Contacts of the helix formed by residues 335 - 346 (chain A) in PDB entry 5LK5
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 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.6 39.2 - - + +
92A VAL* 4.0 3.6 - - - -
333A THR* 3.5 12.0 + - - +
334A ASN* 1.3 82.3 - - - +
336A GLU* 1.3 57.8 + - - +
337A ALA* 3.0 22.8 + - - +
338A TYR* 3.1 15.7 + - + +
339A ALA* 3.0 23.9 + - - +
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Residues in contact with GLU 336 (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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90A THR* 4.2 12.7 + - + +
92A VAL* 4.0 8.2 - - + +
175A ILE* 3.7 34.6 - - + +
177A ARG* 2.7 47.0 + - - +
183A GLU* 4.4 1.6 - - - +
185A LYS* 5.5 6.0 + - - +
334A ASN 4.2 0.6 + - - -
335A ASP* 1.3 70.4 + - - +
337A ALA* 1.3 66.6 + - - +
339A ALA* 3.3 4.7 + - - +
340A GLU* 3.0 23.0 + - - +
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Residues in contact with ALA 337 (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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335A ASP* 3.0 10.5 + - - +
336A GLU* 1.3 79.2 - - - +
338A TYR* 1.3 64.2 + - - +
340A GLU* 3.2 9.6 + - - +
341A GLU* 3.0 34.4 + - - +
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Residues in contact with TYR 338 (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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19A PRO* 4.2 17.9 - - + -
21A VAL* 4.0 23.6 - - + +
24A LYS* 2.6 27.1 + - - -
331A LEU* 4.1 21.8 - - + -
333A THR* 4.0 16.4 - - - -
335A ASP* 3.1 27.1 + - + +
336A GLU 3.3 0.2 - - - -
337A ALA* 1.3 80.4 - - - +
339A ALA* 1.3 56.9 - - - +
341A GLU* 3.1 27.3 + - + +
342A PHE* 2.9 38.4 + - + +
345A GLU* 5.2 5.6 + - - -
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Residues in contact with ALA 339 (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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92A VAL* 3.6 31.4 - - + -
94A GLN* 2.9 34.1 + - - +
173A THR* 4.8 2.5 - - + -
175A ILE* 6.1 0.7 - - + -
331A LEU* 3.8 15.0 - - + -
333A THR* 4.2 4.7 - - + +
335A ASP 3.0 11.7 + - - +
336A GLU 3.5 9.2 - - - +
337A ALA 3.3 0.2 - - - -
338A TYR* 1.3 76.5 - - - +
340A GLU* 1.3 56.2 + - - +
342A PHE 3.5 0.2 + - - -
343A GLY* 2.9 13.9 + - - -
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Residues in contact with GLU 340 (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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185A LYS* 3.8 20.0 + - - +
188A ASN* 3.1 44.6 + - - +
336A GLU 3.0 13.5 + - - +
337A ALA* 3.2 11.5 + - - +
339A ALA* 1.3 78.5 - - - +
341A GLU* 1.3 61.6 + - + +
343A GLY 3.3 0.2 + - - -
344A ASN* 3.0 30.6 + - - +
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Residues in contact with GLU 341 (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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337A ALA* 3.0 27.9 + - - +
338A TYR* 3.4 29.5 - - + +
340A GLU* 1.3 76.6 - - - +
342A PHE* 1.3 58.8 + - - +
344A ASN* 3.1 8.8 + - - +
345A GLU* 2.9 41.2 + - - +
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Residues in contact with PHE 342 (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* 3.5 35.9 - - + -
26A GLN* 3.6 33.0 - - + -
94A GLN* 4.1 6.5 - - - -
329A ASN* 3.9 16.2 - - + -
330A PHE 4.1 2.9 - - - -
331A LEU* 3.7 40.2 - - + -
338A TYR* 2.9 24.3 + - + +
339A ALA 3.8 3.6 - - - +
341A GLU* 1.3 77.0 - - - +
343A GLY* 1.3 51.6 + - - +
345A GLU* 3.3 16.0 + - + -
346A THR* 2.7 59.7 + - + +
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Residues in contact with GLY 343 (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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94A GLN* 3.6 11.0 - - - +
171A LEU* 3.8 17.7 - - - -
188A ASN* 3.9 5.2 - - - -
339A ALA 2.9 15.7 + - - -
340A GLU 3.7 4.3 - - - -
341A GLU 3.2 0.4 - - - -
342A PHE* 1.3 76.9 - - - +
344A ASN* 1.3 57.6 + - - +
346A THR* 3.6 5.4 - - - -
347A TRP* 3.0 15.6 + - - +
348A GLY 3.0 20.3 + - - -
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Residues in contact with ASN 344 (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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188A ASN* 3.0 22.0 + - - +
340A GLU* 3.0 26.4 + - - +
341A GLU* 3.1 9.2 + - - +
343A GLY* 1.3 77.4 - - - +
345A GLU* 1.3 58.1 + - + +
347A TRP* 4.1 13.3 - - - -
348A GLY* 3.3 26.1 - - - -
349A VAL* 3.5 5.4 + - - +
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Residues in contact with GLU 345 (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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338A TYR* 5.2 5.7 + - - -
341A GLU* 2.9 26.7 + - - +
342A PHE* 3.8 21.7 + - + +
344A ASN* 1.3 76.3 - - + +
346A THR* 1.3 63.7 + - + +
349A VAL* 3.4 22.7 - - + +
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Residues in contact with THR 346 (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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26A GLN* 3.9 6.3 - - - +
171A LEU* 4.8 4.0 - - - +
329A ASN* 3.4 42.8 - - - +
342A PHE* 2.7 49.3 + - + +
343A GLY* 3.3 7.4 + - - -
345A GLU* 1.3 82.1 - - + +
347A TRP* 1.3 73.3 + - - +
348A GLY 3.2 0.4 - - - -
349A VAL* 3.0 5.7 + - - +
350A THR* 3.0 26.9 + - - -
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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