Contacts of the helix formed by residues 334 - 340 (chain M) in PDB entry 2JA7
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 334 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327M ALA 5.6 0.4 - - - -
328M ARG 3.6 14.4 - - - -
329M LEU 3.5 7.9 - - - +
330M LYS 3.8 8.0 - - - +
332M LYS 2.6 14.0 + - - -
333M GLU* 1.3 77.7 - - - +
335M ARG* 1.3 72.1 + - - -
336M ILE* 2.7 4.9 + - - -
337M ARG* 2.9 14.4 + - - +
338M GLY 3.7 5.3 - - - +
339M ASN* 4.1 0.9 - - - -
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Residues in contact with ARG 335 (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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328M ARG* 3.4 22.2 + - - +
329M LEU* 3.5 22.7 - - + -
334M GLY* 1.3 65.7 - - - -
336M ILE* 1.3 74.2 + - - +
339M ASN* 2.7 56.8 + - + +
340M LEU* 3.0 8.4 + - + -
1114N LEU* 4.0 22.8 - - - +
1115N THR* 4.7 4.9 + - - -
1199N ALA* 3.8 19.7 - - - +
1202N LEU* 2.8 33.9 - - - +
1203N LEU* 3.9 17.5 - - + +
1206N GLU* 3.0 34.7 + - - +
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Residues in contact with ILE 336 (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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329M LEU* 4.3 8.0 + - + +
331M GLY* 6.2 0.2 - - - -
334M GLY 2.7 4.7 + - - +
335M ARG* 1.3 83.3 - - - +
337M ARG* 1.3 60.9 + - + +
340M LEU* 3.4 12.1 + - + +
341M MET* 3.1 26.4 + - + +
1397M LEU* 5.0 0.4 - - + -
1400M CYS* 3.6 22.0 - - - +
1401M SER* 3.7 37.2 - - - -
1405M THR* 3.7 24.2 - - + -
1409M LEU* 5.0 2.0 - - + -
1429M ILE* 4.5 10.1 - - + -
1203N LEU* 3.4 43.1 - - + -
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Residues in contact with ARG 337 (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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165 T 4.6 2.8 + - - -
175 T 3.5 28.1 + - - -
185 TT 4.1 9.5 - - - -
329M LEU 4.8 0.2 + - - -
331M GLY* 4.0 11.1 - - - -
332M LYS* 3.2 56.3 - - - +
334M GLY 2.9 6.9 + - - -
336M ILE* 1.3 85.2 - - + +
338M GLY* 1.3 55.3 + - - -
341M MET* 3.8 17.8 - - + +
342M GLY 3.9 5.0 + - - -
839M ARG* 2.9 38.2 - - - +
1401M SER* 5.3 4.7 - - - +
1402M PHE* 5.4 1.8 - - - +
1403M GLU* 4.5 12.5 - - - +
1129N ARG* 4.0 4.9 + - - -
1132N GLU* 2.7 44.7 + - + +
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Residues in contact with GLY 338 (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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333M GLU* 4.3 8.3 - - - -
334M GLY 3.2 22.3 + - - +
337M ARG* 1.3 76.0 - - - +
339M ASN* 1.3 67.7 + - - +
342M GLY 3.0 14.4 - - - +
343M LYS* 4.9 0.3 - - - -
1117N GLN* 4.8 1.9 - - - +
1129N ARG* 3.4 28.8 + - - -
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Residues in contact with ASN 339 (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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333M GLU 5.1 2.6 + - - -
334M GLY* 4.1 2.2 - - - -
335M ARG* 2.7 59.6 + - - +
337M ARG 3.6 0.2 - - - -
338M GLY* 1.3 77.5 + - - +
340M LEU* 1.3 58.8 + - - +
342M GLY 3.5 5.8 - - - -
343M LYS* 3.0 17.8 - - - +
1112N GLN* 5.0 1.9 - - - +
1115N THR* 3.4 19.5 + - - +
1117N GLN* 2.7 42.0 + - - +
1156N ASP* 3.8 1.2 - - - +
1199N ALA* 3.9 11.7 - - + +
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Residues in contact with LEU 340 (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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335M ARG* 3.0 7.9 + - + +
336M ILE* 3.5 20.6 - - + +
339M ASN* 1.3 80.2 - - - +
341M MET* 1.3 62.6 + - - +
342M GLY* 3.0 5.3 + - - -
343M LYS* 3.8 15.7 - - - +
1428M VAL* 3.8 15.9 - - - +
1429M ILE* 3.5 33.9 - - + +
1151N LEU* 4.4 2.1 - - - +
1197N PRO* 3.8 14.8 - - + -
1199N ALA* 3.4 14.6 - - + +
1200N ALA* 3.0 37.2 - - + +
1203N LEU* 3.9 29.8 - - + -
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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