Contacts of the helix formed by residues 1645 - 1649 (chain L) in PDB entry 6LTJ
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 SER1645 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1641L PHE* 4.9 1.8 - - - -
1642L PRO* 2.8 24.5 + - - +
1643L PRO 3.2 1.4 - - - +
1644L GLY* 1.3 81.4 - - - +
1646L VAL* 1.3 68.7 + - - +
1647L GLU* 3.1 20.0 - - - -
1648L ALA* 2.9 18.2 + - - +
1649L THR* 3.6 3.7 + - - -
667O SER* 3.6 5.1 - - - -
669O SER* 2.2 32.7 + - - -
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Residues in contact with VAL1646 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1644L GLY 4.4 0.4 + - - -
1645L SER* 1.3 71.7 - - - +
1647L GLU* 1.3 59.1 + - - +
1649L THR* 2.7 39.6 + - - +
664O ILE* 3.3 15.9 - - + +
665O PRO 3.2 23.1 - - - +
666O PHE 3.6 17.7 - - - +
667O SER* 3.8 10.0 + - - -
463P LEU* 3.5 18.4 - - + -
196Q PHE* 3.6 5.9 - - + -
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Residues in contact with GLU1647 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1641L PHE* 3.4 35.7 - - + -
1645L SER* 3.1 5.8 + - - -
1646L VAL* 1.3 75.1 - - - +
1648L ALA* 1.3 58.3 + - - +
1649L THR 3.4 1.3 + - - +
666O PHE* 3.1 10.4 - - - -
667O SER* 2.8 44.4 + - - -
669O SER 3.2 9.1 - - - +
670O GLY* 3.3 10.4 - - - -
671O ASN* 3.5 15.5 + - - +
196Q PHE* 3.9 11.7 - - - -
197Q GLN* 4.6 11.3 + - - +
200Q HIS* 3.4 41.3 - - + +
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Residues in contact with ALA1648 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1641L PHE* 4.4 11.9 - - + +
1642L PRO 3.9 6.1 - - - +
1643L PRO* 3.7 32.0 - - + +
1645L SER 2.9 13.1 + - - +
1647L GLU* 1.3 76.2 - - - +
1649L THR* 1.3 58.9 + - - +
1650L GLN* 2.5 35.7 + - - +
197Q GLN* 5.6 2.7 - - - +
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Residues in contact with THR1649 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1645L SER 3.6 2.6 + - - -
1646L VAL* 2.7 36.3 + - - +
1647L GLU 3.4 2.3 - - - +
1648L ALA* 1.3 79.1 - - - +
1650L GLN* 1.3 75.0 + - - +
1651L PRO* 4.5 1.2 - - - +
463P LEU* 4.3 12.5 - - + +
466P MET* 3.8 14.4 - - - +
467P THR* 3.9 23.3 - - + -
193Q THR* 4.8 0.3 - - - +
196Q PHE* 4.9 3.8 - - - -
197Q GLN* 4.5 9.2 + - - -
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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