Contacts of the helix formed by residues 307 - 315 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305C PRO* 4.0 3.2 + - - +
306C VAL* 1.4 69.9 - - - +
308C PRO* 1.4 60.9 - - + +
309C GLN* 3.3 3.1 - - + +
310C THR* 2.8 45.7 + - + +
311C ALA 3.1 9.2 + - - -
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Residues in contact with PRO 308 (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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306C VAL 3.6 5.8 - - - +
307C HIS* 1.4 79.8 - - + +
309C GLN* 1.3 64.3 + - - +
311C ALA* 3.5 11.6 + - + +
312C PHE* 3.2 20.4 + - - +
401C PHE* 3.5 33.4 - - + -
412C GLN* 3.9 22.4 - - + +
416C PHE* 4.1 7.1 - - + -
420C TYR* 3.6 25.3 - - + +
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Residues in contact with GLN 309 (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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307C HIS* 3.2 3.2 + - + +
308C PRO* 1.3 78.3 - - - +
310C THR* 1.3 66.5 + - + +
312C PHE* 3.2 9.0 + - - +
313C CYS* 3.3 20.9 + - - -
419C THR* 4.8 3.4 + - - +
420C TYR* 2.9 68.9 + - + +
423C GLY* 3.7 20.6 - - - +
424C CYS* 3.5 0.9 - - - -
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Residues in contact with THR 310 (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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306C VAL* 5.5 3.5 - - - +
307C HIS* 2.8 34.9 + - + +
309C GLN* 1.3 77.6 - - + +
311C ALA* 1.3 62.6 + - - +
313C CYS* 3.3 7.9 + - - +
314C ASN* 3.0 47.9 + - - +
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Residues in contact with ALA 311 (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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306C VAL* 4.3 15.9 - - + +
307C HIS 3.1 9.9 + - - +
308C PRO* 3.6 11.9 - - + +
309C GLN 3.4 0.2 - - - -
310C THR* 1.3 71.0 - - - +
312C PHE* 1.3 62.7 + - - +
314C ASN* 3.9 4.6 - - - +
315C SER* 2.5 34.0 + - - +
386C ALA* 4.6 5.4 - - + -
401C PHE* 3.6 33.2 - - + +
416C PHE* 5.8 0.9 - - + -
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Residues in contact with PHE 312 (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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308C PRO 3.2 13.3 + - - +
309C GLN 3.4 9.2 - - - +
310C THR 3.2 0.6 - - - -
311C ALA* 1.3 79.7 - - - +
313C CYS* 1.3 53.8 + - - +
315C SER* 3.4 6.8 + - - +
318C VAL* 3.8 24.2 - - + -
346C TYR* 3.8 20.2 - - + -
347C LYS* 2.8 49.7 + - + +
386C ALA* 5.3 0.2 - - - -
416C PHE* 3.6 39.7 - + + -
420C TYR* 3.8 20.4 - - + -
421C THR* 3.5 41.1 - - + -
424C CYS* 3.9 15.3 - - - -
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Residues in contact with CYS 313 (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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309C GLN* 3.3 20.8 + - - -
310C THR* 3.3 10.0 + - - +
312C PHE* 1.3 78.4 - - - +
314C ASN* 1.3 64.9 + - - +
315C SER 3.9 0.5 - - - +
347C LYS* 2.9 16.3 + - - +
423C GLY 3.9 3.6 - - - -
424C CYS* 2.1 59.5 - - + +
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Residues in contact with ASN 314 (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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306C VAL* 6.2 1.6 - - - +
310C THR* 3.0 33.8 + - - +
311C ALA* 4.1 5.3 - - - +
313C CYS* 1.3 81.2 - - - +
315C SER* 1.3 62.8 + - - +
316C ASP* 4.0 3.6 + - - +
388C LYS* 3.8 24.7 - - - +
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Residues in contact with SER 315 (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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311C ALA* 2.5 24.1 + - - -
312C PHE 3.4 4.9 + - - -
313C CYS 3.9 0.5 - - - +
314C ASN* 1.3 80.0 - - - +
316C ASP* 1.3 59.7 + - - +
317C LEU 3.7 7.4 - - - -
318C VAL* 4.0 4.0 - - - -
347C LYS* 2.9 27.8 + - - -
386C ALA* 3.1 25.1 + - - +
387C GLY* 3.2 24.7 - - - -
388C LYS* 4.7 2.6 - - - +
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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