Contacts of the helix formed by residues 309 - 317 (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 PHE 309 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D TYR 4.9 4.4 + - - -
323D LEU* 5.1 5.8 - - + -
29I LEU* 3.8 22.7 - - + -
32I GLN* 3.9 24.5 - - + +
69I LEU* 4.5 11.4 - - + -
70I LEU* 4.5 13.7 - - + -
73I ILE* 4.5 16.8 - - + -
291J ILE* 4.2 12.6 - - + -
299J LEU* 3.5 35.9 - - + -
307J PRO 3.9 0.2 + - - -
308J PRO* 1.3 89.7 - - + +
310J ILE* 1.3 64.0 + - - +
311J TYR 3.3 2.9 - - - +
312J ARG* 3.5 3.1 + - - +
313J MET* 3.0 39.8 + - - +
401J BR 3.6 32.0 - - + +
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Residues in contact with ILE 310 (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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315D GLN 4.6 1.1 - - - +
316D LEU 3.9 10.8 - - - +
317D GLY* 4.3 2.0 - - - -
288J PRO* 4.1 29.4 - - + -
289J GLY* 4.2 7.2 - - - +
307J PRO* 3.5 40.1 + - + +
308J PRO 3.0 7.9 + - - +
309J PHE* 1.3 78.3 - - - +
311J TYR* 1.3 63.8 + - - +
313J MET* 3.3 7.5 + - + +
314J ARG* 2.9 66.9 + - - +
306N LEU* 5.4 6.3 - - + -
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Residues in contact with TYR 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL 4.6 2.9 - - - -
64A PRO* 2.8 21.1 + - + +
65A TYR* 3.5 50.0 - + + -
68A ASN* 2.8 28.9 + - + -
316D LEU* 3.5 33.7 + - + +
317D GLY* 4.7 1.2 - - - -
318D TYR 4.4 5.1 + - - +
320D PRO* 3.8 23.3 - - + -
309J PHE 3.3 0.8 - - - +
310J ILE* 1.3 81.5 - - - +
312J ARG* 1.3 65.3 + - + +
314J ARG* 3.5 15.0 + - + +
315J GLN* 3.2 43.7 + - + +
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Residues in contact with ARG 312 (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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61A VAL* 3.6 36.5 - - - +
64A PRO* 6.3 0.4 - - - +
320D PRO* 3.8 13.2 - - + -
68I ASN* 3.5 25.0 + - - +
69I LEU* 3.7 20.9 + - + +
309J PHE 3.5 2.0 + - - +
310J ILE 3.3 0.4 - - - -
311J TYR* 1.3 76.2 - - - +
313J MET* 1.3 59.9 + - - +
315J GLN* 2.8 30.4 + - - +
316J LEU* 2.8 63.5 + - + +
401J BR 3.2 27.6 - - + -
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Residues in contact with MET 313 (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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32I GLN* 4.1 25.8 - - - +
65I TYR* 3.6 17.9 - - - +
69I LEU* 3.8 16.8 - - + +
286J PHE* 3.8 6.3 - - + -
288J PRO* 3.8 19.3 - - + +
309J PHE* 3.0 28.0 + - - +
310J ILE* 3.8 5.2 - - + +
312J ARG* 1.3 76.2 - - - +
314J ARG* 1.3 57.8 + - - +
316J LEU* 4.4 0.9 - - - +
317J GLY* 2.8 31.0 + - - +
319J PRO* 3.8 26.0 - - + -
306N LEU* 3.4 39.4 - - + +
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Residues in contact with ARG 314 (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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315D GLN 2.9 26.7 + - - -
316D LEU* 4.5 8.2 - - - +
310J ILE* 2.9 48.6 + - + +
311J TYR* 3.6 13.5 - - + +
312J ARG 3.1 0.2 - - - -
313J MET* 1.3 76.2 - - - +
315J GLN* 1.3 61.2 + - + +
305N SER* 3.9 33.1 - - - +
306N LEU* 3.6 17.4 - - + +
307N PRO* 4.1 17.4 - - - +
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Residues in contact with GLN 315 (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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64A PRO* 3.5 21.3 - - - +
311J TYR* 3.2 52.4 + - + +
312J ARG* 2.8 30.7 + - - +
314J ARG* 1.3 79.6 - - + +
316J LEU* 1.3 66.6 + - + +
317J GLY* 3.2 2.4 + - - -
307N PRO* 5.7 1.2 - - - +
314N ARG* 3.3 22.7 + - - -
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Residues in contact with LEU 316 (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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65I TYR* 3.8 23.3 - - + +
68I ASN* 4.2 9.2 - - + -
69I LEU* 3.9 43.1 - - + +
312J ARG* 2.8 51.4 + - - +
315J GLN* 1.3 75.2 - - + +
317J GLY* 1.3 57.9 + - - +
310N ILE* 5.8 0.2 - - - -
311N TYR* 3.2 48.6 + - + +
314N ARG* 4.6 4.9 + - - +
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Residues in contact with GLY 317 (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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65I TYR* 2.7 25.4 + - - -
313J MET* 2.8 16.8 + - - +
314J ARG 4.3 0.2 - - - -
315J GLN 3.2 3.4 - - - -
316J LEU* 1.3 79.6 - - - +
318J TYR* 1.3 65.0 + - - -
319J PRO* 3.8 0.5 - - - +
306N LEU* 4.8 1.6 - - - -
307N PRO* 3.1 24.7 - - - -
310N ILE* 5.4 1.8 - - - -
311N TYR* 4.8 4.9 - - - -
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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