Contacts of the helix formed by residues 356 - 360 (chain C) in PDB entry 3IML
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 GLU 356 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C GLN* 3.9 16.8 - - + +
26C ASP* 3.7 11.7 - - - +
27C ALA* 3.6 26.3 - - - +
30C ASP* 3.0 18.7 + - - +
73C THR* 3.6 15.6 + - - +
76C ARG* 2.8 43.4 + - - +
355C TYR* 1.3 75.4 - - - +
357C LYS* 1.3 58.0 + - - +
359C ALA* 3.1 21.5 + - - +
360C ALA 4.3 1.0 + - - -
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Residues in contact with LYS 357 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354C ILE* 3.9 12.9 + - - +
355C TYR 3.1 0.6 - - - -
356C GLU* 1.3 79.2 - - - +
358C THR* 1.3 59.2 + - - +
359C ALA 3.3 0.7 + - - -
360C ALA* 3.6 4.2 + - - +
366C ARG* 2.9 39.6 + - - +
368C GLU* 3.7 24.6 - - + +
369C PRO* 4.8 5.3 - - - +
370C GLU* 5.3 7.3 - - + +
371C PHE* 3.8 19.1 - - + -
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Residues in contact with THR 358 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ASP* 3.8 0.2 + - - -
276C ARG* 3.1 19.2 + - - -
280C TYR* 4.0 4.3 - - - +
354C ILE 3.8 9.2 - - - +
355C TYR* 2.7 23.1 + - + +
357C LYS* 1.3 76.7 - - - +
359C ALA* 1.3 55.3 + - - +
360C ALA 3.2 7.1 + - - +
362C GLY 3.9 2.4 + - - +
363C HIS* 3.1 37.3 + - - -
366C ARG* 3.9 10.3 + - - +
371C PHE* 3.6 30.1 - - + -
373C TRP* 3.7 23.3 - - + -
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Residues in contact with ALA 359 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LYS* 2.9 30.1 + - - +
22C ASP* 3.8 10.3 - - - +
23C GLN* 3.6 22.4 - - + +
26C ASP* 3.6 21.3 - - + +
267C SER* 3.8 8.1 - - - +
355C TYR 4.0 0.7 - - - +
356C GLU 3.1 15.8 + - - +
358C THR* 1.3 79.2 + - - +
360C ALA* 1.3 58.8 + - - +
363C HIS* 4.2 7.4 - - - -
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Residues in contact with ALA 360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C SER 5.1 0.4 - - - -
14C GLU* 3.8 23.8 - - + +
19C LYS* 4.1 7.6 - - + -
23C GLN* 3.9 10.5 - - - +
356C GLU 4.3 1.4 + - - +
357C LYS 3.6 2.6 + - - +
358C THR 3.2 0.4 - - - -
359C ALA* 1.3 81.1 - - - +
361C TYR* 1.3 83.4 + - + +
362C GLY 3.3 2.9 - - - +
366C ARG* 2.6 32.1 + - - -
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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