0.2 - - - -
385B LEU* 3.5 45.4 + - + +
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Residues in contact with SER 376 (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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17A A 6.1 0.3 - - - -
18A A 3.0 32.0 - - - +
372B ARG* 2.4 46.2 + - - +
373B GLN 3.4 0.3 + - - -
374B LEU 3.1 0.8 + - - -
375B TYR* 1.3 72.0 - - - +
377B LEU* 1.3 78.4 + - - +
378B ILE 3.7 0.7 - - - -
379B GLY 5.6 0.4 - - - -
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Residues in contact with LEU 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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17A A 6.1 4.9 - - + -
373B GLN* 2.8 48.2 + - + +
376B SER* 1.3 97.8 + - - +
378B ILE* 1.3 73.4 + - + +
442B ALA* 5.8 2.9 - - - +
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Residues in contact with ILE 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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373B GLN* 3.2 7.2 + - - +
374B LEU* 3.1 6.0 + - - +
377B LEU* 1.3 105.6 - - + +
379B GLY* 1.3 73.0 + - - +
380B TYR* 2.7 22.2 + - + +
383B LEU* 4.4 9.0 - - + -
385B LEU* 5.3 5.4 - - + -
437B MET* 5.4 1.1 - - - -
438B LEU* 3.2 57.7 - - + +
441B TYR* 3.3 41.3 - - + -
442B ALA* 5.0 4.9 - - + +
445B ARG* 4.7 5.6 + - + +
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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