Contacts of the strand formed by residues 306 - 312 (chain M) in PDB entry 6CM9
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 THR 306 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304M ARG 4.3 6.1 + - - -
305M SER* 1.3 74.8 - - - +
307M ALA* 1.3 60.7 + - - +
308M ASN* 2.9 24.9 + - - +
347M SER* 3.3 27.6 - - - +
348M PHE 3.9 15.3 - - - +
349M PRO* 4.5 9.4 - - + +
382M ILE* 4.4 3.1 - - - +
383M PRO* 3.4 20.7 + - - +
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Residues in contact with ALA 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277M ILE* 4.6 2.2 - - + -
301M PHE* 3.6 19.5 - - + -
305M SER 4.0 1.6 + - - -
306M THR* 1.3 67.3 - - - +
308M ASN* 1.3 66.3 + - - +
309M ASN 3.6 1.4 + - - -
310M VAL* 3.7 22.4 - - + +
346M LYS 3.6 1.2 - - - +
348M PHE* 3.1 45.8 + - + +
380M PHE* 4.9 1.1 - - + -
381M GLU 4.0 0.7 - - - +
382M ILE* 3.7 19.7 - - + -
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Residues in contact with ASN 308 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306M THR* 2.9 25.4 + - - +
307M ALA* 1.3 74.9 - - - +
309M ASN* 1.3 79.0 + - + +
310M VAL 3.2 1.0 + - - -
346M LYS* 3.5 7.8 - - + +
347M SER* 5.3 1.4 - - - -
381M GLU* 3.0 25.7 + - + +
383M PRO* 3.4 16.6 - - - +
6T TYR* 2.4 39.0 + - - +
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Residues in contact with ASN 309 (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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308M ASN* 1.3 92.0 - - - +
310M VAL* 1.3 65.4 + - - +
311M GLU* 3.6 11.9 + - + +
345M VAL 3.3 10.5 - - - -
346M LYS* 2.9 40.4 + - + +
379M LYS 3.5 11.3 - - - +
381M GLU* 3.6 25.1 + - - +
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Residues in contact with VAL 310 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277M ILE* 3.8 11.7 - - + -
307M ALA* 3.7 28.7 - - + +
308M ASN 4.2 0.4 - - - +
309M ASN* 1.3 76.4 - - - +
311M GLU* 1.3 64.2 + - - +
312M ILE* 4.4 20.6 - - + -
344M SER* 3.5 0.7 - - - -
345M VAL* 3.0 56.7 + - + +
348M PHE* 4.2 11.2 - - + -
378M VAL* 5.7 1.1 - - + -
379M LYS 5.4 0.2 - - - +
380M PHE* 3.6 33.0 - - + +
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Residues in contact with GLU 311 (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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309M ASN* 3.6 14.0 + - + +
310M VAL* 1.3 80.1 - - - +
312M ILE* 1.3 61.0 + - - +
313M HIS* 2.9 33.9 + - + -
333M LYS* 4.7 6.2 + - - -
342M VAL* 3.9 15.7 - - + +
343M TRP 3.6 6.7 - - - -
344M SER* 3.7 20.2 + - - +
378M VAL* 3.6 0.3 - - - -
379M LYS* 3.4 33.8 + - + +
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Residues in contact with ILE 312 (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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277M ILE* 5.0 4.0 - - + -
279M ILE* 3.7 27.6 - - + -
297M ALA* 3.7 9.0 - - + -
310M VAL* 4.4 19.5 - - + -
311M GLU* 1.3 70.0 - - - +
313M HIS* 1.3 63.6 + - - +
314M ILE* 3.4 16.7 + - + +
341M ILE 3.2 13.0 - - - +
343M TRP* 3.0 54.0 + - + +
345M VAL* 5.4 1.1 - - + -
348M PHE* 5.6 1.3 - - + -
376M ILE* 3.8 26.2 - - + -
378M VAL* 4.0 20.0 - - + +
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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
------------------------------------------------------------
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