Contacts of the helix formed by residues 344 - 355 (chain A) in PDB entry 5ODS
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 ASN 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A THR* 3.9 25.7 + - - +
338A ILE* 2.9 21.5 + - + +
342A LEU* 3.7 22.2 - - + +
343A GLN* 1.3 75.8 - - - +
345A PRO* 1.3 64.0 - - - +
346A ASP* 4.1 0.5 - - - +
347A LEU* 3.1 28.4 + - + +
348A ALA 3.2 8.8 + - - -
224B ALA* 3.4 30.3 + - - +
225B GLY* 3.6 11.2 - - - +
227B LYS* 4.7 3.2 - - - +
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Residues in contact with PRO 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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338A ILE 4.5 0.2 - - - -
339A THR* 4.7 7.6 - - + +
343A GLN* 3.3 11.0 - - - +
344A ASN* 1.3 87.6 - - - +
346A ASP* 1.3 56.2 + - - +
348A ALA* 3.1 10.2 + - + +
349A LEU* 2.9 39.2 + - + +
363A LEU* 3.8 25.1 - - + -
367A LYS* 6.1 0.7 - - - -
176B ARG* 5.3 4.3 - - - +
222B GLY 4.0 2.7 - - - +
223B GLN* 3.2 43.1 - - - +
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Residues in contact with ASP 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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344A ASN* 4.1 0.2 - - - +
345A PRO* 1.3 71.9 - - - +
347A LEU* 1.3 58.6 + - - +
349A LEU* 3.6 6.7 + - - +
350A ARG* 3.1 26.7 + - - +
367A LYS* 3.9 21.4 + - - -
223B GLN* 2.8 49.6 + - - +
224B ALA* 3.7 16.7 + - + +
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Residues in contact with LEU 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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286A ASP* 3.4 34.3 - - + +
289A THR* 4.3 6.5 - - + +
291A THR* 4.1 24.5 - - + +
293A ILE* 4.2 15.7 - - + -
338A ILE* 3.9 28.0 - - + -
342A LEU* 5.1 2.2 - - + -
344A ASN* 3.1 24.0 + - + +
346A ASP* 1.3 76.0 - - - +
348A ALA* 1.3 60.6 + - - +
350A ARG* 3.3 10.0 + - + +
351A MET* 2.8 36.3 + - + +
354A ARG* 5.4 1.3 - - - +
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Residues in contact with ALA 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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335A ILE* 3.9 13.2 - - + +
338A ILE* 3.6 19.2 - - + +
339A THR* 3.2 28.5 - - - +
344A ASN 3.2 6.6 + - - +
345A PRO* 3.1 10.2 + - + +
347A LEU* 1.3 77.8 - - - +
349A LEU* 1.3 56.3 + - - +
351A MET* 3.3 5.6 + - - +
352A ALA* 3.0 31.9 + - - +
360A ALA* 5.2 0.2 - - - -
363A LEU* 3.9 9.4 - - + -
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Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PRO* 2.9 28.5 + - + +
346A ASP* 3.8 7.9 - - - +
348A ALA* 1.3 76.9 - - - +
350A ARG* 1.3 63.0 + - - +
352A ALA* 4.0 3.1 - - - +
353A VAL* 3.3 25.4 + - - +
360A ALA* 5.3 0.2 - - - -
363A LEU* 3.8 38.4 - - + +
364A PHE* 3.8 41.3 - - + -
367A LYS* 3.8 37.0 - - + -
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Residues in contact with ARG 350 (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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204A PHE* 5.1 2.0 - - - -
205A LYS 5.3 2.0 + - - -
206A MET 5.1 1.6 - - - -
207A GLU* 3.9 41.2 + - - +
286A ASP* 5.8 0.7 - - - +
288A GLU* 3.0 38.7 + - - +
289A THR* 6.6 0.4 - - + -
346A ASP 3.1 16.0 + - - +
347A LEU* 3.7 10.5 - - + +
349A LEU* 1.3 78.2 - - - +
351A MET* 1.3 59.5 + - - +
353A VAL* 3.2 23.7 - - - +
354A ARG* 2.9 66.3 + - - +
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Residues in contact with MET 351 (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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270A HIS* 4.1 11.0 - - + +
272A VAL* 3.6 29.6 - - + -
286A ASP* 5.0 1.3 - - - +
293A ILE* 4.7 4.9 - - + -
334A ILE* 3.7 31.9 - - + -
335A ILE* 3.8 16.4 - - + -
338A ILE* 3.8 15.7 - - + -
347A LEU* 2.8 28.7 + - + +
348A ALA* 3.7 4.5 - - - +
349A LEU 3.3 0.2 - - - -
350A ARG* 1.3 76.4 - - - +
352A ALA* 1.3 59.4 + - - +
354A ARG* 3.7 19.3 - - - +
355A ASN* 3.0 45.4 + - - +
357A LEU* 3.9 6.5 - - + +
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Residues in contact with ALA 352 (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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335A ILE* 3.9 12.5 - - + +
348A ALA 3.0 13.3 + - - +
349A LEU 4.0 3.6 - - - +
350A ARG 3.4 0.2 - - - -
351A MET* 1.3 76.7 - - - +
353A VAL* 1.3 56.2 + - - +
355A ASN 2.7 16.8 - - - +
356A ASN* 4.0 1.7 - - - +
357A LEU* 3.5 23.9 + - - +
360A ALA* 3.5 32.3 - - + -
364A PHE* 4.4 5.8 - - + -
388A PRO* 3.8 12.9 - - + +
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Residues in contact with VAL 353 (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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207A GLU* 5.3 4.3 - - - +
349A LEU 3.3 12.6 + - - +
350A ARG* 3.2 30.7 - - - +
352A ALA* 1.3 80.7 - - - +
354A ARG* 1.3 68.0 + - - +
355A ASN 4.2 1.6 - - - +
356A ASN* 5.0 3.6 + - - +
364A PHE* 4.5 8.7 - - + -
386A ASN* 3.5 36.8 - - + +
387A ALA 5.4 0.2 - - - -
388A PRO* 5.2 7.4 - - + -
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Residues in contact with ARG 354 (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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204A PHE* 4.1 9.9 - - + -
205A LYS 5.9 1.8 - - - +
270A HIS 3.3 22.2 + - - -
271A ASP* 3.4 32.0 + - - +
286A ASP* 3.0 30.5 + - - -
288A GLU* 2.9 27.6 + - - +
347A LEU* 5.4 0.8 - - - +
350A ARG* 2.9 54.6 + - - +
351A MET* 3.7 22.7 - - - +
353A VAL* 1.3 81.0 - - - +
355A ASN* 1.3 66.5 + - - +
356A ASN 4.1 0.3 + - - -
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Residues in contact with ASN 355 (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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269A LYS 2.9 29.0 + - - +
270A HIS* 3.3 22.8 - - + +
271A ASP* 3.1 23.8 + - - -
351A MET* 3.0 22.0 + - - +
352A ALA 2.7 14.4 - - - +
353A VAL 4.4 0.9 - - - -
354A ARG* 1.3 90.9 + - - +
356A ASN* 1.3 59.7 + - - +
357A LEU* 2.7 26.6 + - + +
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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