Contacts of the helix formed by residues 340 - 349 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.6 43.2 + - - +
117A ASP* 3.5 32.3 + - - +
309A ALA* 3.9 8.1 - - + +
310A GLU* 3.7 45.9 + - - +
338A ASP* 2.6 37.7 + - - +
339A LEU* 1.3 78.3 - - - +
341A PRO* 1.3 77.4 - - + +
342A LYS 3.2 0.2 - - - -
343A GLY 2.9 13.2 + - - +
344A ILE* 2.9 11.1 + - - +
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Residues in contact with PRO 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN* 4.2 8.5 - - - +
119A GLY 4.6 2.5 - - - +
120A ALA* 3.7 36.8 - - + +
121A GLY 5.7 0.2 - - - +
271A PRO 5.2 0.7 - - - +
272A SER* 5.2 8.2 - - - +
274A VAL* 3.9 19.7 - - + -
277A SER* 4.7 4.9 + - - +
304A TYR* 3.9 7.0 - - + -
309A ALA* 3.2 22.9 - - - +
339A LEU 4.6 0.7 - - - +
340A ARG* 1.3 86.8 - - + +
342A LYS* 1.3 64.7 + - + +
344A ILE* 3.6 15.9 + - + +
345A ILE* 3.6 18.1 + - - +
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Residues in contact with LYS 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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38A TYR* 6.3 0.8 - - - -
40A ARG* 5.9 3.8 - - - +
115A ASN* 3.2 36.0 + - - +
116A LEU* 4.1 15.3 + - + +
118A GLN* 3.7 36.8 + - + +
340A ARG* 3.2 1.4 - - - +
341A PRO* 1.3 81.4 - - + +
343A GLY* 1.3 65.5 + - - +
345A ILE* 3.6 20.3 + - + +
346A GLN* 3.3 21.3 + - - +
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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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116A LEU* 4.6 9.3 + - - +
338A ASP* 3.6 33.7 - - - +
340A ARG* 2.9 11.6 + - - +
342A LYS* 1.3 77.4 - - - +
344A ILE* 1.3 58.1 + - - +
346A GLN* 3.4 5.4 + - - +
347A MET* 2.9 30.3 + - - +
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Residues in contact with ILE 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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274A VAL* 6.1 0.7 - - + -
277A SER* 3.2 38.8 - - - +
278A ALA* 4.0 8.5 - - + +
281A ALA* 3.7 28.7 - - + -
304A TYR* 3.5 25.1 - - + +
338A ASP 3.5 15.0 - - - +
339A LEU* 3.6 9.4 - - + +
340A ARG 2.9 15.2 + - - +
341A PRO* 3.8 7.6 - - + +
342A LYS 3.3 0.2 - - - -
343A GLY* 1.3 75.1 - - - +
345A ILE* 1.3 55.1 + - - +
347A MET* 3.3 6.0 + - + +
348A LEU* 2.8 45.7 + - + +
350A LEU* 4.2 2.0 - - + -
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Residues in contact with ILE 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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271A PRO* 3.9 42.2 - - + +
272A SER* 4.0 9.9 - - - +
277A SER* 5.0 0.4 - - - -
341A PRO 3.6 13.7 + - - +
342A LYS* 3.6 22.6 + - + +
343A GLY 3.4 0.2 - - - -
344A ILE* 1.3 77.7 - - - +
346A GLN* 1.3 54.7 + - - +
349A ASP* 2.7 34.1 + - - -
350A LEU* 3.0 17.1 + - + +
351A LEU* 3.8 36.6 - - + -
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Residues in contact with GLN 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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116A LEU* 5.5 8.5 - - + -
342A LYS 3.3 11.2 + - - +
343A GLY* 3.8 8.5 - - - +
345A ILE* 1.3 79.7 - - - +
347A MET* 1.3 62.9 + - - +
348A LEU 3.3 0.7 + - - -
349A ASP* 3.4 11.4 + - - +
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Residues in contact with MET 347 (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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281A ALA* 4.3 17.3 - - + -
284A TYR* 3.8 33.0 + - + +
285A VAL* 5.8 0.2 - - + -
337A PHE* 3.8 24.9 - - + -
338A ASP* 3.5 42.2 - - + +
339A LEU* 4.6 2.9 - - + -
343A GLY 2.9 18.0 + - - +
344A ILE* 3.6 10.8 - - - +
346A GLN* 1.3 76.8 - - - +
348A LEU* 1.3 65.1 + - + +
372A SER* 4.6 2.4 + - - -
378A LYS* 4.7 9.2 - - - -
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Residues in contact with LEU 348 (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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280A TYR* 4.1 14.8 - - + +
281A ALA* 3.9 24.9 - - + +
284A TYR* 3.8 19.5 - - + -
344A ILE* 2.8 38.4 + - + +
347A MET* 1.3 84.9 - - + +
349A ASP* 1.3 72.5 + - - +
350A LEU* 3.4 18.7 + - + +
352A ARG* 3.5 2.4 + - - -
372A SER* 3.2 33.0 + - - +
373A TRP* 3.7 30.3 - - + +
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Residues in contact with ASP 349 (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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37A LYS* 6.0 0.3 + - - -
345A ILE 2.7 17.3 + - - -
346A GLN* 3.4 10.3 + - - +
347A MET 3.6 0.6 - - - -
348A LEU* 1.3 74.9 - - - +
350A LEU* 1.3 57.4 + - - +
351A LEU* 3.3 7.0 + - - +
352A ARG* 2.7 61.5 + - - +
372A SER* 5.1 1.6 - - - +
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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