Contacts of the helix formed by residues 1506 - 1511 (chain H) in PDB entry 6C3P
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 GLU1506 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1426H GLN* 3.1 34.2 + - - +
1505H ASP* 1.3 66.5 - - - +
1507H ALA* 1.3 65.7 + - - +
1508H THR 3.0 4.2 + - - -
1509H ALA* 3.1 10.0 + - - +
1535H ILE* 3.1 38.7 + - + +
1536H ALA* 4.2 0.7 - - - +
1537H HIS* 3.5 33.4 - - + +
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Residues in contact with ALA1507 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1424H ILE* 3.6 19.3 - - + -
1425H LEU 4.9 0.2 - - - -
1426H GLN 5.1 0.6 - - - +
1487H GLN* 3.3 19.7 - - - +
1491H LEU* 3.6 31.2 - - + -
1504H MET* 4.4 15.6 - - + +
1505H ASP 3.1 5.8 + - - +
1506H GLU* 1.3 77.7 - - - +
1508H THR* 1.3 58.3 + - - +
1509H ALA 3.2 1.8 + - - -
1510H SER 4.0 1.4 + - - -
1511H ILE* 3.1 18.4 - - - +
1535H ILE 4.2 2.8 + - - -
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Residues in contact with THR1508 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491H LEU* 6.3 0.2 - - - -
1506H GLU 3.0 1.6 + - - -
1507H ALA* 1.3 74.7 - - - +
1509H ALA* 1.3 64.7 + - - +
1510H SER 3.2 3.6 - - - -
1511H ILE* 2.9 34.1 + - - +
1516H GLU* 4.2 29.3 - - - +
1519H LEU* 6.5 1.3 - - - -
1536H ALA* 6.4 1.6 - - - -
1537H HIS 6.3 1.3 - - - -
1538H ARG* 4.8 11.8 + - - +
1541H THR* 4.9 9.2 - - - -
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Residues in contact with ALA1509 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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857H SER* 3.6 34.7 + - - +
888H HIS* 4.4 9.5 - - - +
1426H GLN* 3.6 17.0 - - - +
1506H GLU 3.1 16.8 + - - +
1507H ALA 3.2 0.4 - - - -
1508H THR* 1.3 77.7 - - - +
1510H SER* 1.3 61.6 + - - +
1511H ILE 3.4 3.8 + - - +
1537H HIS* 4.1 20.2 - - + +
1538H ARG* 5.0 11.6 + - - +
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Residues in contact with SER1510 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715H VAL* 5.0 1.2 - - - +
857H SER* 3.6 15.2 + - - -
888H HIS* 3.0 29.6 - - - -
1426H GLN 5.1 2.6 + - - -
1428H PRO* 4.9 6.2 - - - +
1483H GLN* 4.6 11.3 + - - +
1484H GLY* 4.2 19.1 + - - -
1487H GLN* 4.2 32.2 + - - +
1507H ALA 4.0 2.4 + - - -
1508H THR 3.2 0.4 - - - -
1509H ALA* 1.3 78.4 - - - +
1511H ILE* 1.3 58.5 + - - +
1512H ASP 3.8 0.2 + - - -
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Residues in contact with ILE1511 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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715H VAL* 5.4 4.7 - - + -
888H HIS* 4.1 7.2 - - - +
1484H GLY* 4.9 1.8 - - - +
1487H GLN* 3.6 19.5 - - + -
1488H LEU* 3.5 28.7 - - + -
1491H LEU* 4.9 9.0 - - + -
1507H ALA 3.1 28.0 - - - +
1508H THR* 2.9 24.5 + - - +
1509H ALA 4.0 3.8 - - - +
1510H SER* 1.3 81.4 - - - +
1512H ASP* 1.3 84.0 + - - +
1515H THR* 3.8 10.5 - - + -
1516H GLU* 3.3 28.4 - - + +
1519H LEU* 5.2 4.7 - - + -
1538H ARG* 5.2 3.8 + - - -
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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