Contacts of the helix formed by residues 336 - 348 (chain E) in PDB entry 6G2T
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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E MET* 5.1 5.1 - - + +
17E LYS* 3.6 32.1 - - + +
26E PRO* 4.3 22.9 - - + -
29E VAL* 3.8 28.7 - - + +
304E MET* 6.0 3.6 - - + -
333E GLU* 3.1 38.5 + - + +
335E LYS* 1.3 92.9 + - + +
337E SER* 1.3 64.1 + - - +
338E VAL 3.3 2.0 - - - -
339E TRP* 3.3 7.5 + - - +
340E ILE* 3.0 25.7 + - + +
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Residues in contact with SER 337 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E LEU 3.7 1.9 - - - +
140E SER* 4.2 15.7 - - - -
143E ALA* 3.3 27.1 - - - +
144E SER* 5.7 1.0 + - - -
299E SER* 4.9 2.2 - - - -
331E PRO* 5.2 6.6 - - - +
333E GLU 3.2 6.0 + - - -
334E ARG* 3.1 33.2 + - - +
336E TYR* 1.3 78.0 - - - +
338E VAL* 1.3 57.8 + - - +
340E ILE* 3.1 6.4 + - - +
341E GLY 2.8 25.8 + - - -
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Residues in contact with VAL 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ASP* 3.1 28.7 - - + +
105E THR* 3.8 20.2 - - - +
136E GLN* 3.7 28.5 - - + +
139E LEU* 3.3 14.3 - - + +
140E SER* 4.0 16.2 - - - +
153E ASP* 3.9 16.8 - - - +
299E SER* 4.7 6.5 - - - +
300E GLY* 5.4 3.8 - - - +
335E LYS 4.4 7.0 + - - +
336E TYR 3.3 0.6 - - - -
337E SER* 1.3 76.0 - - - +
339E TRP* 1.3 62.6 + - - +
342E GLY 3.1 16.6 + - - -
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Residues in contact with TRP 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E VAL* 2.9 44.5 + - + +
10E ASP* 3.6 11.0 + - + -
17E LYS* 3.5 36.8 - - + -
18E ALA 3.6 0.8 - - - -
19E GLY* 3.4 29.6 - - - +
20E PHE 3.6 18.4 - - - -
23E ASP* 3.0 29.8 - - + -
24E ASP 3.7 8.3 - - - -
25E ALA 3.7 3.6 - - - -
26E PRO* 3.4 43.5 - - + -
139E LEU* 5.6 0.2 - - - -
336E TYR 3.3 8.7 + - - +
338E VAL* 1.3 78.6 - - - +
340E ILE* 1.3 66.3 + - + +
342E GLY* 3.0 3.3 + - - -
343E SER* 2.9 33.0 + - - -
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Residues in contact with ILE 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E ASP* 3.5 23.1 - - - +
26E PRO* 5.6 0.4 - - + -
143E ALA* 3.6 21.3 - - + +
333E GLU* 3.2 33.7 - - + +
336E TYR* 3.0 26.0 + - + +
337E SER* 3.4 11.9 - - - +
339E TRP* 1.3 79.4 - - + +
341E GLY* 1.3 65.2 + - - +
343E SER* 2.7 25.7 + - - +
344E ILE* 3.0 12.7 + - + +
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Residues in contact with GLY 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E LEU* 3.0 34.1 - - - -
142E TYR* 3.8 4.1 - - - +
143E ALA 4.1 2.2 - - - -
337E SER 2.8 11.5 + - - -
340E ILE* 1.3 77.1 - - - +
342E GLY* 1.3 56.5 + - - +
344E ILE* 3.0 13.2 - - - +
345E LEU* 2.8 31.7 + - - +
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Residues in contact with GLY 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E VAL* 3.5 11.3 - - - +
103E LEU* 3.3 21.4 - - - +
139E LEU* 3.5 21.4 - - - +
338E VAL 3.1 7.7 + - - -
339E TRP 3.0 8.7 + - - -
341E GLY* 1.3 76.1 - - - +
343E SER* 1.3 55.9 + - - +
345E LEU* 3.5 0.8 + - - -
346E ALA* 3.1 25.3 + - - +
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Residues in contact with SER 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E VAL* 3.7 10.0 - - - +
21E ALA* 4.0 5.2 - - - +
22E GLY* 3.4 16.5 + - - -
23E ASP 3.4 24.2 + - - -
24E ASP* 5.3 0.2 - - - -
339E TRP* 2.9 24.6 + - - -
340E ILE* 2.7 25.0 + - - +
342E GLY* 1.3 73.1 - - - +
344E ILE* 1.3 63.0 + - - +
346E ALA* 3.7 1.6 + - - +
347E SER* 2.8 27.8 + - - -
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Residues in contact with ILE 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142E TYR* 3.5 43.7 - - + +
143E ALA* 5.4 0.7 - - - -
340E ILE* 3.0 18.1 + - + +
341E GLY* 3.0 23.3 - - - +
343E SER* 1.3 74.7 + - - +
345E LEU* 1.3 63.4 + - - +
347E SER* 3.2 14.9 + - - -
348E LEU* 2.9 38.3 + - + +
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Residues in contact with LEU 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 3.4 37.0 - - + -
103E LEU* 4.0 15.0 - - + -
132E TYR* 4.6 0.9 - - + -
134E ALA* 4.3 20.0 - - + -
138E VAL* 6.2 0.9 - - + -
139E LEU* 4.5 10.8 - - + -
142E TYR* 4.2 24.7 - - + -
341E GLY 2.8 17.8 + - - +
342E GLY 3.6 3.8 - - - +
344E ILE* 1.3 82.0 - - + +
346E ALA* 1.3 61.4 + - - +
348E LEU* 3.6 9.0 + - + +
351E PHE* 3.2 50.5 - - + +
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Residues in contact with ALA 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E ALA* 4.2 6.5 - - + +
8E VAL* 4.5 3.8 - - + -
21E ALA* 3.6 25.4 - - + -
103E LEU* 4.8 1.3 - - + +
342E GLY 3.1 14.3 + - - +
345E LEU* 1.3 79.8 - - - +
347E SER* 1.3 63.0 + - - +
348E LEU 3.5 7.4 + - - +
351E PHE* 3.9 12.9 - - - -
352E GLN* 4.1 17.5 + - - +
355E TRP* 4.0 22.7 - - + -
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Residues in contact with SER 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E ALA* 4.2 1.6 - - - +
22E GLY* 3.2 25.8 + - - -
343E SER 2.8 16.8 + - - -
344E ILE* 3.2 15.9 + - - -
346E ALA* 1.3 77.1 - - - +
348E LEU* 1.3 67.0 + - - +
349E SER* 3.5 2.1 + - - -
352E GLN* 5.0 5.1 + - - +
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Residues in contact with LEU 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C VAL* 4.4 33.2 - - + +
45C GLY* 5.0 5.6 - - - -
142E TYR* 5.4 8.5 - - + -
344E ILE* 2.9 44.1 + - + +
345E LEU* 3.6 8.5 + - - +
346E ALA 3.4 9.3 - - - +
347E SER* 1.3 80.1 - - - +
349E SER* 1.3 65.7 + - - +
350E THR* 3.4 6.1 - - - +
351E PHE* 3.4 12.0 + - - +
352E GLN* 3.8 4.9 + - - +
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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