Contacts of the helix formed by residues 309 - 317 (chain N) 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 PHE 309 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M LEU* 3.4 34.1 - - + -
32M GLN* 3.1 30.5 - - - +
69M LEU* 4.5 3.6 - - + -
70M LEU* 3.5 24.2 - - + -
73M ILE* 4.4 26.5 - - + -
289N GLY* 4.8 5.8 - - - -
291N ILE* 6.0 6.3 - - + -
307N PRO 3.7 0.2 - - - -
308N PRO* 1.3 94.9 - - + +
310N ILE* 1.3 64.5 + - - +
311N TYR 3.5 0.7 - - - -
312N ARG* 3.7 4.9 + - - +
313N MET* 3.2 35.6 + - + +
401N BR 4.3 14.1 - - + -
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Residues in contact with ILE 310 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315J GLN 5.4 0.2 - - - +
316J LEU 5.2 2.0 - - - +
317J GLY* 5.4 0.4 - - - -
288N PRO* 3.4 24.0 - - + +
289N GLY* 3.4 36.3 - - - +
307N PRO* 4.4 21.3 + - + +
308N PRO 3.4 2.2 - - - -
309N PHE* 1.3 77.6 - - - +
311N TYR* 1.3 61.2 + - - +
313N MET* 3.7 7.1 - - + +
314N ARG* 2.8 75.2 + - + +
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Residues in contact with TYR 311 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I VAL 5.0 2.0 - - - -
64I PRO* 3.1 34.7 + - + +
65I TYR* 3.3 44.3 - + + -
68I ASN* 4.1 8.5 - - + +
316J LEU* 3.2 47.4 + - + +
317J GLY* 4.8 1.7 - - - -
318J TYR 4.7 11.0 - - - +
320J PRO* 5.1 12.3 - - + -
308N PRO 4.5 3.1 + - - +
309N PHE 3.5 0.2 - - - -
310N ILE* 1.3 79.8 - - - +
312N ARG* 1.3 65.7 + - + +
314N ARG* 3.5 11.4 + - - +
315N GLN* 3.5 31.7 + - - +
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Residues in contact with ARG 312 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320J PRO* 5.4 4.5 - - + +
68M ASN 6.0 0.7 - - - +
69M LEU* 5.6 8.3 - - + +
308N PRO 5.2 0.8 + - - -
309N PHE 3.7 5.3 + - - +
310N ILE 3.4 0.4 - - - -
311N TYR* 1.3 82.7 - - + +
313N MET* 1.3 58.3 + - - +
315N GLN* 3.2 15.7 - - - +
316N LEU* 2.9 45.5 + - + +
401N BR 4.3 21.3 - - + -
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Residues in contact with MET 313 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M GLN* 4.0 35.7 - - + +
33M ALA* 5.3 0.9 - - - -
65M TYR* 3.3 28.7 - - + +
69M LEU* 5.9 7.2 - - + +
70M LEU* 6.6 0.2 - - + -
286N PHE* 4.2 11.7 - - - -
288N PRO* 3.7 29.4 - - - -
309N PHE* 3.2 36.0 + - + +
310N ILE* 3.2 10.5 + - + +
312N ARG* 1.3 78.9 - - - +
314N ARG* 1.3 57.0 + - + +
316N LEU* 4.6 1.6 - - - -
317N GLY 2.9 35.3 + - - +
318N TYR* 5.7 0.4 - - - -
319N PRO* 4.8 4.9 - - + -
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Residues in contact with ARG 314 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315J GLN 3.3 25.5 + - - -
316J LEU* 4.6 5.1 + - - +
310N ILE* 2.8 46.0 + - + +
311N TYR* 4.0 5.8 - - - +
312N ARG 3.3 0.2 - - - -
313N MET* 1.3 77.6 - - + +
315N GLN* 1.3 59.9 + - - +
317N GLY* 3.9 6.7 + - - -
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Residues in contact with GLN 315 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I VAL* 6.1 3.4 - - - +
64I PRO* 4.5 18.6 - - - +
311N TYR* 3.5 32.5 + - - +
312N ARG* 3.2 20.2 + - - +
314N ARG* 1.3 78.6 - - - +
316N LEU* 1.3 77.1 + - + +
317N GLY* 3.2 2.3 + - - -
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Residues in contact with LEU 316 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65M TYR* 4.1 28.1 - - + +
68M ASN* 4.3 23.8 - - + +
69M LEU* 4.0 35.9 - - + +
312N ARG* 2.9 28.4 + - + +
313N MET* 5.0 0.2 - - - -
315N GLN* 1.3 87.3 - - + +
317N GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 317 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65M TYR* 2.6 31.7 + - - -
313N MET* 2.9 16.4 + - - +
314N ARG 3.9 6.7 + - - -
315N GLN 3.2 3.8 - - - -
316N LEU* 1.3 78.4 - - - +
318N TYR* 1.3 61.8 + - - -
319N PRO* 3.9 0.2 - - - +
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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