Contacts of the helix formed by residues 309 - 317 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.4 33.7 - - + -
32A GLN* 3.9 28.3 - - + +
69A LEU* 4.1 12.3 - - + +
70A LEU* 4.0 6.5 - - + -
73A ILE* 3.3 29.4 - - + -
318C TYR 5.1 3.4 + - - -
323C LEU* 3.4 14.0 - - + +
291D ILE* 4.8 4.9 - - + -
299D LEU* 3.8 25.4 - - + -
307D PRO 3.9 0.6 + - - -
308D PRO* 1.3 80.5 - - + +
310D ILE* 1.3 62.5 + - - +
311D TYR* 3.3 3.4 + - - +
312D ARG* 3.6 3.1 + - - -
313D MET* 3.1 42.1 + - + +
401D BR 3.5 27.2 - - + +
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Residues in contact with ILE 310 (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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315C GLN 5.3 1.3 - - - +
316C LEU 5.0 3.1 - - - +
317C GLY* 5.0 0.7 - - - -
288D PRO* 3.5 31.6 - - + +
289D GLY* 3.7 20.6 - - - +
307D PRO* 3.6 32.2 + - + +
308D PRO 3.1 1.2 + - - -
309D PHE* 1.3 76.3 - - - +
311D TYR* 1.3 66.3 + - - +
313D MET* 3.3 5.8 + - - +
314D ARG* 3.0 61.1 + - + +
304J LYS* 5.9 2.7 - - + -
306J LEU* 4.5 10.1 - - + -
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Residues in contact with TYR 311 (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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61B VAL 4.7 1.8 - - - -
64B PRO* 3.1 8.3 - - - +
65B TYR* 3.1 58.7 + + + -
68B ASN* 3.0 30.7 + - - -
316C LEU* 3.2 37.6 + - + +
317C GLY* 4.8 1.6 - - - -
318C TYR 4.3 16.1 + - - +
320C PRO* 3.9 18.4 - - + -
309D PHE 3.3 1.2 - - - +
310D ILE* 1.3 80.4 - - - +
312D ARG* 1.3 63.6 + - + +
314D ARG* 3.3 22.0 - - + +
315D GLN* 3.1 31.9 + - + +
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Residues in contact with ARG 312 (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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68A ASN* 3.5 26.3 + - - +
69A LEU* 4.3 17.5 + - + -
61B VAL* 3.6 32.0 - - + +
320C PRO* 3.8 28.3 - - + -
324C LYS* 3.7 14.5 - - - +
309D PHE 3.6 3.7 + - - +
310D ILE 3.3 0.2 - - - -
311D TYR* 1.3 74.9 - - + +
313D MET* 1.3 62.3 + - - +
314D ARG 3.1 1.8 - - - -
315D GLN* 2.8 28.5 + - - +
316D LEU* 2.7 58.2 + - + +
401D BR 4.1 11.9 - - + -
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Residues in contact with MET 313 (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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32A GLN* 3.5 45.1 - - + +
65A TYR* 3.4 23.6 - - - +
69A LEU* 3.9 18.4 - - + +
286D PHE* 4.3 6.3 - - + -
288D PRO* 3.7 25.6 - - + -
309D PHE* 3.1 34.8 + - + +
310D ILE* 3.3 4.9 + - - +
312D ARG* 1.3 75.5 - - - +
314D ARG* 1.3 54.5 + - - +
316D LEU* 4.4 1.6 - - - +
317D GLY* 2.7 37.4 + - - +
319D PRO* 4.8 2.0 - - - -
306J LEU* 3.7 22.1 - - + +
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Residues in contact with ARG 314 (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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315C GLN* 2.7 31.9 + - - +
316C LEU* 4.0 13.7 + - - +
310D ILE* 3.0 35.6 + - - +
311D TYR* 3.3 16.8 - - + +
312D ARG 3.1 0.6 - - - -
313D MET* 1.3 76.3 - - - +
315D GLN* 1.3 59.9 + - + +
304J LYS* 3.8 23.0 + - - +
305J SER* 4.3 10.7 + - - +
306J LEU* 3.7 17.7 - - + +
307J PRO* 3.5 24.5 - - + +
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Residues in contact with GLN 315 (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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61B VAL* 5.3 3.0 + - - +
64B PRO* 4.1 17.9 - - - +
311D TYR* 3.1 49.3 + - + +
312D ARG* 2.8 31.1 + - - +
314D ARG* 1.3 78.4 - - + +
316D LEU* 1.3 66.0 + - + +
317D GLY 3.2 2.3 + - - -
307J PRO* 5.4 1.0 - - - +
310J ILE* 4.6 1.7 - - - +
314J ARG* 2.9 28.8 + - - +
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Residues in contact with LEU 316 (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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65A TYR* 3.9 23.3 - - + +
68A ASN* 4.2 15.5 - - + +
69A LEU* 4.1 44.2 - - + +
312D ARG* 2.7 51.4 + - - +
315D GLN* 1.3 75.6 - - + +
317D GLY* 1.3 58.6 + - - +
310J ILE* 3.9 5.0 - - - +
311J TYR* 3.5 41.0 + - + +
314J ARG* 4.5 6.6 + - - +
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Residues in contact with GLY 317 (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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65A TYR* 2.9 24.4 + - - -
313D MET 2.7 21.8 + - - +
314D ARG 4.1 0.4 + - - -
315D GLN 3.2 3.6 + - - -
316D LEU* 1.3 76.0 - - - +
318D TYR* 1.3 64.4 + - - -
319D PRO* 3.8 0.7 - - - +
306J LEU* 4.6 1.8 - - - -
307J PRO* 3.2 26.0 - - - -
310J ILE* 4.3 4.9 - - - -
311J TYR 4.7 0.7 - - - -
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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