Contacts of the helix formed by residues 341 - 355 (chain A) in PDB entry 3OMA
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 SER 341 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A GLY 3.7 2.8 + - - -
340A LEU* 1.3 77.2 - - - +
342A LEU* 1.3 58.7 + - - +
343A THR* 3.4 8.7 + - - -
344A GLN* 3.2 37.1 + - - +
345A GLN* 3.0 25.2 + - - +
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Residues in contact with LEU 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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341A SER* 1.3 74.5 - - - +
343A THR* 1.3 55.5 + - - +
345A GLN* 3.8 6.6 - - - +
346A SER* 2.8 36.6 + - - -
123B LEU* 3.7 39.3 - - + +
124B PHE* 3.6 44.6 - - + -
127B GLN* 4.0 23.5 - - + +
128B GLU* 4.0 21.1 - - + +
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Residues in contact with THR 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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341A SER* 3.2 8.0 + - - -
342A LEU* 1.3 77.0 - - - +
344A GLN* 1.3 67.6 + - + +
346A SER* 3.3 5.9 + - - -
347A TYR* 3.0 24.6 + - + +
124B PHE* 6.3 0.9 - - - -
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Residues in contact with GLN 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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277A HIS* 4.9 10.7 + - - -
339A GLY 5.1 0.3 - - - +
340A LEU* 3.9 25.1 - - + +
341A SER* 3.2 36.0 + - - +
343A THR* 1.3 78.2 - - + +
345A GLN* 1.3 56.1 + - - +
347A TYR* 3.2 5.4 + - - +
348A PHE* 3.0 54.4 + - + -
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Residues in contact with GLN 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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336A TYR* 3.8 39.5 + - + +
340A LEU* 2.5 40.5 + - + -
341A SER 3.0 17.6 + - - +
342A LEU* 3.8 6.3 - - - +
344A GLN* 1.3 75.9 - - - +
346A SER* 1.3 57.0 + - - +
349A MET* 3.1 30.0 + - - +
404A ALA* 3.9 3.7 - - + +
408A ARG* 2.7 29.1 + - - -
123B LEU* 3.6 17.8 - - + +
127B GLN* 3.3 23.7 + - - +
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Residues in contact with SER 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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342A LEU 2.8 22.9 + - - -
343A THR* 3.7 5.8 - - - -
345A GLN* 1.3 73.4 - - - +
347A TYR* 1.3 66.2 + - - +
349A MET* 3.5 3.3 + - - +
350A MET* 3.1 36.7 + - - +
120B LEU* 3.4 28.0 - - - +
123B LEU* 3.7 10.1 - - - +
124B PHE* 3.7 14.0 - - - -
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Residues in contact with TYR 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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329A VAL* 2.9 47.2 + - - +
331A TRP* 6.2 0.2 - + - -
343A THR* 3.0 18.4 + - + +
344A GLN* 3.7 4.7 - - - +
346A SER* 1.3 76.5 - - - +
348A PHE* 1.3 95.1 + + - +
350A MET* 2.9 15.3 + - + +
351A ALA* 2.9 40.6 + - + -
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Residues in contact with PHE 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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277A HIS* 5.7 2.9 - + - -
329A VAL 3.7 18.8 - - - -
330A VAL 3.5 19.3 - - - -
331A TRP* 3.9 35.4 - + - -
332A ALA* 3.5 33.9 - - + -
333A HIS 4.3 12.8 - - - +
336A TYR* 3.7 9.9 - - + -
340A LEU* 4.8 1.1 - - + -
344A GLN* 3.0 46.5 + - + +
345A GLN 4.4 1.8 - - - +
347A TYR* 1.3 95.1 - + - +
349A MET* 1.3 58.3 + - - +
351A ALA* 4.2 2.1 - - - +
352A THR* 2.7 34.0 + - - -
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Residues in contact with MET 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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336A TYR* 3.2 12.7 + - + +
345A GLN 3.1 18.0 + - - +
346A SER 3.6 3.8 - - - +
348A PHE* 1.3 79.0 - - - +
350A MET* 1.3 62.3 + - + +
352A THR* 3.7 3.2 - - - -
353A MET* 3.1 40.4 + - + +
402A SER 3.4 15.6 - - - +
403A GLN* 3.1 27.4 - - - +
404A ALA 3.9 18.4 - - - +
405A SER 5.3 0.2 - - - -
116B GLY* 4.6 4.5 - - - -
119B SER* 3.2 21.1 - - - +
120B LEU* 4.1 24.2 - - + +
123B LEU* 4.3 19.7 - - - -
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Residues in contact with MET 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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346A SER* 3.1 29.5 + - - +
347A TYR* 2.9 11.4 + - + +
349A MET* 1.3 78.1 - - + +
351A ALA* 1.3 63.4 + - - +
353A MET* 3.1 30.9 + - + +
354A VAL* 3.5 18.9 + - - +
4B TRD 3.9 34.7 - - + +
120B LEU* 3.9 19.5 - - + -
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Residues in contact with ALA 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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326A LEU* 4.7 5.9 - - + +
329A VAL* 3.8 15.3 - - + +
330A VAL* 3.6 12.7 - - + +
347A TYR* 2.9 47.3 + - + +
348A PHE 4.2 2.5 - - - +
350A MET* 1.3 73.3 - - - +
352A THR* 1.3 63.4 + - - +
354A VAL* 3.6 20.3 + - - +
355A ILE* 4.0 5.2 + - - +
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Residues in contact with THR 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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2A HEA 3.6 24.3 - - + +
330A VAL* 3.5 15.2 + - + +
333A HIS* 2.8 38.3 + - + +
348A PHE 2.7 24.0 + - - -
349A MET* 3.7 4.5 - - - -
350A MET 3.3 0.2 - - - -
351A ALA* 1.3 73.2 - - - +
353A MET* 1.3 65.4 + - - +
355A ILE* 3.3 22.8 + - + +
356A ALA 4.3 1.0 + - - -
399A ILE* 4.4 0.2 - - - +
402A SER* 3.5 23.6 - - - -
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Residues in contact with MET 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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349A MET* 3.1 27.7 + - + +
350A MET* 3.1 48.0 - - + +
351A ALA 3.4 0.4 - - - -
352A THR* 1.3 75.8 - - - +
354A VAL* 1.3 62.0 + - - +
356A ALA* 3.1 15.1 + - - +
399A ILE* 4.2 10.1 - - + -
402A SER* 3.8 6.7 - - - +
403A GLN* 3.2 28.3 - - - +
4B TRD 3.8 26.5 - - + -
112B LEU* 3.3 42.6 - - + +
115B ILE* 4.9 2.9 - - - -
116B GLY* 4.7 4.3 - - - -
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Residues in contact with VAL 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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326A LEU* 3.6 28.0 - - + -
350A MET 3.5 16.4 - - - +
351A ALA* 3.6 12.1 - - - +
352A THR 3.2 0.4 - - - -
353A MET* 1.3 76.7 - - - +
355A ILE* 1.3 56.0 + - - +
357A VAL* 2.9 31.1 + - + +
358A PRO* 3.2 8.9 - - + +
4B TRD 4.3 14.1 - - + -
112B LEU* 4.9 1.3 - - - -
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Residues in contact with ILE 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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2A HEA 3.6 26.0 - - - +
284A HIS* 4.7 0.7 - - + -
288A TYR* 3.6 28.3 - - + +
323A ILE* 4.6 11.2 - - + +
326A LEU* 3.7 44.2 - - + +
327A GLY 4.3 2.0 - - - +
330A VAL* 4.1 17.5 - - + -
351A ALA 4.1 5.4 - - - +
352A THR* 3.5 16.4 - - + +
353A MET 3.2 0.6 - - - -
354A VAL* 1.3 76.9 - - - +
356A ALA* 1.3 59.5 + - - +
357A VAL 3.1 1.0 + - - -
358A PRO* 3.4 12.2 - - - +
359A THR* 2.8 29.5 + - - +
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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