Contacts of the helix formed by residues 337 - 347 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16I MET* 5.5 0.2 - - - +
18I LYS* 3.9 22.0 - - + -
26I ALA* 5.6 4.7 - - + -
27I PRO* 4.0 30.7 - - + -
30I VAL* 3.4 22.6 - - + +
334I GLU* 2.8 4.3 + - + +
336I LYS* 1.3 120.7 + - + +
338I SER* 1.3 61.7 + - - -
339I VAL* 3.4 2.5 - - - -
340I TRP* 3.1 15.3 + - + -
341I ILE* 3.1 33.3 + - + +
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Residues in contact with SER 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I LEU 3.9 2.1 - - - +
141I SER* 3.6 31.9 + - - -
144I ALA* 4.1 7.1 - - - +
300I SER* 5.0 0.8 - - - -
332I PRO* 5.2 5.4 - - - +
334I GLU* 3.7 12.2 + - - +
335I ARG* 4.0 18.6 - - - -
336I LYS 3.7 1.6 - - - -
337I TYR* 1.3 72.9 - - - +
339I VAL* 1.3 64.8 + - - +
340I TRP 3.1 0.5 + - - -
341I ILE* 3.1 4.5 + - - +
342I GLY* 3.0 22.5 + - - -
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Residues in contact with VAL 339 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ASP* 3.4 33.4 - - - +
106I THR* 4.0 9.6 - - + -
137I GLN* 3.4 45.1 - - + +
140I LEU* 3.3 22.7 - - + +
141I SER* 3.2 22.7 - - - +
154I ASP* 4.4 2.2 - - - +
301I GLY* 5.0 13.0 - - - +
335I ARG 5.4 1.5 + - - +
336I LYS 5.4 0.4 + - - -
337I TYR 3.4 0.8 - - - -
338I SER* 1.3 74.1 - - - +
340I TRP* 1.3 64.0 + - - +
342I GLY 3.5 0.2 + - - -
343I GLY 3.4 3.6 + - - -
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Residues in contact with TRP 340 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I VAL* 3.2 36.0 + - + +
11I ASP* 4.1 12.1 + - + +
18I LYS* 3.3 43.3 - - + -
19I ALA 3.7 0.6 - - - -
20I GLY* 3.4 32.7 - - - +
21I PHE 3.8 10.8 - - - -
24I ASP* 3.2 30.3 - - + -
25I ASP 3.8 1.6 - - - -
26I ALA* 3.4 24.7 - - - -
27I PRO* 3.4 26.7 - - + -
337I TYR* 3.1 10.3 + - - +
339I VAL* 1.3 79.4 - - - +
341I ILE* 1.3 63.0 + - + +
343I GLY* 3.3 1.4 + - - -
344I SER* 3.0 37.8 + - - -
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Residues in contact with ILE 341 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I ASP 4.4 6.3 - - - +
25I ASP 3.2 27.6 - - - +
26I ALA* 4.8 1.1 - - + -
27I PRO* 5.1 1.3 - - + -
144I ALA* 4.0 7.9 - - + -
337I TYR* 3.1 43.0 + - + +
338I SER* 4.3 3.4 - - - +
340I TRP* 1.3 86.0 - - + +
342I GLY* 1.3 61.1 + - - +
344I SER* 3.9 2.9 - - - -
345I ILE* 3.2 21.5 + - + +
99P MET* 4.4 7.4 - - + -
101P PHE* 3.8 29.2 - - + -
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Residues in contact with GLY 342 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I LEU* 3.1 32.9 - - - +
143I TYR* 4.6 6.1 - - - +
144I ALA* 3.4 14.0 - - - +
338I SER 3.0 10.8 + - - -
341I ILE* 1.3 79.9 - - - +
343I GLY* 1.3 55.7 + - - +
345I ILE* 3.8 3.8 - - - +
346I LEU* 3.2 27.4 + - - +
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Residues in contact with GLY 343 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I VAL* 3.8 14.4 - - - -
104I LEU* 4.1 6.2 - - - +
140I LEU* 3.6 21.4 - - - +
339I VAL 3.4 5.9 + - - -
340I TRP 3.3 5.8 + - - -
342I GLY* 1.3 73.7 - - - +
344I SER* 1.3 59.9 + - - +
346I LEU* 3.3 4.1 + - - +
347I ALA* 2.8 34.4 + - - +
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Residues in contact with SER 344 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I VAL* 3.4 15.2 - - - +
21I PHE 3.8 0.3 + - - -
22I ALA* 3.7 5.9 - - - +
23I GLY* 3.1 12.0 + - - -
24I ASP 2.7 41.9 + - - -
340I TRP* 3.0 32.3 + - - -
341I ILE* 3.9 6.5 - - - +
343I GLY* 1.3 73.1 - - - +
345I ILE* 1.3 49.4 + - - +
347I ALA 4.3 0.2 - - - -
348I SER* 2.8 23.9 + - - -
101P PHE* 5.6 1.9 - - - -
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Residues in contact with ILE 345 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I TYR* 4.0 22.7 - - + +
144I ALA* 4.0 22.2 - - - +
341I ILE 3.2 14.3 + - - +
342I GLY* 3.8 4.3 - - - +
343I GLY 3.2 0.8 - - - -
344I SER* 1.3 71.8 - - - +
346I LEU* 1.3 70.0 + - - +
348I SER* 2.6 20.1 + - - -
349I LEU* 3.2 21.0 - - + +
101P PHE* 1.9 97.8 - - + -
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Residues in contact with LEU 346 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G GLN* 5.0 9.0 - - + -
104I LEU* 3.5 22.2 - - + -
133I TYR* 5.1 4.7 - - + -
135I ALA* 5.3 4.9 - - + -
140I LEU* 5.7 3.8 - - + -
143I TYR* 4.7 22.9 - - + -
342I GLY 3.2 17.7 + - - +
343I GLY* 3.6 4.9 - - - +
345I ILE* 1.3 80.9 - - + +
347I ALA* 1.3 55.1 + - - +
348I SER 2.8 8.0 + - - -
349I LEU* 3.0 28.9 + - + +
351I THR* 6.0 1.3 - - + -
352I PHE* 3.3 52.7 - - + +
355I MET* 4.8 5.6 - - - -
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Residues in contact with ALA 347 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I ALA* 5.8 0.3 - - - -
7I ALA* 3.9 22.5 + - + +
9I VAL* 4.8 2.5 - - + -
22I ALA* 3.6 21.1 - - + +
104I LEU* 4.4 13.2 - - + -
343I GLY 2.8 20.6 + - - +
346I LEU* 1.3 70.1 - - - +
348I SER* 1.3 55.9 + - - +
349I LEU 3.6 1.0 - - - +
352I PHE* 3.7 18.0 - - + -
356I TRP* 4.1 14.4 - - + -
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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