Contacts of the helix formed by residues 1414 - 1421 (chain E) in PDB entry 6BAA
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 PRO1414 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1412E LYS 4.6 2.2 - - - +
1413E LEU* 1.3 81.9 - - + +
1415E LEU* 1.3 64.2 + - - +
1416E HIS* 3.4 2.2 - - + +
1417E THR* 3.4 13.5 + - - +
1418E LEU* 3.0 23.0 + - - +
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Residues in contact with LEU1415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1394E ARG* 5.9 6.7 - - + -
1410E ILE 5.0 5.2 - - - +
1413E LEU 3.1 8.1 + - - +
1414E PRO* 1.3 72.0 - - - +
1416E HIS* 1.3 58.6 + - - +
1418E LEU* 4.3 5.4 - - - -
1419E ARG* 2.9 37.2 + - + +
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Residues in contact with HIS1416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513E ALA* 5.4 0.2 - - - +
1414E PRO* 3.4 1.5 - - + -
1415E LEU* 1.3 80.0 - - - +
1417E THR* 1.3 60.9 + - - +
1420E SER* 3.2 23.0 + - - -
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Residues in contact with THR1417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1414E PRO* 3.4 16.2 + - - +
1416E HIS* 1.3 78.3 - - - +
1418E LEU* 1.3 66.7 + - - +
1420E SER* 3.8 2.6 - - - -
1421E ARG* 3.0 25.4 + - - +
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Residues in contact with LEU1418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1410E ILE* 4.7 16.2 - - + +
1413E LEU* 3.7 22.7 - - + -
1414E PRO 3.0 19.4 + - - +
1415E LEU* 3.9 4.5 - - - +
1417E THR* 1.3 76.4 - - - +
1419E ARG* 1.3 59.3 + - - +
1421E ARG* 3.0 24.9 + - - +
1422E LEU* 3.7 6.8 + - - +
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Residues in contact with ARG1419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511E LEU 4.2 5.6 - - - +
1392E PHE 5.9 0.7 - - - +
1393E PHE 4.2 19.3 - - - +
1394E ARG* 4.4 13.9 - - + -
1410E ILE* 5.8 2.8 - - + +
1415E LEU* 2.9 19.7 + - + +
1416E HIS* 5.7 0.2 - - - -
1418E LEU* 1.3 73.9 - - - +
1420E SER* 1.3 61.3 + - - +
1422E LEU* 3.4 23.2 + - - +
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Residues in contact with SER1420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510E LYS 6.1 0.4 - - - -
511E LEU 4.9 4.7 - - - +
512E TYR* 4.4 9.9 - - - +
513E ALA* 3.4 32.1 - - - +
1416E HIS 3.2 22.6 + - - -
1417E THR* 3.5 3.8 + - - -
1418E LEU 3.3 0.6 - - - -
1419E ARG* 1.3 78.9 - - - +
1421E ARG* 1.3 62.0 + - - +
1422E LEU 3.4 5.3 + - - +
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Residues in contact with ARG1421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1417E THR 3.0 16.2 + - - +
1418E LEU* 3.0 11.0 + - - +
1420E SER* 1.3 77.5 - - - +
1422E LEU* 1.3 56.2 + - - +
1423E SER 4.1 1.3 + - - -
1500E THR* 5.7 3.1 - - - -
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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