Contacts of the helix formed by residues 356 - 361 (chain B) in PDB entry 4LT6
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 356 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LYS* 4.9 18.0 + - - +
44B ALA* 5.3 2.9 - - - +
350B ILE* 3.7 7.9 - - - +
355B SER* 1.3 79.3 + - - +
357B TRP* 1.3 77.5 + - - +
358B SER* 3.5 24.4 + - - +
359B LYS* 2.8 21.4 + - + +
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Residues in contact with TRP 357 (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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37B TYR* 2.9 23.5 + + - +
40B LYS* 3.4 32.9 - - + +
41B LEU* 3.4 30.5 - - + +
44B ALA* 3.8 18.8 - - + -
265B SER* 3.7 42.4 - - - -
268B VAL* 4.2 13.2 - - + -
347B THR* 4.3 9.9 - - + -
350B ILE* 3.5 45.8 - - + +
351B LEU* 4.4 10.1 - - + -
356B ASP* 1.3 77.3 + - - +
358B SER* 1.3 63.7 + - - +
360B LEU* 2.8 49.4 + - + +
361B LEU* 3.8 6.1 + - + +
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Residues in contact with SER 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA* 4.3 8.5 - - - +
356B ASP* 3.1 22.0 + - - +
357B TRP* 1.3 78.7 - - - +
359B LYS* 1.3 63.9 + - - +
361B LEU* 3.2 26.5 + - - +
362B GLU* 3.6 10.2 + - - +
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Residues in contact with LYS 359 (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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346B VAL* 4.0 25.5 - - + +
349B GLU* 3.4 26.7 + - - +
355B SER* 3.2 21.9 + - - +
356B ASP* 2.8 15.6 + - + +
358B SER* 1.3 82.3 + - - +
360B LEU* 1.3 63.8 + - - +
361B LEU 3.0 1.4 + - - -
362B GLU* 3.2 44.0 + - - +
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Residues in contact with LEU 360 (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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41B LEU* 5.9 2.7 - - + -
225B ALA* 5.8 3.4 - - + +
229B TRP* 3.3 40.3 - - + +
233B ARG* 3.9 13.1 + - - +
268B VAL* 4.2 12.3 - - + -
272B PHE* 4.1 14.1 - - + -
343B GLY* 4.4 10.1 - - - +
346B VAL* 3.7 16.9 - - + +
347B THR* 3.9 26.7 - - + -
350B ILE* 4.7 1.8 - - + -
357B TRP* 2.8 33.2 + - + +
359B LYS* 1.3 78.0 - - - +
361B LEU* 1.3 72.0 + - + +
362B GLU 3.6 1.0 + - - +
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Residues in contact with LEU 361 (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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41B LEU* 5.8 3.4 - - + -
44B ALA* 4.3 17.5 - - + +
45B MET* 4.9 4.0 - - + -
48B PHE* 3.9 25.0 - - + -
225B ALA 5.3 1.1 - - - +
228B LEU* 3.5 34.5 - - + -
229B TRP* 4.3 20.2 - - + -
232B ARG* 2.4 46.9 + - + +
357B TRP* 4.1 13.5 - - + +
358B SER* 3.6 14.6 - - - +
359B LYS 3.0 1.0 - - - -
360B LEU* 1.3 96.3 - - + +
362B GLU* 1.3 52.9 + - - +
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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