Contacts of the helix formed by residues 319 - 323 (chain J) in PDB entry 5LXY
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 PRO 319 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32I GLN 3.5 20.6 - - - +
33I ALA 3.0 23.8 - - - +
65I TYR* 3.6 27.8 - - + +
286J PHE* 3.5 25.4 - - + -
313J MET* 3.8 14.8 - - + -
317J GLY 3.4 0.6 - - - -
318J TYR* 1.3 83.9 - - + +
320J PRO* 1.3 65.5 - - - +
321J GLY 3.2 0.4 - - - -
322J TRP* 3.0 23.3 + - + +
323J LEU* 3.6 6.9 + - - +
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Residues in contact with PRO 320 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I ALA 4.8 0.6 - - - -
59I HIS* 5.2 1.0 - - - -
61I VAL* 4.3 27.4 - - + +
62I SER* 5.9 0.2 - - - -
65I TYR* 4.7 7.0 - - + -
318J TYR 3.1 6.3 - - - +
319J PRO* 1.3 71.3 - - - +
321J GLY* 1.3 62.5 + - - +
322J TRP 3.3 1.0 + - - -
323J LEU* 3.3 20.2 + - + +
73M ILE* 5.7 0.5 - - - +
311N TYR* 5.1 14.6 - - + -
312N ARG* 5.4 4.5 - - + -
401N BR 3.9 25.6 - - + -
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Residues in contact with GLY 321 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I ALA 4.6 1.6 + - - -
34I GLY* 4.8 0.4 - - - -
35I PRO* 3.2 23.8 - - - +
58I LYS* 4.8 1.9 + - - +
59I HIS* 3.6 28.4 + - - -
61I VAL* 5.6 0.4 - - - -
62I SER* 3.1 30.2 + - - +
319J PRO 3.2 1.4 - - - -
320J PRO* 1.3 78.6 - - - +
322J TRP* 1.3 58.4 + - - +
323J LEU 4.8 2.1 - - - +
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Residues in contact with TRP 322 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I HIS* 2.8 39.9 + - + -
32I GLN 3.7 1.4 + - - -
34I GLY* 3.2 13.4 - - - +
35I PRO* 3.6 38.1 - - + -
286J PHE* 3.5 59.8 - + + -
318J TYR* 6.5 0.2 - - + -
319J PRO* 3.0 32.0 + - + +
321J GLY* 1.3 75.8 - - - +
323J LEU* 1.3 65.2 + - - +
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Residues in contact with LEU 323 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I HIS* 5.9 2.3 + - - -
318J TYR* 6.4 1.6 - - + -
319J PRO 3.6 5.2 + - - +
320J PRO* 3.3 19.0 + - + +
321J GLY 4.8 1.7 - - - +
322J TRP* 1.3 82.8 - - - +
72M GLY 4.5 4.0 - - - +
73M ILE* 4.1 26.4 - - + +
74M LYS* 4.3 39.8 + - - +
299N LEU* 5.9 7.2 - - - -
308N PRO* 5.6 9.6 - - + -
309N PHE* 6.2 0.7 - - + -
401N BR 4.6 9.6 - - + -
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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