Contacts of the helix formed by residues 336 - 348 (chain C) in PDB entry 5JLH
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 TYR 336 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C MET* 5.1 5.2 - - + +
17C LYS* 3.5 28.3 - - + +
26C PRO* 4.9 16.4 - - + -
29C VAL* 4.5 23.5 - - + +
333C GLU* 3.2 26.0 + - + +
334C ARG 3.1 0.6 - - - -
335C LYS* 1.4 108.5 + - + +
337C SER* 1.3 64.9 + - - +
338C VAL 3.2 2.2 - - - -
339C TRP* 2.8 17.3 + - + -
340C ILE* 3.0 24.9 + - + +
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Residues in contact with SER 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C SER* 3.7 27.1 - - - -
143C ALA* 3.3 18.9 - - - +
144C SER* 5.3 2.3 + - - -
298C LEU 5.0 0.9 + - - -
299C SER* 4.3 6.2 - - - -
331C PRO* 4.7 6.9 - - - +
333C GLU 3.5 3.7 + - - -
334C ARG* 2.9 36.6 + - - +
335C LYS 3.3 0.6 - - - -
336C TYR* 1.3 76.2 - - - +
338C VAL* 1.3 64.4 + - - +
340C ILE* 3.2 5.3 + - - +
341C GLY* 2.9 19.6 + - - -
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Residues in contact with VAL 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ASP* 3.2 29.8 - - + +
17C LYS* 5.1 2.7 - - - +
105C THR* 3.3 29.4 - - + +
136C GLN* 3.8 25.6 - - + +
139C LEU* 3.6 19.1 - - + +
140C SER* 4.3 3.8 - - - +
153C ASP* 5.3 1.1 - - - +
299C SER* 4.6 16.4 - - - +
300C GLY* 5.4 3.1 - - - +
335C LYS 4.8 1.9 + - - +
336C TYR 3.0 0.6 + - - -
337C SER* 1.3 77.1 - - - +
339C TRP* 1.3 64.0 + - - +
341C GLY* 3.2 1.7 + - - -
342C GLY 2.9 17.7 + - - -
401C ADP 5.3 0.2 - - - +
402C MG 4.2 13.9 - - - -
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Residues in contact with TRP 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 3.1 39.5 + - + +
10C ASP* 4.3 8.4 + - + -
17C LYS* 3.1 41.9 - - + +
18C ALA 3.5 0.4 - - - -
19C GLY* 3.3 36.0 - - - +
20C PHE 3.5 20.0 - - - -
23C ASP 3.6 18.8 - - - -
24C ASP 4.1 1.6 - - - -
25C ALA* 3.3 14.8 - - - -
26C PRO* 3.2 44.0 - - + -
336C TYR 2.8 9.2 + - - +
338C VAL* 1.3 81.3 - - - +
340C ILE* 1.3 70.9 + - + +
342C GLY* 3.0 3.8 + - - -
343C SER* 2.9 25.6 + - - -
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Residues in contact with ILE 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ASP* 3.8 22.4 - - - +
26C PRO* 5.5 0.7 - - + -
143C ALA* 3.8 20.2 - - + +
333C GLU* 3.6 34.3 - - + +
336C TYR* 3.0 26.0 + - + +
337C SER* 3.7 10.1 - - - +
339C TRP* 1.3 82.6 - - + +
341C GLY* 1.3 64.8 + - - +
343C SER* 2.6 30.8 + - - +
344C ILE* 2.9 9.7 + - + +
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Residues in contact with GLY 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 3.1 34.0 - - - +
143C ALA* 3.7 3.7 - - - +
337C SER 2.9 10.5 + - - -
338C VAL 3.6 2.9 - - - -
340C ILE* 1.3 77.4 - - - +
342C GLY* 1.3 60.6 + - - +
344C ILE* 2.9 28.9 - - - +
345C LEU* 2.9 13.0 + - - +
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Residues in contact with GLY 342 (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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8C VAL* 3.8 9.3 - - - +
103C LEU* 3.3 31.3 - - - +
139C LEU* 3.6 10.9 - - - +
338C VAL 2.9 11.3 + - - -
339C TRP 3.0 5.1 + - - -
341C GLY* 1.3 77.0 - - - +
343C SER* 1.3 55.9 + - - +
345C LEU* 3.2 1.1 + - - -
346C ALA* 2.9 28.8 + - - +
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Residues in contact with SER 343 (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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8C VAL* 4.1 2.8 - - - +
21C ALA* 4.1 11.3 - - - +
22C GLY* 3.7 10.2 + - - -
23C ASP 3.3 26.0 + - - -
24C ASP* 5.2 0.2 - - - -
339C TRP* 2.9 25.4 + - - -
340C ILE* 2.6 25.3 + - - +
342C GLY* 1.3 75.9 - - - +
344C ILE* 1.3 63.1 + - - +
346C ALA* 3.4 0.9 + - - -
347C SER* 2.6 34.0 + - - -
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Residues in contact with ILE 344 (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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142C TYR* 3.8 38.4 - - + +
143C ALA* 5.0 2.7 - - - -
145C GLY* 6.5 0.2 - - - -
340C ILE* 2.9 8.7 + - + +
341C GLY* 2.9 34.3 - - - +
343C SER* 1.3 82.4 + - - +
345C LEU* 1.3 63.0 + - - +
347C SER* 3.2 9.0 + - - -
348C LEU* 3.0 43.3 + - + +
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Residues in contact with LEU 345 (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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103C LEU* 4.6 6.5 - - + -
132C TYR* 5.1 2.5 - - + -
134C ALA* 5.1 8.1 - - + -
138C VAL* 5.8 1.3 - - + -
139C LEU* 4.4 18.4 - - + -
142C TYR* 3.3 54.3 - - + +
341C GLY 2.9 15.8 + - - +
342C GLY* 3.2 6.7 + - - +
344C ILE* 1.3 78.1 - - - +
346C ALA* 1.3 62.6 + - - +
348C LEU* 3.1 19.4 + - + +
351C PHE* 3.2 50.0 - - + +
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Residues in contact with ALA 346 (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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6C ALA* 3.8 17.6 - - + +
8C VAL* 4.4 6.1 - - + -
21C ALA* 3.5 27.4 - - + -
103C LEU* 4.9 2.4 - - + +
342C GLY 2.9 12.9 + - - +
345C LEU* 1.3 78.7 - - - +
347C SER* 1.3 59.9 + - - +
348C LEU 3.2 6.0 + - - +
351C PHE* 3.8 10.3 - - + -
352C GLN* 4.2 16.8 + - - +
355C TRP* 4.0 16.9 - - + -
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Residues in contact with SER 347 (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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3C GLU* 5.4 6.1 - - - +
21C ALA* 4.0 0.8 - - - -
22C GLY* 3.2 27.2 + - - -
343C SER 2.6 23.1 + - - -
344C ILE* 3.5 10.2 - - - -
345C LEU 3.1 0.4 - - - -
346C ALA* 1.3 73.9 - - - +
348C LEU* 1.3 66.3 + - - +
349C SER* 3.4 4.9 + - - -
352C GLN* 5.6 2.6 + - - -
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Residues in contact with LEU 348 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C TYR* 4.7 20.9 - - + +
344C ILE* 3.0 43.3 + - + +
345C LEU* 3.1 18.3 + - + +
346C ALA 3.8 1.2 - - - +
347C SER* 1.3 80.2 - - - +
349C SER* 1.3 65.2 + - - +
350C THR* 4.7 4.0 - - - +
351C PHE* 3.5 23.0 + - + +
352C GLN* 3.7 10.9 + - - +
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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