Contacts of the helix formed by residues 340 - 349 (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 ARG 340 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C LEU 3.2 30.9 + - - +
117C ASP* 2.7 33.4 + - - +
309C ALA* 3.9 23.1 - - + +
310C GLU* 4.4 17.2 + - + +
311C PRO* 4.8 2.2 - - - +
338C ASP* 3.0 35.7 + - - +
339C LEU* 1.3 79.1 - - - +
341C PRO* 1.3 68.3 - - + +
342C LYS 3.4 0.4 - - - -
343C GLY* 2.6 27.2 + - - +
344C ILE 2.8 9.9 + - - -
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Residues in contact with PRO 341 (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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118C GLN* 4.1 18.6 - - + +
119C GLY 4.4 2.0 - - - +
120C ALA* 4.2 16.4 - - - -
271C PRO 5.8 0.2 - - - -
272C SER* 4.9 11.2 - - - +
274C VAL* 3.8 28.7 - - + -
277C SER* 4.7 5.6 + - - +
304C TYR* 4.1 8.1 - - + +
309C ALA 3.5 15.0 - - - +
339C LEU 3.7 0.4 - - - +
340C ARG* 1.3 89.9 - - + +
342C LYS* 1.3 61.4 + - + +
344C ILE* 3.1 22.8 + - + +
345C ILE* 3.2 17.7 + - + +
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Residues in contact with LYS 342 (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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40C ARG* 5.7 8.3 - - - +
116C LEU* 3.6 44.0 + - + +
118C GLN* 4.0 23.4 + - + +
340C ARG* 3.4 1.2 - - - +
341C PRO* 1.3 78.8 - - + +
343C GLY* 1.3 64.1 + - - +
345C ILE* 3.4 27.9 + - + +
346C GLN* 3.4 20.0 + - + +
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Residues in contact with GLY 343 (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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116C LEU 4.6 4.3 + - - +
338C ASP* 3.5 37.0 - - - +
340C ARG* 2.6 21.9 + - - +
342C LYS* 1.3 70.2 - - - +
344C ILE* 1.3 63.0 + - - -
346C GLN* 3.7 2.9 + - - +
347C MET* 3.3 22.7 + - - +
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Residues in contact with ILE 344 (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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274C VAL* 6.5 0.2 - - + -
277C SER* 3.2 42.2 - - - +
278C ALA* 4.8 3.4 - - + -
281C ALA* 3.4 28.0 - - + -
304C TYR* 4.9 1.6 - - - +
338C ASP 3.0 23.1 - - - +
339C LEU* 3.5 23.6 - - + +
340C ARG 2.8 19.2 + - - +
341C PRO* 3.3 10.5 - - + +
343C GLY* 1.3 71.8 - - - +
345C ILE* 1.3 62.7 + - - +
347C MET* 3.2 9.0 + - + +
348C LEU* 3.1 35.2 + - + +
350C LEU* 4.0 2.9 - - + -
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Residues in contact with ILE 345 (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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271C PRO* 3.9 37.9 - - + +
272C SER* 4.2 9.6 - - - +
341C PRO* 3.2 15.2 + - + +
342C LYS* 3.7 23.6 - - + +
343C GLY 3.2 1.0 - - - -
344C ILE* 1.3 77.8 - - + +
346C GLN* 1.3 65.5 + - + +
349C ASP* 2.7 31.2 + - - -
350C LEU* 3.2 23.3 + - + +
351C LEU* 3.9 34.1 - - + -
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Residues in contact with GLN 346 (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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342C LYS 3.4 15.1 + - - +
343C GLY* 4.5 2.0 - - - +
345C ILE* 1.3 88.1 - - + +
347C MET* 1.3 65.8 + - - +
348C LEU 3.5 0.2 + - - -
349C ASP* 3.6 11.0 + - - +
351C LEU* 5.1 6.6 - - - +
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Residues in contact with MET 347 (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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281C ALA* 4.8 7.2 - - + -
284C TYR* 4.1 27.4 + - + +
285C VAL* 5.6 0.4 - - + -
337C PHE* 3.9 29.6 - - + -
338C ASP* 3.5 35.2 - - + +
339C LEU* 5.2 0.9 - - + -
343C GLY 3.3 14.2 + - - +
344C ILE* 3.2 18.7 + - + +
346C GLN* 1.3 79.9 - - - +
348C LEU* 1.3 66.3 + - + +
349C ASP* 5.3 0.3 - - - +
372C SER* 5.4 1.0 - - - -
378C LYS* 4.4 11.4 - - - +
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Residues in contact with LEU 348 (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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280C TYR* 4.1 8.3 - - + +
281C ALA* 4.1 17.7 - - - +
284C TYR* 3.8 38.4 - - + -
344C ILE* 3.1 32.3 + - + +
347C MET* 1.3 87.0 - - + +
349C ASP* 1.3 73.2 + - - +
350C LEU* 3.3 19.0 + - + +
352C ARG* 3.6 2.3 + - - -
372C SER* 2.6 39.6 + - - +
373C TRP* 4.0 21.8 - - + -
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Residues in contact with ASP 349 (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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345C ILE 2.7 16.9 + - - -
346C GLN* 3.6 8.9 + - - +
347C MET 3.5 3.0 - - - +
348C LEU* 1.3 73.4 - - - +
350C LEU* 1.3 58.2 + - - +
351C LEU* 3.4 5.7 + - - +
352C ARG* 2.9 51.2 + - - +
372C SER* 5.6 1.1 - - - -
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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