Contacts of the helix formed by residues 335 - 352 (chain E) in PDB entry 5TJ4
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 GLN 335 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E GLN* 4.9 1.2 - - - +
169E PHE* 3.6 26.4 - - + -
178E ILE* 3.9 21.0 - - + +
333E ILE* 3.2 13.8 - - + +
334E PRO* 1.3 94.6 - - - +
336E MET* 1.3 59.0 + - - +
337E SER 3.2 0.2 - - - -
338E ALA* 2.9 21.8 + - - +
339E PHE 3.0 9.7 + - - -
1221E SER* 3.3 39.2 + - - +
1224E LEU* 3.9 29.5 + - + -
1225E ASP* 3.9 9.3 - - - +
1227E HIS* 5.7 4.4 - - - -
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Residues in contact with MET 336 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E ASP* 4.1 16.6 - - + +
168E ALA* 3.7 17.0 - - + -
169E PHE* 3.6 29.7 - - + -
258E PHE* 4.7 1.8 - - + -
330E MET* 5.0 4.0 - - - -
331E PRO* 3.3 59.0 - - + +
333E ILE* 3.3 15.0 + - + +
334E PRO 3.1 0.2 - - - -
335E GLN* 1.3 76.4 - - - +
337E SER* 1.3 63.7 + - - +
339E PHE* 3.5 16.7 - - + +
340E TRP* 2.9 47.0 + - + -
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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
----------------------------------------------------------
66E ARG* 4.6 25.7 + - - +
69E GLY* 5.6 4.0 - - - -
334E PRO* 3.4 14.5 + - - +
336E MET* 1.3 78.7 - - - +
338E ALA* 1.3 62.7 + - - +
340E TRP* 3.3 4.9 + - - +
341E TYR* 3.0 46.1 + - - -
1224E LEU* 5.4 7.2 - - - +
1365E VAL* 5.5 3.8 - - - -
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Residues in contact with ALA 338 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334E PRO 4.5 0.2 + - - -
335E GLN 2.9 12.1 + - - +
337E SER* 1.3 79.2 - - - +
339E PHE* 1.3 64.8 + - - +
341E TYR* 3.4 6.4 + - - +
342E ALA* 3.1 25.4 + - - +
368E ALA* 3.9 5.1 - - - +
1220E MET* 3.7 33.2 - - + -
1221E SER* 3.6 22.2 - - - +
1224E LEU* 4.3 7.3 - - + +
1361E GLN* 4.4 3.1 + - - +
1365E VAL* 5.8 0.2 - - - -
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Residues in contact with PHE 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158E TRP* 3.6 37.9 - + - -
168E ALA* 3.5 34.1 - - + -
169E PHE* 4.0 16.2 - + + -
181E VAL* 4.7 5.8 - - + -
183E VAL* 3.8 10.5 - - + -
258E PHE* 3.8 13.9 - + - -
335E GLN 3.0 7.5 + - - +
336E MET* 3.5 17.3 - - - +
338E ALA* 1.3 79.8 - - - +
340E TRP* 1.3 100.4 + + - +
342E ALA* 3.3 2.1 + - - +
343E VAL* 3.1 42.7 + - + +
368E ALA* 4.3 11.1 - - + +
1221E SER* 4.7 0.8 + - - -
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Residues in contact with TRP 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E ASP* 3.1 27.9 + - - -
66E ARG* 4.6 9.0 - - - +
154E PRO* 3.6 27.8 - - + +
155E TYR* 3.7 33.0 - + - -
158E TRP* 4.7 7.0 - + + -
258E PHE* 3.6 35.4 - + + -
330E MET* 3.8 16.2 - - + -
336E MET* 2.9 39.1 + - + +
337E SER* 3.8 3.6 - - - +
339E PHE* 1.3 94.9 - + - +
341E TYR* 1.3 57.7 + - - +
343E VAL* 3.3 3.6 + - + +
344E ARG* 2.9 36.0 + - - +
2O GLC 3.7 34.0 + - - +
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Residues in contact with TYR 341 (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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45E GLU* 3.4 28.3 - - + +
66E ARG* 3.9 16.1 + - - -
337E SER* 3.0 43.7 + - - +
338E ALA* 4.0 4.5 - - - +
340E TRP* 1.3 76.5 - - + +
342E ALA* 1.3 64.1 + - - +
344E ARG* 3.2 34.8 + - - +
345E THR* 3.2 25.4 + - - +
1220E MET* 6.5 0.2 - - + -
1361E GLN* 4.5 16.2 - - + +
1364E SER* 4.6 18.2 + - - +
1365E VAL* 3.8 31.4 - - + +
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Residues in contact with ALA 342 (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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338E ALA 3.1 17.7 + - - +
339E PHE 3.5 4.3 - - - +
341E TYR* 1.3 77.8 - - - +
343E VAL* 1.3 60.5 + - + +
345E THR* 2.7 19.6 + - - -
346E ALA* 3.1 12.6 + - - +
364E ALA* 3.5 35.3 - - + +
368E ALA* 3.8 8.7 - - + -
1361E GLN* 3.6 21.0 - - - +
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Residues in contact with VAL 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154E PRO* 3.7 21.1 - - + -
158E TRP* 4.4 17.5 - - + -
161E ILE* 4.9 3.4 - - + -
183E VAL* 3.9 17.7 - - + -
339E PHE* 3.1 44.9 + - + +
340E TRP* 3.8 4.3 - - + +
342E ALA* 1.3 74.4 - - + +
344E ARG* 1.3 68.9 + - - +
346E ALA* 3.0 8.1 + - + +
347E VAL* 2.8 37.4 + - + +
361E LEU* 6.0 4.0 - - + -
364E ALA* 4.7 2.2 - - + -
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Residues in contact with ARG 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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44E GLU* 5.6 2.8 + - - -
66E ARG* 4.4 4.2 - - - +
152E GLN 3.8 16.6 - - - +
153E GLU* 3.1 33.5 + - - -
154E PRO* 3.8 16.7 - - + +
340E TRP* 2.9 21.9 + - - +
341E TYR* 3.2 49.6 - - - +
343E VAL* 1.3 76.9 - - - +
345E THR* 1.4 61.7 + - + +
347E VAL* 3.9 3.3 - - - +
348E ILE* 3.1 38.1 + - + +
2O GLC 3.4 25.7 + - - -
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Residues in contact with THR 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341E TYR 3.2 11.5 + - - +
342E ALA 2.7 22.0 + - - -
344E ARG* 1.4 73.5 - - + +
346E ALA* 1.3 64.5 + - - +
348E ILE* 3.1 7.4 + - - +
349E ASN* 2.8 40.4 + - - +
355E GLN* 5.9 0.2 - - - -
364E ALA* 5.8 0.2 - - - -
1357E LEU* 5.3 11.2 - - + -
1360E ASP* 6.5 1.6 - - + -
1361E GLN* 3.6 20.8 + - + +
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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
----------------------------------------------------------
192E LEU* 4.9 1.6 - - + -
342E ALA 3.1 13.3 + - - +
343E VAL* 3.0 10.6 + - - +
345E THR* 1.3 76.4 + - - +
347E VAL* 1.3 59.2 + - + +
349E ASN* 3.8 1.7 - - - -
350E ALA* 2.9 32.5 + - - +
355E GLN* 5.0 1.6 - - - -
360E ALA* 3.6 38.1 - - + +
361E LEU* 4.3 12.8 - - + +
364E ALA* 3.8 9.6 - - + -
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Residues in contact with VAL 347 (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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151E LEU* 4.0 21.1 - - + +
152E GLN 6.2 0.2 - - - +
154E PRO* 5.0 4.9 - - + -
157E THR* 3.9 25.6 - - + +
161E ILE* 4.0 22.2 - - + -
192E LEU* 4.3 13.1 - - + +
195E LEU* 4.4 10.8 - - + -
343E VAL* 2.8 39.1 + - + +
344E ARG* 3.9 4.0 - - - +
346E ALA* 1.3 72.4 - - + +
348E ILE* 1.3 58.1 + - + +
350E ALA* 3.3 1.7 + - - +
351E ALA* 2.9 31.9 + - + +
361E LEU* 6.3 0.4 - - + -
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Residues in contact with ILE 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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151E LEU 4.6 7.9 - - - +
152E GLN* 3.8 44.9 - - + +
344E ARG* 3.1 27.1 + - + +
345E THR* 3.7 4.5 - - - +
347E VAL* 1.3 75.3 - - + +
349E ASN* 1.3 62.0 + - - +
351E ALA* 3.7 5.4 - - - +
352E SER* 2.8 41.8 + - - +
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Residues in contact with ASN 349 (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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345E THR* 2.8 31.5 + - - +
346E ALA 3.8 2.2 - - - +
348E ILE* 1.3 81.6 - - - +
350E ALA* 1.3 57.2 + - - +
352E SER* 3.6 5.8 + - - -
353E GLY 3.2 3.3 + - - -
354E ARG* 3.0 56.9 + - + +
355E GLN* 2.8 43.6 + - + +
1357E LEU* 4.1 18.0 - - - +
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Residues in contact with ALA 350 (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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192E LEU* 4.1 17.9 - - + -
196E VAL* 3.7 33.0 - - + +
200E LYS* 5.8 0.5 - - - -
346E ALA 2.9 18.7 + - - +
347E VAL 3.8 2.5 - - - +
349E ASN* 1.3 73.7 - - - +
351E ALA* 1.3 65.1 + - - +
353E GLY* 3.4 10.2 + - - -
355E GLN 3.6 14.2 - - - +
357E VAL* 4.3 14.0 - - + +
360E ALA* 4.3 3.8 - - + +
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Residues in contact with ALA 351 (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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84A ALA* 3.7 13.3 - - - +
151E LEU* 5.4 4.7 - - + -
192E LEU* 5.9 0.2 - - - +
195E LEU* 5.8 2.7 - - + -
196E VAL* 4.4 8.2 - - + +
199E ILE* 3.6 35.4 - - + +
206E ALA* 3.9 21.1 - - + +
347E VAL* 2.9 22.2 + - + +
348E ILE* 3.7 6.3 - - - +
350E ALA* 1.3 79.2 - - - +
352E SER* 1.3 60.2 + - - +
353E GLY 3.2 0.9 + - - -
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Residues in contact with SER 352 (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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84A ALA* 3.6 15.6 - - - +
85A PHE* 3.8 11.1 + - - +
88A LYS* 3.2 39.5 + - - +
206E ALA* 4.4 8.0 - - - +
348E ILE* 2.8 29.9 + - - +
349E ASN* 3.5 11.8 + - - -
351E ALA* 1.3 73.7 - - - +
353E GLY* 1.3 58.6 + - - +
354E ARG* 3.2 10.2 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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