Contacts of the helix formed by residues 322 - 332 (chain M) in PDB entry 5MS0
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 GLY 322 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318M ILE* 3.4 16.8 - - - -
319M GLY 3.3 6.0 + - - -
320M ARG 3.2 1.2 - - - -
321M ASN* 1.3 77.4 - - - +
323M GLN* 1.3 58.3 + - - +
325M VAL* 3.7 4.9 + - - +
326M ARG* 2.9 31.8 + - - +
29R G 3.3 29.7 + - - -
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Residues in contact with GLN 323 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233M ARG* 5.9 7.2 - - + -
318M ILE 3.3 2.0 + - - -
319M GLY* 4.1 1.0 - - - -
320M ARG 3.5 19.8 + - - +
321M ASN* 4.3 2.5 - - + +
322M GLY* 1.3 75.6 - - - +
324M ASN* 1.3 63.0 + - - +
326M ARG* 4.0 4.4 - - - +
327M LEU* 2.9 33.3 + - - +
20R A 5.9 4.3 - - - +
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Residues in contact with ASN 324 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288M MET* 5.1 8.1 - - - +
289M ALA 5.5 4.5 - - - +
316M GLN 4.1 6.3 - - - +
317M ALA 3.3 23.1 - - - +
318M ILE 2.9 9.9 + - - +
319M GLY* 3.8 7.9 - - - +
323M GLN* 1.3 77.7 - - - +
325M VAL* 1.3 51.5 + - - +
327M LEU* 5.1 1.8 - - - -
328M ALA* 2.7 41.0 + - - +
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Residues in contact with VAL 325 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317M ALA 4.2 2.6 + - - +
318M ILE* 3.1 25.8 + - + +
322M GLY* 3.7 5.6 + - - +
324M ASN* 1.3 76.2 - - - +
326M ARG* 1.3 51.1 + - - +
328M ALA* 3.9 4.2 - - - +
329M SER* 2.7 37.5 + - - -
336M LEU* 4.9 8.5 - - + +
338M VAL* 5.2 11.9 - - + +
29N SER* 4.1 14.1 - - - -
29R G 5.8 1.3 - - - +
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Residues in contact with ARG 326 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322M GLY 2.9 21.6 + - - +
323M GLN* 4.0 4.5 - - - +
324M ASN 3.2 0.2 - - - -
325M VAL* 1.3 77.2 - - - +
327M LEU* 1.3 60.5 + - - +
329M SER* 3.0 8.3 + - - -
330M GLN* 2.9 27.1 + - - +
29N SER* 5.1 5.2 - - - -
30N ALA 5.8 1.1 - - - -
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Residues in contact with LEU 327 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227M ALA* 3.4 23.6 - - + +
228M ARG 5.4 6.1 - - - +
233M ARG* 5.8 4.0 - - + +
234M ALA 5.8 0.9 - - - -
235M LYS* 4.8 13.6 - - + +
323M GLN 2.9 18.1 + - - +
324M ASN* 4.6 1.3 - - - +
326M ARG* 1.3 76.0 - - - +
328M ALA* 1.3 57.7 + - - +
330M GLN* 3.1 6.8 + - - -
331M LEU* 2.9 26.7 + - - +
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Residues in contact with ALA 328 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287M ALA* 3.8 31.0 - - + +
288M MET* 4.7 7.2 - - + -
324M ASN 2.7 24.0 + - - +
325M VAL* 4.3 3.8 - - - -
327M LEU* 1.3 74.8 - - - +
329M SER* 1.3 53.9 - - - +
330M GLN 3.1 4.3 + - - -
331M LEU* 3.9 11.7 + - - +
332M SER* 4.1 14.4 + - - -
334M TRP 4.8 3.3 - - - +
336M LEU* 5.3 4.1 - - - +
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Residues in contact with SER 329 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325M VAL 2.7 23.4 + - - -
326M ARG* 3.0 10.9 + - - -
328M ALA* 1.3 74.7 - - - +
330M GLN* 1.3 56.1 + - - +
332M SER 5.4 0.7 - - - -
333M GLY 5.9 1.8 - - - -
334M TRP 4.7 9.7 - - - +
335M GLU* 5.4 2.1 - - - -
336M LEU* 4.6 15.0 - - - -
29N SER* 4.2 17.9 - - - -
30N ALA 4.3 9.6 - - - +
31N LYS* 4.3 20.5 - - - +
32N PRO 5.1 1.0 - - - -
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Residues in contact with GLN 330 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225M ALA* 5.6 0.3 - - - +
226M ALA 5.1 3.1 - - - +
227M ALA* 3.8 16.7 - - + +
228M ARG 5.8 0.2 - - - +
326M ARG 2.9 12.5 + - - +
327M LEU* 3.1 8.7 + - - +
329M SER* 1.3 80.5 - - - +
331M LEU* 1.3 63.6 + - - +
332M SER 3.6 0.9 - - - -
333M GLY 5.1 1.5 + - - -
34N ASN* 4.5 20.1 - - - +
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Residues in contact with LEU 331 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225M ALA* 3.3 30.6 - - + +
226M ALA 5.5 0.2 - - - -
227M ALA* 4.2 12.1 - - + +
235M LYS* 5.0 12.3 - - + +
237M ALA* 5.9 4.9 - - + -
287M ALA* 4.9 13.0 - - + -
327M LEU 2.9 14.7 + - - +
328M ALA* 3.9 7.7 + - - +
330M GLN* 1.3 79.6 - - - +
332M SER* 1.3 66.7 + - - +
34N ASN* 6.0 0.3 - - - +
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Residues in contact with SER 332 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280M PRO 5.6 3.4 - - - -
283M PHE* 5.5 5.6 - - - -
284M VAL* 5.1 21.8 - - - -
287M ALA* 5.5 4.5 - - - -
328M ALA 4.1 12.6 + - - -
329M SER 5.4 0.2 - - - -
330M GLN 3.6 0.6 - - - -
331M LEU* 1.3 83.5 - - - +
333M GLY* 1.3 60.5 + - - +
334M TRP* 4.2 11.9 - - - -
34N ASN* 5.9 0.7 - - - -
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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