Contacts of the helix formed by residues 1739 - 1745 (chain D) in PDB entry 6X34
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 THR1739 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1737D PRO* 3.3 27.1 + - - +
1738D LEU* 1.3 76.9 - - - +
1740D PRO* 1.3 70.5 - - + +
1741D GLU* 3.5 23.1 - - + +
1742D THR* 2.9 35.5 + - - -
1743D ARG* 3.7 2.9 + - - +
2147D PRO* 5.0 5.5 - - + +
2150D VAL* 5.6 1.2 - - - +
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Residues in contact with PRO1740 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1738D LEU 3.7 7.0 - - - +
1739D THR* 1.3 90.3 - - + +
1741D GLU* 1.3 59.6 + - - +
1743D ARG* 3.3 22.0 + - + +
1744D ALA* 4.2 2.8 + - - +
2147D PRO* 5.2 8.3 - - + -
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Residues in contact with GLU1741 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1739D THR* 3.1 16.2 - - + +
1740D PRO* 1.3 78.9 - - - +
1742D THR* 1.3 61.8 + - - +
1743D ARG 3.2 0.7 + - - -
1744D ALA* 3.5 18.1 + - - +
1745D ILE 4.5 1.2 + - - -
1768D VAL* 5.0 8.4 - - - +
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Residues in contact with THR1742 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1736D VAL* 5.5 8.3 - - - -
1737D PRO* 6.2 0.7 - - - -
1738D LEU* 5.7 0.4 - - - -
1739D THR* 2.9 24.9 + - - -
1741D GLU* 1.3 75.8 - - - +
1743D ARG* 1.3 62.8 + - - +
1744D ALA 3.2 0.7 - - - -
1745D ILE* 3.3 19.7 + - - +
1768D VAL* 5.6 2.0 - - - -
1770D THR* 3.7 32.8 - - - +
1957D GLU 5.3 1.8 - - - +
1961D ALA* 3.7 16.1 - - - +
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Residues in contact with ARG1743 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1739D THR 3.7 3.1 + - - +
1740D PRO* 3.3 17.2 + - + +
1741D GLU 3.2 0.8 - - - -
1742D THR* 1.3 79.0 - - - +
1744D ALA* 1.3 59.4 + - - +
1745D ILE 3.2 3.1 + - - +
1961D ALA* 4.2 10.7 - - + +
1965D ARG* 2.8 37.2 + - + +
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Residues in contact with ALA1744 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1740D PRO 4.2 2.3 + - - +
1741D GLU* 3.5 14.4 + - - +
1742D THR 3.2 1.2 - - - -
1743D ARG* 1.3 76.8 - - - +
1745D ILE* 1.3 62.7 + - - +
1746D THR* 3.7 4.2 + - - -
1768D VAL* 6.5 0.2 - - + -
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Residues in contact with ILE1745 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1741D GLU 4.5 1.0 + - - -
1742D THR* 3.3 15.3 + - - +
1743D ARG 3.2 11.5 - - - +
1744D ALA* 1.3 81.0 - - - +
1746D THR* 1.3 59.3 + - - +
1768D VAL* 4.2 25.0 - - + +
1770D THR* 5.8 4.0 - - + -
1954D HIS* 4.6 16.8 - - + +
1957D GLU* 6.1 2.7 - - + -
1958D SER* 4.2 11.5 + - - +
1961D ALA* 4.8 4.7 - - - +
1965D ARG* 4.3 8.0 + - - -
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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
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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