Contacts of the helix formed by residues 341 - 355 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339C GLY 3.6 2.0 + - - -
340C LEU* 1.3 76.4 - - - +
342C LEU* 1.3 59.0 + - - +
343C THR* 3.5 8.3 + - - -
344C GLN* 3.1 37.6 + - - +
345C GLN* 2.9 27.9 + - - +
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Residues in contact with LEU 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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340C LEU 4.0 0.4 + - - -
341C SER* 1.3 75.1 - - - +
343C THR* 1.3 57.7 + - - +
345C GLN* 3.7 8.3 - - - +
346C SER* 2.9 32.2 + - - -
123D LEU* 3.7 39.9 - - + +
124D PHE* 3.5 47.8 - - + -
127D GLN* 3.9 19.2 - - + +
128D GLU* 3.9 22.0 - - + +
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Residues in contact with THR 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341C SER* 3.2 7.7 + - - -
342C LEU* 1.3 75.4 - - - +
344C GLN* 1.3 67.6 + - + +
346C SER* 3.1 8.0 + - - -
347C TYR* 2.9 24.8 + - + +
124D PHE* 6.1 2.1 - - - -
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Residues in contact with GLN 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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277C HIS* 4.3 14.3 + - - -
339C GLY 5.0 0.3 - - - +
340C LEU* 3.8 29.5 - - + +
341C SER* 3.1 40.0 + - - +
343C THR* 1.3 80.6 - - + +
345C GLN* 1.3 61.2 + - - +
347C TYR* 3.3 4.3 + - - -
348C PHE* 3.0 45.9 + - + -
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Residues in contact with GLN 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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336C TYR* 3.8 38.6 + - + +
340C LEU* 3.0 37.6 + - + -
341C SER 2.9 19.2 + - - +
342C LEU* 3.7 5.8 - - - +
344C GLN* 1.3 75.0 - - - +
346C SER* 1.3 58.0 + - - +
348C PHE 3.7 0.2 + - - -
349C MET* 3.1 31.0 + - - +
404C ALA* 3.7 4.6 - - + +
408C ARG* 2.6 30.5 + - - -
123D LEU* 3.4 16.7 - - + +
127D GLN* 3.2 26.5 + - - +
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Residues in contact with SER 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342C LEU 2.9 22.3 + - - -
343C THR* 3.1 8.3 + - - -
345C GLN* 1.3 75.1 - - - +
347C TYR* 1.3 65.3 + - - +
349C MET* 3.6 2.1 - - - +
350C MET* 3.2 36.2 + - - +
120D LEU* 3.6 24.3 - - - +
123D LEU* 3.7 10.8 - - - +
124D PHE* 3.6 17.5 - - - -
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Residues in contact with TYR 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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329C VAL* 2.8 48.1 + - - +
331C TRP* 5.9 0.6 - + - -
343C THR* 2.9 17.5 + - + +
344C GLN* 3.9 4.5 - - - +
346C SER* 1.3 74.5 - - - +
348C PHE* 1.3 93.3 + + - +
350C MET* 3.1 14.0 + - + +
351C ALA* 2.9 41.6 + - + +
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Residues in contact with PHE 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C HIS* 5.9 1.3 - + - -
329C VAL 3.6 16.8 - - - -
330C VAL* 3.6 14.4 - - - -
331C TRP* 3.8 35.0 - + - -
332C ALA* 3.5 43.5 - - + -
333C HIS 4.4 11.7 - - - +
336C TYR* 3.7 8.5 - - + -
340C LEU* 4.8 0.2 - - + -
344C GLN* 3.0 46.3 + - + +
345C GLN 4.3 1.8 - - - +
347C TYR* 1.3 95.2 - + - +
349C MET* 1.3 61.6 + - - +
351C ALA* 4.1 1.9 - - - +
352C THR* 2.6 34.4 + - - -
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Residues in contact with MET 349 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C TYR* 3.2 13.1 + - + +
345C GLN 3.1 18.2 + - - +
346C SER 3.6 4.5 - - - +
348C PHE* 1.3 79.9 - - - +
350C MET* 1.3 57.4 - - + +
352C THR* 3.5 3.2 - - - -
353C MET* 3.1 48.5 + - + +
402C SER* 3.2 16.6 - - - +
403C GLN* 3.8 13.2 - - - +
404C ALA 3.9 18.6 - - - -
405C SER 5.5 0.2 - - - -
116D GLY* 4.7 1.6 - - - +
119D SER* 3.7 26.0 - - - +
120D LEU* 3.5 37.5 - - + +
123D LEU* 4.2 15.7 - - - -
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Residues in contact with MET 350 (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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346C SER* 3.2 31.2 + - - +
347C TYR* 3.1 11.5 + - + +
349C MET* 1.3 80.3 - - + +
351C ALA* 1.3 65.7 + - - +
353C MET* 3.2 34.7 + - + +
354C VAL* 3.3 17.4 + - - +
14D TRD 4.2 23.3 - - + +
120D LEU* 4.1 20.4 - - + -
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Residues in contact with ALA 351 (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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326C LEU* 4.8 5.2 - - + +
329C VAL* 4.0 14.1 - - + +
330C VAL* 3.7 11.7 - - + +
347C TYR* 2.9 48.8 + - + +
348C PHE* 4.1 3.6 - - - +
350C MET* 1.3 75.8 - - - +
352C THR* 1.3 62.0 + - - +
354C VAL* 3.4 21.9 + - - +
355C ILE* 4.1 4.5 + - - +
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Residues in contact with THR 352 (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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2C HEA 3.6 23.5 - - + +
330C VAL* 3.6 14.9 + - + +
333C HIS* 2.7 39.0 + - + +
348C PHE 2.6 23.5 + - - -
349C MET* 3.5 5.2 - - - -
351C ALA* 1.3 73.8 - - - +
353C MET* 1.3 66.8 + - - +
355C ILE* 3.3 23.1 + - + +
356C ALA 4.4 1.0 + - - -
399C ILE* 4.5 0.3 - - - +
402C SER* 3.5 24.9 - - - -
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Residues in contact with MET 353 (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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349C MET* 3.1 25.9 + - + +
350C MET* 3.2 48.9 + - + +
352C THR* 1.3 77.6 - - - +
354C VAL* 1.3 60.8 + - - +
356C ALA* 3.2 15.1 + - - +
399C ILE* 4.3 9.2 - - + -
402C SER* 3.8 6.3 - - - +
403C GLN* 3.1 32.3 - - - +
14D TRD 3.7 25.1 - - + -
112D LEU* 3.3 46.9 - - + +
115D ILE* 5.1 2.0 - - - -
116D GLY* 4.6 5.6 - - - -
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Residues in contact with VAL 354 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C LEU* 3.8 27.1 - - + -
350C MET 3.5 15.0 - - - +
351C ALA* 3.5 14.1 - - - +
352C THR 3.2 0.6 - - - -
353C MET* 1.3 76.9 - - - +
355C ILE* 1.3 57.1 + - - +
357C VAL* 2.9 30.8 + - + +
358C PRO* 3.3 7.9 - - + +
14D TRD 3.9 21.3 - - + -
109D ILE* 6.3 1.1 - - + -
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Residues in contact with ILE 355 (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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2C HEA 3.6 26.2 - - - +
284C HIS* 5.0 0.4 - - + -
288C TYR* 3.8 21.3 - - + +
323C ILE* 4.0 14.6 - - + +
326C LEU* 3.6 32.5 - - + -
327C GLY 4.3 2.5 - - - +
330C VAL* 3.9 34.8 - - + -
351C ALA 4.4 2.2 - - - +
352C THR* 3.3 14.6 + - + +
353C MET 3.2 1.2 - - - -
354C VAL* 1.3 75.9 - - - +
356C ALA* 1.3 60.8 + - - +
357C VAL 3.0 1.7 + - - -
358C PRO* 3.4 9.0 - - - +
359C THR* 2.9 35.3 + - - +
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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