Contacts of the helix formed by residues 309 - 317 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.5 31.9 - - + -
32B GLN* 4.1 28.7 - - + +
69B LEU* 4.3 9.9 - - + -
70B LEU* 3.7 20.6 - - + -
73B ILE* 4.2 14.4 - - + -
289C GLY* 4.7 3.1 - - - -
291C ILE* 4.5 5.6 - - + -
299C LEU* 4.0 18.6 - - + -
308C PRO* 1.3 93.9 - - + +
310C ILE* 1.3 65.2 + - - +
311C TYR 3.3 2.2 - - - -
312C ARG* 3.2 7.8 + - - +
313C MET* 2.9 41.4 + - + +
401C BR 3.5 19.5 - - + -
323F LEU* 4.2 11.2 - - + -
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Residues in contact with ILE 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C PRO* 3.8 36.6 - - + +
289C GLY* 4.0 8.0 - - - +
307C PRO* 3.9 28.0 - - + -
308C PRO 3.4 2.4 - - - -
309C PHE* 1.3 75.8 - - - +
311C TYR* 1.3 66.8 + - - +
313C MET* 3.0 8.8 + - - -
314C ARG* 2.9 68.6 + - - +
303D ASP* 4.4 13.2 - - - +
306D LEU* 4.7 7.9 - - + -
315F GLN 4.7 0.7 - - - +
316F LEU 3.9 9.4 - - - +
317F GLY* 4.5 2.7 - - - -
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Residues in contact with TYR 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C PRO 4.8 0.8 + - - -
309C PHE 3.3 0.8 - - - -
310C ILE* 1.3 80.7 - - - +
312C ARG* 1.3 63.7 + - - +
314C ARG* 3.9 12.2 - - - +
315C GLN* 3.5 40.5 + - - +
61E VAL 4.5 2.9 - - - -
64E PRO* 3.0 36.0 + - + +
65E TYR* 3.5 39.9 - + + -
68E ASN* 3.6 25.1 + - - -
316F LEU* 3.1 38.6 + - + +
317F GLY* 4.6 1.4 - - - -
318F TYR 4.4 11.7 - - - +
320F PRO* 4.0 19.1 - - + -
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Residues in contact with ARG 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 4.0 21.2 + - - +
69B LEU* 4.4 15.6 + - + +
309C PHE 3.2 7.7 + - - +
311C TYR* 1.3 83.5 - - - +
313C MET* 1.3 61.8 + - - +
314C ARG 3.3 0.2 - - - -
315C GLN* 3.4 28.4 + - - +
316C LEU* 3.2 47.8 + - + +
401C BR 3.8 19.3 - - + -
61E VAL* 4.1 30.7 - - - +
320F PRO* 4.7 9.3 - - + +
324F LYS* 4.7 12.6 - - - +
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Residues in contact with MET 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLN* 4.0 22.9 - - + +
65B TYR* 3.1 23.8 - - - +
69B LEU* 3.6 34.9 - - + +
286C PHE* 4.6 8.1 - - - -
288C PRO* 4.1 25.4 - - - -
289C GLY 5.4 0.2 - - - +
309C PHE* 2.9 30.7 + - + +
310C ILE* 3.0 8.3 + - - +
312C ARG* 1.3 74.6 - - - +
314C ARG* 1.3 55.2 + - - +
316C LEU* 3.7 1.3 - - - +
317C GLY 2.8 42.2 + - - +
319C PRO* 4.6 4.5 - - + -
306D LEU* 3.8 18.3 - - + +
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Residues in contact with ARG 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C ILE* 2.9 40.9 + - + +
311C TYR* 3.9 10.3 - - - +
313C MET* 1.3 76.7 - - - +
315C GLN* 1.3 60.6 + - + +
317C GLY 3.7 0.2 + - - -
303D ASP* 4.7 6.1 + - - -
305D SER* 2.8 37.2 + - - +
306D LEU* 3.6 21.1 - - + -
307D PRO* 3.1 29.3 - - - +
315F GLN 3.2 27.7 + - - -
316F LEU* 4.0 16.4 + - - +
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Residues in contact with GLN 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C TYR* 3.5 47.4 + - + +
312C ARG* 3.4 26.8 + - - +
313C MET 3.2 0.6 - - - -
314C ARG* 1.3 79.1 - - + +
316C LEU* 1.3 58.3 + - - +
317C GLY* 3.1 1.7 + - - -
307D PRO* 5.9 0.2 - - - +
310D ILE* 5.3 1.0 - - - +
314D ARG* 2.7 36.1 + - - +
64E PRO* 4.1 14.7 - - - +
68E ASN* 5.8 0.2 - - - +
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B TYR* 3.6 28.9 - - + +
68B ASN* 4.1 14.8 - - + +
69B LEU* 4.1 38.4 - - + +
312C ARG* 3.2 41.9 + - + +
313C MET 3.9 0.2 - - - +
315C GLN* 1.3 78.8 - - + +
317C GLY* 1.3 58.2 + - - +
310D ILE* 4.5 1.0 - - - -
311D TYR* 3.2 44.9 + - + +
314D ARG* 4.0 11.5 + - - +
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Residues in contact with GLY 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B TYR* 2.8 25.8 + - - -
313C MET* 2.8 14.2 + - - +
314C ARG 3.7 0.8 + - - -
315C GLN 3.1 4.4 - - - -
316C LEU* 1.3 79.6 - - - +
318C TYR* 1.3 64.5 + - - -
319C PRO* 3.9 0.2 - - - +
306D LEU* 5.0 1.1 - - - -
307D PRO* 3.3 27.6 - - - -
310D ILE* 5.0 2.2 - - - -
311D TYR* 4.8 4.5 - - - -
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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