Contacts of the helix formed by residues 388 - 396 (chain A) in PDB entry 1LWT
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 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A ILE* 3.5 23.3 + - - +
387A GLY* 1.3 82.8 - - - +
389A ASP* 1.3 64.0 + - - -
391A LEU* 2.9 12.5 + - - +
392A LEU* 3.2 9.4 + - - -
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Residues in contact with ASP 389 (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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387A GLY 3.2 1.0 + - - -
388A GLY* 1.3 68.9 - - - -
390A VAL* 1.3 55.2 + - + +
392A LEU* 2.6 38.7 + - - +
393A ASN* 2.6 17.7 + - - +
408A PRO* 3.5 18.9 - - + +
409A ALA* 5.0 5.6 + - - +
412A PHE* 3.2 35.5 - - + +
413A ALA 5.7 1.1 - - - +
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Residues in contact with VAL 390 (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* 5.0 1.4 - - - +
357A LEU* 3.9 9.3 - - + +
358A GLY* 4.7 1.8 - - - +
359A LEU* 3.5 32.3 - - + +
387A GLY 3.7 6.5 - - - +
388A GLY 3.1 1.4 + - - -
389A ASP* 1.3 74.7 - - + +
391A LEU* 1.3 61.6 + - - +
393A ASN* 3.8 4.7 + - - +
394A VAL* 3.6 19.6 + - - +
412A PHE* 3.6 23.9 - - + -
413A ALA 4.5 7.9 - - - +
414A ARG* 3.7 33.5 + - + +
417A ARG* 3.8 20.0 - - - +
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Residues in contact with LEU 391 (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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319A LEU* 5.4 0.4 - - + -
323A ILE* 4.9 6.7 - - + -
335A ILE* 3.5 34.8 - - + +
336A LYS* 3.7 9.6 - - - -
337A ALA* 4.0 20.0 - - + +
359A LEU* 3.3 25.4 - - + -
385A MSE 4.4 4.3 - - + -
386A SER* 3.6 20.6 - - - +
387A GLY 4.0 4.0 - - - +
388A GLY 2.9 10.0 + - - +
390A VAL* 1.3 77.0 - - - +
392A LEU* 1.3 67.0 + - - +
394A VAL* 2.9 21.8 + - + +
395A LEU* 3.0 33.9 + - + +
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Residues in contact with LEU 392 (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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331A ASP* 5.9 1.1 - - - +
335A ILE* 3.8 20.8 - - + +
388A GLY* 3.2 4.5 + - - +
389A ASP* 2.6 33.0 + - - +
391A LEU* 1.3 69.7 - - - +
393A ASN* 1.3 54.7 + - - +
394A VAL 2.7 5.8 + - - -
395A LEU* 2.6 42.2 + - + +
396A SER* 2.7 13.6 + - - -
405A ARG* 3.7 23.7 - - + +
406A PRO 3.7 14.6 - - - +
408A PRO* 3.5 15.3 - - + -
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Residues in contact with ASN 393 (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* 3.0 29.7 + - - +
389A ASP 2.6 14.2 + - - +
390A VAL 3.9 4.5 - - - +
392A LEU* 1.3 72.0 - - - +
394A VAL* 1.3 58.2 + - - +
396A SER* 2.5 18.8 + - - -
397A LYS* 3.3 20.5 + - - +
407A ALA* 4.1 8.7 - - - +
408A PRO* 3.2 24.4 - - + +
412A PHE* 3.4 37.9 - - + -
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Residues in contact with VAL 394 (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* 4.0 22.4 - - + +
319A LEU* 4.1 11.0 - - + -
320A ALA* 3.9 26.2 - - - +
323A ILE* 4.0 19.7 - - + -
357A LEU* 4.2 23.6 - - + -
359A LEU* 4.8 1.8 - - + -
390A VAL 3.6 14.6 - - - +
391A LEU* 2.9 13.6 + - + +
392A LEU 2.7 1.8 + - - -
393A ASN* 1.3 77.0 - - - +
395A LEU* 1.3 55.9 + - + +
397A LYS* 2.7 38.1 + - - +
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Residues in contact with LEU 395 (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 ILE* 4.9 7.0 - - + -
329A VAL* 3.9 28.0 - - + -
335A ILE* 3.6 15.7 - - + -
337A ALA* 5.1 0.7 - - + -
391A LEU* 3.0 43.3 - - + +
392A LEU* 2.6 25.1 + - + +
394A VAL* 1.3 68.7 - - + +
396A SER* 1.3 51.1 + - - +
397A LYS 2.7 6.6 + - - -
398A CYS* 2.6 45.3 + - - +
403A LYS 3.6 19.5 - - - +
404A PHE* 3.9 0.7 - - - -
405A ARG* 3.5 23.5 + - + +
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Residues in contact with SER 396 (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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392A LEU 2.7 11.2 + - - -
393A ASN* 2.5 30.1 + - - -
395A LEU* 1.3 70.2 - - - +
397A LYS* 1.3 63.3 + - - +
398A CYS 3.2 3.8 + - - +
404A PHE* 3.7 15.5 - - - -
405A ARG 2.7 22.0 + - - -
407A ALA* 3.3 36.8 - - - +
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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