Contacts of the helix formed by residues 359 - 366 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I PHE* 3.7 46.6 + - + +
125I GLU* 4.7 6.1 - - - +
128I ASN* 3.8 20.0 + - - +
129I THR 3.7 14.8 - - - +
130I PRO* 3.0 20.0 + - + +
358I SER* 1.3 69.4 - - - +
360I GLN* 1.3 65.3 + - + +
362I TYR* 3.0 23.8 + - + +
363I ASP* 3.1 30.9 + - - +
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Residues in contact with GLN 360 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358I SER* 3.2 24.4 + - - +
359I LYS* 1.3 77.7 - - + +
361I GLU* 1.3 65.6 + - + +
363I ASP* 3.2 11.6 + - - +
364I GLU* 2.9 29.3 + - - +
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Residues in contact with GLU 361 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356I TRP 4.3 2.8 - - - +
357I ILE* 4.2 0.4 - - + -
358I SER* 2.9 38.7 + - - +
360I GLN* 1.3 78.2 + - + +
362I TYR* 1.3 57.4 + - - +
364I GLU* 3.2 22.4 + - - +
365I SER* 2.7 40.1 + - - -
369I ILE* 3.6 18.6 - - + +
373I LYS* 3.3 37.3 + - - +
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Residues in contact with TYR 362 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I THR* 3.7 17.3 - - + -
121I GLN* 3.3 23.7 + - - -
124I PHE* 3.3 48.0 - + + -
125I GLU* 2.8 34.3 + - + -
357I ILE* 4.6 1.3 - - + +
358I SER 2.9 9.4 + - - +
359I LYS* 3.3 19.3 - - + +
361I GLU* 1.3 78.0 - - - +
363I ASP* 1.3 58.6 + - - +
366I GLY* 2.6 61.7 + - - -
367I PRO* 3.4 24.0 - - + +
369I ILE* 4.6 4.5 - - + -
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Residues in contact with ASP 363 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359I LYS* 3.1 35.5 + - - +
360I GLN* 3.2 10.1 + - - +
362I TYR* 1.3 78.5 - - - +
364I GLU* 1.4 69.6 - - - +
365I SER 4.4 0.5 - - - -
366I GLY* 4.3 2.3 + - - -
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Residues in contact with GLU 364 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360I GLN* 2.9 10.5 + - - +
361I GLU* 3.2 28.5 - - - +
363I ASP* 1.4 84.7 - - - +
365I SER* 1.3 73.4 + - - +
369I ILE* 5.0 2.3 - - - +
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Residues in contact with SER 365 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361I GLU 2.7 18.6 + - - -
363I ASP 4.4 0.9 - - - -
364I GLU* 1.3 92.8 + - - +
366I GLY* 1.3 58.4 + - - +
368I SER* 5.3 5.3 - - - -
369I ILE* 3.7 32.7 - - - +
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Residues in contact with GLY 366 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362I TYR* 2.6 38.0 + - - +
363I ASP 4.3 1.3 + - - -
365I SER* 1.3 74.8 - - - +
367I PRO* 1.3 71.8 - - - +
368I SER 3.5 2.0 - - - -
369I ILE* 3.5 12.1 - - - +
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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