Contacts of the helix formed by residues 307 - 315 (chain B) in PDB entry 3MA2
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 HIS 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305B PRO* 5.4 2.2 + - - +
306B VAL* 1.3 77.8 - - - +
308B PRO* 1.4 81.5 - - + +
309B GLN* 4.1 18.6 - - + +
310B THR* 3.0 35.3 + - + +
311B ALA* 2.8 22.2 + - - +
401B PHE* 4.6 3.8 - - - -
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Residues in contact with PRO 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B HIS* 1.4 86.8 - - + +
309B GLN* 1.3 58.1 + - - +
311B ALA* 3.3 5.4 + - + +
312B PHE* 2.8 30.7 + - - +
401B PHE* 3.7 29.6 - - + -
408B LEU* 5.0 0.2 - - + -
412B GLN* 3.8 28.7 - - + +
416B PHE* 3.5 26.1 - - + -
420B TYR* 3.3 22.7 - - + +
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Residues in contact with GLN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B HIS* 3.3 16.3 - - + +
308B PRO* 1.3 78.6 - - - +
310B THR* 1.3 60.2 + - - +
312B PHE* 3.4 1.2 - - - +
313B CYS* 2.9 40.9 + - - -
419B THR 4.6 0.9 - - - +
420B TYR* 3.1 63.8 + - + +
423B GLY* 3.7 19.2 + - - -
424B CYS* 3.6 0.6 - - - -
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Residues in contact with THR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B PRO 4.8 4.3 - - - +
306B VAL* 4.4 8.3 - - + -
307B HIS* 3.0 50.7 + - + +
309B GLN* 1.3 79.8 - - - +
311B ALA* 1.3 68.6 + - - +
313B CYS* 3.0 6.8 + - - +
314B ASN* 2.9 42.0 + - - +
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B VAL* 3.9 12.1 - - + -
307B HIS 2.8 16.2 + - - +
308B PRO 3.5 4.9 - - - +
310B THR* 1.3 79.6 - - - +
312B PHE* 1.3 62.5 + - - +
314B ASN* 4.8 4.3 - - - +
315B SER* 2.6 32.2 + - - +
386B ALA* 4.4 9.4 - - + -
401B PHE* 3.6 31.6 - - + +
416B PHE* 5.7 0.9 - - + -
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Residues in contact with PHE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B PRO 2.8 17.6 + - - +
309B GLN 3.4 6.5 - - - +
310B THR 3.1 0.2 - - - -
311B ALA* 1.3 79.9 - - - +
313B CYS* 1.3 64.6 + - - +
314B ASN 3.2 0.2 + - - -
315B SER* 3.5 3.5 + - - +
318B VAL* 4.1 13.2 - - + -
346B TYR* 3.9 26.9 - - + -
347B LYS* 3.0 44.6 + - + +
415B GLY 5.1 0.4 - - - -
416B PHE* 3.7 44.1 - + + -
420B TYR* 3.7 21.5 - - + -
421B THR* 3.7 37.5 - - - -
424B CYS* 3.9 12.6 - - - -
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Residues in contact with CYS 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B GLN* 2.9 30.7 + - - +
310B THR* 3.0 5.5 + - - +
312B PHE* 1.3 77.2 - - - +
314B ASN* 1.3 65.1 + - - +
315B SER 4.1 0.2 - - - +
347B LYS* 3.1 16.2 + - - +
424B CYS* 2.0 65.9 - - + +
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Residues in contact with ASN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B THR* 2.9 33.1 + - - +
311B ALA* 4.2 4.6 - - - +
313B CYS* 1.3 82.6 - - - +
315B SER* 1.3 62.1 + - - +
316B ASP* 4.0 2.8 + - - +
388B LYS* 3.8 25.6 - - - +
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B ALA* 2.6 23.5 + - - -
312B PHE 3.5 0.2 + - - -
313B CYS 3.4 0.8 - - - +
314B ASN* 1.3 80.5 - - - +
316B ASP* 1.3 62.2 + - - +
317B LEU 3.7 12.8 - - - -
318B VAL* 3.9 10.1 - - - -
347B LYS* 2.8 27.4 + - - +
386B ALA* 3.4 19.9 + - - +
387B GLY* 3.1 16.3 + - - -
388B LYS* 4.3 6.0 - - - +
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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