Contacts of the helix formed by residues 337 - 347 (chain C) in PDB entry 3LUE
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 337 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C MET* 5.5 0.2 - - - +
18C LYS* 3.9 20.9 - - + -
26C ALA* 5.6 4.5 - - + -
27C PRO* 4.0 32.8 - - + -
30C VAL* 3.4 22.9 - - + +
334C GLU* 2.8 4.3 + - + +
336C LYS* 1.3 119.8 + - + +
338C SER* 1.3 60.9 + - - -
339C VAL 3.4 2.5 - - - -
340C TRP* 3.1 15.8 + - + -
341C ILE* 3.1 33.5 + - + +
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Residues in contact with SER 338 (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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140C LEU 3.9 2.4 - - - +
141C SER* 3.6 30.2 + - - -
144C ALA* 4.1 6.1 - - - +
300C SER* 5.0 1.9 - - - -
332C PRO* 5.2 5.5 - - - +
334C GLU* 3.7 12.5 + - - +
335C ARG* 4.0 18.5 - - - -
336C LYS 3.7 1.8 + - - -
337C TYR* 1.3 73.1 - - - +
339C VAL* 1.3 66.5 + - - +
340C TRP 3.1 0.7 + - - -
341C ILE* 3.1 4.4 + - - +
342C GLY* 3.0 22.0 + - - -
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Residues in contact with VAL 339 (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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11C ASP* 3.4 33.0 - - - +
106C THR* 4.0 9.6 - - + -
137C GLN* 3.4 44.6 - - + +
140C LEU* 3.3 22.8 - - + +
141C SER* 3.2 23.1 - - - +
154C ASP* 4.4 2.0 - - - +
301C GLY* 5.0 13.0 - - - +
335C ARG 5.4 1.1 - - - +
336C LYS 5.4 0.4 + - - -
337C TYR 3.4 0.8 - - - -
338C SER* 1.3 74.3 - - - +
340C TRP* 1.3 63.4 + - - +
342C GLY 3.5 0.3 + - - -
343C GLY 3.4 3.6 + - - -
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Residues in contact with TRP 340 (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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9C VAL* 3.2 36.2 + - + +
11C ASP* 4.1 11.2 + - + +
18C LYS* 3.3 43.3 - - + -
19C ALA 3.7 1.0 - - - -
20C GLY* 3.4 33.6 - - - +
21C PHE 3.8 10.3 - - - -
24C ASP* 3.2 28.9 - - + -
25C ASP 3.8 1.6 - - - -
26C ALA* 3.4 25.4 - - - -
27C PRO* 3.4 26.7 - - + -
106C THR* 6.2 0.2 - - - -
337C TYR* 3.1 10.3 + - - +
339C VAL* 1.3 81.2 - - - +
341C ILE* 1.3 62.7 + - + +
343C GLY* 3.3 1.2 + - - -
344C SER* 3.0 38.3 + - - -
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Residues in contact with ILE 341 (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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24C ASP 4.4 5.6 - - - +
25C ASP 3.2 27.8 - - - +
26C ALA* 4.8 1.1 - - + -
27C PRO* 5.1 1.1 - - + -
144C ALA* 4.0 7.4 - - + -
337C TYR* 3.1 42.4 + - + +
338C SER* 4.3 3.6 - - - +
340C TRP* 1.3 86.5 - - + +
342C GLY* 1.3 62.1 + - - +
343C GLY 3.3 0.2 - - - -
344C SER* 4.0 2.2 - - - -
345C ILE* 3.2 22.6 + - + +
99K MET* 4.3 7.2 - - + -
101K PHE* 3.8 29.8 - - + -
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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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140C LEU* 3.1 32.9 - - - +
143C TYR* 4.6 6.2 - - - +
144C ALA* 3.4 12.9 - - - +
338C SER 3.0 10.1 + - - -
341C ILE* 1.3 79.0 - - - +
343C GLY* 1.3 55.7 + - - +
345C ILE* 3.7 4.1 + - - +
346C LEU* 3.2 27.2 + - - +
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Residues in contact with GLY 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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9C VAL* 3.8 14.8 - - - -
104C LEU* 4.1 6.5 - - - +
140C LEU* 3.6 22.0 - - - +
339C VAL 3.4 6.5 + - - -
340C TRP 3.3 5.4 + - - -
342C GLY* 1.3 74.4 - - - +
344C SER* 1.3 58.4 + - - +
345C ILE 3.2 0.2 + - - -
346C LEU* 3.3 4.2 + - - -
347C ALA* 2.8 33.8 + - - +
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Residues in contact with SER 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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9C VAL* 3.4 16.3 - - - +
21C PHE 3.8 0.2 + - - -
22C ALA* 3.7 5.4 - - - +
23C GLY* 3.1 10.9 + - - -
24C ASP 2.7 42.4 + - - -
340C TRP* 3.0 32.8 + - - -
341C ILE* 3.9 5.7 - - - +
343C GLY* 1.3 74.0 - - - +
345C ILE* 1.3 49.3 + - - +
347C ALA 4.3 0.2 - - - -
348C SER* 2.8 24.4 + - - -
101K PHE* 5.5 1.9 - - - -
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Residues in contact with ILE 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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143C TYR* 4.0 22.7 - - + +
144C ALA* 4.0 22.4 - - - +
341C ILE 3.2 14.4 + - - +
342C GLY* 3.8 4.9 - - - +
343C GLY 3.2 0.6 - - - -
344C SER* 1.3 71.9 - - - +
346C LEU* 1.3 69.2 - - - +
348C SER* 2.6 20.3 + - - -
349C LEU* 3.2 20.7 - - + +
101K PHE* 1.9 95.6 - - + +
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Residues in contact with LEU 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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41A GLN* 5.0 9.2 - - + -
49A GLN* 5.3 0.2 - - - +
104C LEU* 3.5 22.4 - - + -
133C TYR* 5.1 4.0 - - + -
135C ALA* 5.3 4.9 - - + -
140C LEU* 5.7 4.3 - - + -
143C TYR* 4.7 23.1 - - + -
342C GLY 3.2 16.4 + - - +
343C GLY* 3.6 4.0 - - - +
345C ILE* 1.3 81.7 - - + +
347C ALA* 1.3 56.8 + - - +
348C SER 2.8 7.8 + - - -
349C LEU* 3.0 28.2 + - + +
351C THR* 6.0 0.9 - - + -
352C PHE* 3.3 52.5 - - + +
355C MET* 4.8 6.5 - - + -
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Residues in contact with ALA 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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6C ALA* 5.8 0.3 - - - -
7C ALA* 3.9 23.2 + - + +
9C VAL* 4.8 2.0 - - + -
22C ALA* 3.6 21.6 - - + +
104C LEU* 4.4 13.2 - - + -
343C GLY 2.8 20.1 + - - +
346C LEU* 1.3 70.7 - - - +
348C SER* 1.3 56.3 + - - +
349C LEU 4.8 0.7 - - - +
352C PHE* 3.7 18.1 - - + +
356C TRP* 4.1 14.0 - - + -
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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