Contacts of the helix formed by residues 359 - 366 (chain H) in PDB entry 3LUE
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 LYS 359 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124H PHE* 3.7 47.9 + - + +
125H GLU* 4.7 5.5 - - - +
128H ASN* 3.8 19.4 + - - +
129H THR 3.7 15.5 - - - +
130H PRO* 3.0 21.4 + - + +
358H SER* 1.3 68.9 - - - +
360H GLN* 1.3 66.0 + - + +
362H TYR* 3.0 23.5 + - + +
363H ASP* 3.2 30.8 + - - +
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Residues in contact with GLN 360 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358H SER* 3.2 24.6 + - - +
359H LYS* 1.3 77.8 - - + +
361H GLU* 1.3 65.7 + - + +
363H ASP* 3.2 11.8 + - - +
364H GLU* 2.9 29.0 + - - +
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Residues in contact with GLU 361 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356H TRP 4.3 2.4 - - - +
357H ILE* 4.2 0.4 - - + -
358H SER* 2.9 39.5 + - - +
360H GLN* 1.3 78.3 + - + +
362H TYR* 1.3 57.7 + - - +
364H GLU* 3.2 22.0 + - - +
365H SER* 2.7 39.9 + - - -
369H ILE* 3.6 17.9 - - + +
373H LYS* 3.3 37.4 + - - +
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Residues in contact with TYR 362 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120H THR* 3.7 16.2 - - + -
121H GLN* 3.3 23.3 + - - -
124H PHE* 3.3 47.8 - + + -
125H GLU* 2.8 34.2 + - + -
357H ILE* 4.6 1.1 - - + +
358H SER 2.9 10.1 + - - +
359H LYS* 3.3 19.3 - - - +
361H GLU* 1.3 78.9 - - - +
363H ASP* 1.3 60.2 + - - +
366H GLY* 2.6 62.5 + - - -
367H PRO* 3.4 24.6 - - + +
369H ILE* 4.7 5.2 - - + -
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Residues in contact with ASP 363 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359H LYS* 3.2 34.9 + - - +
360H GLN* 3.2 10.5 + - - +
362H TYR* 1.3 78.4 - - - +
364H GLU* 1.4 71.0 + - - +
365H SER 4.4 0.2 - - - -
366H GLY* 4.3 2.4 + - - -
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Residues in contact with GLU 364 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360H GLN* 2.9 10.5 + - - +
361H GLU* 3.2 27.8 - - - +
363H ASP* 1.4 84.9 - - - +
365H SER* 1.3 73.5 + - - +
369H ILE* 5.0 2.6 - - - +
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Residues in contact with SER 365 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361H GLU 2.7 19.9 + - - -
363H ASP 4.4 1.1 - - - -
364H GLU* 1.3 93.2 + - - +
366H GLY* 1.3 58.1 + - - +
368H SER* 5.3 5.7 - - - -
369H ILE* 3.7 33.6 - - - +
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Residues in contact with GLY 366 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362H TYR* 2.6 39.4 + - - +
363H ASP 4.3 1.7 + - - -
365H SER* 1.3 74.9 - - - +
367H PRO* 1.3 70.9 - - - +
368H SER* 3.5 2.2 - - - -
369H ILE* 3.5 12.3 - - - +
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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