Contacts of the helix formed by residues 342 - 352 (chain B) in PDB entry 1L5G
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 GLN 342 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LYS* 3.7 43.4 - - + +
138B LEU* 5.9 1.8 - - + -
141B GLN* 2.7 48.6 + - + +
339B ASN* 4.0 17.5 + - - +
340B VAL* 2.7 11.7 + - - -
341B LEU* 1.3 95.9 + - - +
343B LEU* 1.3 66.9 + - - +
344B ILE* 3.0 8.5 - - + +
345B VAL* 2.9 18.8 + - + +
346B ASP* 3.1 8.7 - - - +
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Residues in contact with LEU 343 (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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307B ILE* 5.4 2.5 - - + -
309B ALA* 4.5 15.0 - - + -
331B GLY* 4.0 22.4 - - - +
332B VAL* 2.9 33.9 - - + +
333B LEU* 4.5 4.7 - - + -
339B ASN* 4.0 21.5 - - - +
340B VAL* 3.2 22.4 - - + +
341B LEU* 4.3 7.0 - - + +
342B GLN* 1.3 73.4 - - - +
344B ILE* 1.3 59.7 + - + +
346B ASP* 2.7 16.4 + - - +
347B ALA* 2.4 41.0 + - + +
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Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE* 3.3 34.8 - - + -
116B TYR* 4.2 9.4 - - - +
138B LEU* 3.7 22.9 - - + -
142B MET* 4.2 8.3 - - - -
245B LEU* 4.2 13.0 - - + +
247B VAL* 3.4 41.5 - - + -
307B ILE* 5.0 5.2 - - + -
339B ASN* 5.2 1.6 - - - +
342B GLN* 4.4 6.1 - - + -
343B LEU* 1.3 88.9 - - + +
345B VAL* 1.3 55.0 + - + +
347B ALA* 4.0 5.6 - - - -
348B TYR* 2.6 39.0 + - - +
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Residues in contact with VAL 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 5.3 0.4 - - - +
141B GLN* 3.0 59.0 - - + +
142B MET* 3.2 21.3 - - + -
145B LEU* 5.2 11.3 - - + +
342B GLN* 2.9 13.8 + - + +
344B ILE* 1.3 76.3 - - + +
346B ASP* 1.3 65.8 + - - +
348B TYR* 3.8 2.4 - - - +
349B GLY* 2.9 26.5 + - - -
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Residues in contact with ASP 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLN* 4.6 1.9 + - - -
341B LEU* 3.7 17.7 - - - +
342B GLN 3.1 15.3 - - - +
343B LEU* 2.7 11.1 + - - +
345B VAL* 1.3 82.4 - - - +
347B ALA* 1.3 57.4 + - - +
349B GLY* 3.9 2.5 - - - +
350B LYS* 3.0 31.2 + - - +
674B SER* 5.6 5.9 + - - +
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Residues in contact with ALA 347 (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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307B ILE* 3.7 33.2 - - + -
329B THR* 4.4 8.7 - - - +
330B VAL 6.6 0.2 - - - -
331B GLY* 6.4 0.9 - - - -
343B LEU* 2.4 24.5 + - + +
344B ILE* 3.5 4.9 - - - +
346B ASP* 1.3 71.2 - - - +
348B TYR* 1.3 56.5 + - - +
349B GLY 3.0 1.1 - - - -
350B LYS* 2.8 10.7 + - - +
351B ILE* 2.5 40.5 + - - +
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Residues in contact with TYR 348 (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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110B TYR* 4.3 8.4 + - - +
112B VAL* 3.8 15.5 - - + +
142B MET* 4.0 14.4 - - + -
145B LEU* 3.5 36.1 - - + -
243B SER* 2.9 37.3 + - - -
245B LEU* 3.8 33.1 - - + +
307B ILE* 5.3 0.2 - - - +
344B ILE 2.6 21.3 + - - +
345B VAL 3.8 2.2 - - - +
347B ALA* 1.3 71.8 - - - +
349B GLY* 1.3 63.7 + - - +
351B ILE* 3.7 9.6 - - + +
352B ARG* 3.0 57.3 + - + +
391B ILE* 3.8 11.4 - - + -
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Residues in contact with GLY 349 (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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145B LEU* 5.4 4.0 - - - -
345B VAL 2.9 16.6 + - - -
346B ASP* 4.0 2.0 - - - -
348B TYR* 1.3 83.2 - - - +
350B LYS* 1.3 62.8 + - - +
352B ARG* 3.1 12.2 + - - +
353B SER* 3.1 11.9 + - - -
391B ILE* 5.4 7.4 - - - +
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Residues in contact with LYS 350 (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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329B THR* 3.8 29.4 - - + -
330B VAL 5.2 8.0 + - - -
346B ASP* 3.0 17.6 + - - +
347B ALA* 2.8 15.9 + - - +
349B GLY* 1.3 70.4 - - - +
351B ILE* 1.3 63.8 + - - +
353B SER* 2.5 30.3 + - - +
354B LYS* 4.5 1.7 + - - +
674B SER* 4.2 28.7 + - - -
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Residues in contact with ILE 351 (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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245B LEU* 5.0 3.1 - - + -
305B ASN* 3.2 45.8 - - + +
306B LEU 4.6 1.1 - - - +
307B ILE* 4.1 13.7 - - + -
327B GLY 3.5 22.7 - - - +
329B THR* 3.1 28.0 + - + +
347B ALA 2.5 27.2 + - - +
348B TYR* 3.7 10.3 - - + +
350B LYS* 1.3 72.5 - - - +
352B ARG* 1.3 64.8 + - + +
353B SER 3.4 2.4 + - - -
354B LYS* 4.1 25.5 + - - +
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Residues in contact with ARG 352 (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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82B GLN* 3.9 2.8 + - - -
106B GLN* 2.6 70.6 + - - +
107B VAL 3.1 23.0 + - - -
110B TYR* 4.2 7.6 - - - +
243B SER* 4.4 2.7 - - - +
305B ASN* 6.1 0.2 - - - +
348B TYR* 3.0 51.8 + - + +
349B GLY 3.1 8.6 + - - +
351B ILE* 1.3 79.4 - - + +
353B SER* 1.3 57.5 + - - +
354B LYS 3.4 2.7 - - - +
389B LEU 3.9 8.1 - - - +
391B ILE* 3.2 47.1 + - + +
421B PHE* 3.1 31.0 - - - -
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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