Contacts of the helix formed by residues 2519 - 2527 (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 LEU2519 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2464D LEU* 5.4 15.3 - - + -
2468D VAL* 6.0 7.0 - - + -
2507D LEU* 5.3 13.9 - - + -
2518D PHE* 1.3 74.3 - - - +
2520D LEU* 1.3 58.1 + - - +
2521D HIS 3.4 2.5 - - - -
2522D VAL* 3.5 33.2 + - + +
2523D LEU* 2.9 34.6 + - + +
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Residues in contact with LEU2520 (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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2518D PHE* 3.3 25.3 + - + +
2519D LEU* 1.3 78.3 - - - +
2521D HIS* 1.3 61.8 + - + +
2523D LEU* 3.3 5.7 + - - +
2524D ASP* 2.9 36.9 + - + +
2569D LEU 4.3 4.7 - - - +
2570D PHE* 3.6 45.8 - - + -
2571D ALA* 3.7 26.2 - - + +
2580D VAL* 5.1 11.7 - - + -
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Residues in contact with HIS2521 (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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2518D PHE* 5.0 4.1 + - + +
2519D LEU 3.4 0.6 - - - -
2520D LEU* 1.3 81.6 - - + +
2522D VAL* 1.3 62.4 + - + +
2524D ASP* 3.2 7.4 + - - +
2525D VAL* 2.9 30.0 + - - +
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Residues in contact with VAL2522 (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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2468D VAL* 3.7 30.3 - - + -
2471D ILE* 5.8 0.5 - - - +
2519D LEU* 3.5 31.9 + - + -
2520D LEU 3.4 0.4 - - - -
2521D HIS* 1.3 78.2 - - + +
2523D LEU* 1.3 58.1 + - - +
2525D VAL* 3.2 14.5 - - + +
2526D GLY* 2.9 26.3 + - - -
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Residues in contact with LEU2523 (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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2471D ILE* 6.2 1.1 - - - -
2519D LEU* 2.9 26.0 + - + +
2520D LEU* 3.6 8.1 - - + +
2522D VAL* 1.3 77.2 - - - +
2524D ASP* 1.3 59.8 + - - +
2526D GLY* 5.1 0.4 - - - -
2527D PHE* 3.0 45.4 + - + +
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Residues in contact with ASP2524 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2520D LEU* 2.9 24.1 + - + +
2521D HIS* 3.2 6.9 + - - +
2523D LEU* 1.3 76.2 - - - +
2525D VAL* 1.3 64.9 + - - +
2526D GLY 3.4 0.2 + - - -
2527D PHE* 3.7 17.4 + - - +
2579D MET 5.7 12.1 - - - +
2580D VAL* 6.0 2.5 - - - -
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Residues in contact with VAL2525 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2521D HIS 2.9 16.7 + - - +
2522D VAL* 3.2 26.5 - - + +
2524D ASP* 1.3 77.4 - - - +
2526D GLY* 1.3 62.6 + - - +
2527D PHE 4.6 1.4 - - - -
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Residues in contact with GLY2526 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2471D ILE* 4.0 32.5 - - - +
2472D SER* 5.0 9.7 - - - -
2500D LYS* 4.7 7.1 + - - -
2522D VAL 2.9 16.8 + - - -
2523D LEU 4.0 0.7 - - - -
2524D ASP 3.2 0.2 - - - -
2525D VAL* 1.3 82.7 - - - +
2527D PHE* 1.3 60.7 + - - +
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Residues in contact with PHE2527 (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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2471D ILE* 4.4 21.1 - - + -
2500D LYS* 5.5 4.5 - - + +
2504D VAL* 3.5 26.2 - - + -
2507D LEU* 6.3 4.0 - - + -
2523D LEU* 3.0 39.6 + - + +
2524D ASP* 3.8 14.1 - - - +
2525D VAL 3.6 1.8 - - - -
2526D GLY* 1.3 81.5 - - - +
2554D TYR* 3.3 28.5 - + - -
2559D VAL* 4.0 26.5 - - + -
2562D LEU* 4.8 19.1 - - + -
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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