Contacts of the helix formed by residues 335 - 352 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D GLN* 5.0 1.6 - - - +
169D PHE* 3.6 26.4 - - + -
178D ILE* 3.9 21.2 - - + +
333D ILE* 3.1 13.4 - - + +
334D PRO* 1.3 95.6 - - - +
336D MET* 1.3 64.3 + - - +
337D SER 3.2 0.4 - - - -
338D ALA* 2.9 15.6 + - - +
339D PHE 3.0 10.4 + - - -
1221D SER* 3.3 38.2 + - - +
1224D LEU* 3.9 28.8 + - + +
1225D ASP* 3.9 10.3 - - - +
1227D HIS* 5.6 4.0 - - - -
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Residues in contact with MET 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ASP* 4.1 17.9 - - + +
168D ALA* 3.7 17.7 - - + -
169D PHE* 3.5 33.7 - - + -
258D PHE* 4.7 1.6 - - + -
330D MET* 5.0 4.3 - - - -
331D PRO* 3.3 56.3 - - + +
333D ILE* 3.3 15.0 + - + +
334D PRO 3.1 0.4 - - - -
335D GLN* 1.3 77.1 - - - +
337D SER* 1.3 63.0 + - - +
339D PHE* 3.2 11.9 + - + +
340D TRP* 2.9 51.7 + - + -
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Residues in contact with SER 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ASP 5.6 0.4 + - - -
66D ARG* 4.5 34.6 + - - +
69D GLY* 5.4 4.7 - - - -
334D PRO* 3.4 14.4 + - - +
335D GLN 3.2 0.2 - - - -
336D MET* 1.3 75.7 - - - +
338D ALA* 1.3 64.1 + - - +
340D TRP* 3.8 2.8 - - - +
341D TYR* 3.0 25.1 + - - +
1224D LEU* 5.5 6.6 - - - +
1365D VAL* 5.6 11.2 - - - -
1368D GLN* 5.5 8.6 + - - -
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Residues in contact with ALA 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D PRO 4.5 0.2 + - - -
335D GLN 2.9 12.5 + - - +
337D SER* 1.3 79.7 - - - +
339D PHE* 1.3 64.4 + - - +
341D TYR* 3.4 0.6 + - - -
342D ALA* 3.1 25.1 + - - +
368D ALA* 3.9 3.7 - - - +
1220D MET* 3.7 28.5 - - + -
1221D SER* 3.6 21.3 - - - +
1224D LEU* 4.3 8.0 - - + +
1361D GLN* 3.7 13.2 + - - +
1365D VAL* 6.0 1.6 - - - -
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Residues in contact with PHE 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D TRP* 3.6 36.3 - + - -
168D ALA* 3.5 36.1 - - + -
169D PHE* 4.0 16.4 - - + -
181D VAL* 4.7 5.4 - - + -
183D VAL* 3.8 9.4 - - + -
258D PHE* 3.8 14.1 - + - -
335D GLN 3.0 10.8 + - - +
336D MET* 3.5 15.9 - - - +
338D ALA* 1.3 77.8 - - - +
340D TRP* 1.3 108.7 - + - +
342D ALA* 3.2 2.1 + - - +
343D VAL* 3.1 43.4 + - + +
368D ALA* 4.3 10.9 - - + +
1221D SER* 4.8 0.6 + - - -
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Residues in contact with TRP 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ASP* 3.1 27.6 + - - -
66D ARG* 4.5 8.3 - - - +
154D PRO* 3.6 28.5 - - + +
155D TYR* 3.8 31.9 - + - -
158D TRP* 4.7 6.7 - + + -
258D PHE* 3.6 36.1 - + + -
330D MET* 3.8 15.9 - - + -
336D MET* 2.9 40.1 + - + +
337D SER 3.8 3.1 - - - +
339D PHE* 1.3 93.1 - + - +
341D TYR* 1.3 65.4 + - - +
343D VAL* 3.2 3.3 + - + +
344D ARG* 2.8 29.6 + - - +
2N GLC 3.7 34.7 - - - +
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Residues in contact with TYR 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D GLU* 5.6 4.3 - - - -
337D SER 3.0 16.8 + - - +
338D ALA* 4.0 3.1 - - - +
340D TRP* 1.3 77.4 - - - +
342D ALA* 1.3 62.9 + - - +
344D ARG* 3.4 27.6 + - + +
345D THR* 3.2 33.6 + - - -
1360D ASP* 4.8 6.2 + - + +
1361D GLN* 3.4 31.9 - - + +
1364D SER* 3.0 37.6 + - - -
1365D VAL* 5.3 7.0 - - + -
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Residues in contact with ALA 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D VAL* 6.3 0.2 - - + -
338D ALA 3.1 18.2 + - - +
339D PHE 3.5 3.8 - - - +
341D TYR* 1.3 79.0 - - - +
343D VAL* 1.3 62.6 + - + +
345D THR* 3.6 6.0 - - - +
346D ALA* 3.1 22.0 + - - +
364D ALA* 3.5 35.1 - - + +
367D ASN* 4.8 1.1 - - + -
368D ALA* 3.8 11.0 - - + +
1361D GLN* 3.6 17.2 + - - +
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Residues in contact with VAL 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D PRO* 3.7 20.9 - - + -
158D TRP* 4.4 17.7 - - + -
161D ILE* 4.9 3.4 - - + -
183D VAL* 3.9 18.2 - - + -
339D PHE* 3.1 45.8 + - + +
340D TRP* 3.8 4.9 - - + +
342D ALA* 1.3 74.6 - - + +
344D ARG* 1.3 68.9 + - - +
346D ALA* 2.9 8.1 + - + +
347D VAL* 2.8 36.6 + - + +
361D LEU* 6.0 4.3 - - + -
364D ALA* 4.7 1.6 - - + -
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Residues in contact with ARG 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLU* 5.1 4.4 + - - -
45D GLU* 4.4 14.3 + - - -
66D ARG* 4.3 7.1 - - - +
152D GLN 3.8 16.8 - - - +
153D GLU* 3.1 32.7 + - - -
154D PRO* 3.8 16.0 - - + +
340D TRP* 2.8 19.7 + - - +
341D TYR* 3.4 40.4 + - - +
343D VAL* 1.3 76.2 - - - +
345D THR* 1.3 62.2 + - - +
347D VAL* 3.6 3.1 + - - +
348D ILE* 3.1 38.6 + - + +
2N GLC 3.5 26.5 + - - -
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Residues in contact with THR 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D TYR* 3.2 31.2 + - - -
342D ALA* 3.6 10.5 - - - +
344D ARG* 1.3 76.9 - - - +
346D ALA* 1.3 68.0 + - - +
348D ILE* 3.2 5.8 + - - +
349D ASN* 2.8 49.2 + - - +
355D GLN* 4.8 1.8 - - - +
1357D LEU* 4.2 19.5 - - + -
1361D GLN* 5.5 0.2 + - - -
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Residues in contact with ALA 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D LEU* 4.9 1.6 - - - -
342D ALA 3.1 11.4 + - - +
343D VAL* 2.9 10.6 + - + +
345D THR* 1.3 80.7 - - - +
347D VAL* 1.3 59.2 + - + +
349D ASN* 3.8 1.3 - - - -
350D ALA* 2.9 31.9 + - - +
355D GLN* 5.0 0.9 - - - -
360D ALA* 3.5 38.9 - - + +
361D LEU* 4.3 12.3 - - + +
364D ALA* 3.8 9.6 - - + -
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Residues in contact with VAL 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LEU* 3.9 20.9 - - + +
152D GLN 6.2 0.2 - - - +
154D PRO* 5.0 4.3 - - + -
157D THR* 3.9 26.5 - - + +
161D ILE* 4.0 21.5 - - + -
192D LEU* 4.3 12.8 - - + +
195D LEU* 4.4 10.8 - - + -
343D VAL* 2.8 39.8 + - + +
344D ARG* 3.9 4.5 - - - +
346D ALA* 1.3 72.7 - - + +
348D ILE* 1.3 58.1 + - - +
350D ALA* 3.2 2.3 + - - +
351D ALA* 2.9 32.3 + - + +
361D LEU* 6.3 0.7 - - + -
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Residues in contact with ILE 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LEU 4.6 7.9 - - - +
152D GLN* 3.8 44.6 - - + +
344D ARG* 3.1 27.0 + - + +
345D THR* 3.7 4.3 - - - +
347D VAL* 1.3 77.0 - - + +
349D ASN* 1.3 63.3 + - - +
351D ALA* 3.7 5.4 - - - +
352D SER* 2.8 42.4 + - - +
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Residues in contact with ASN 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345D THR* 2.8 39.1 + - - +
346D ALA 3.8 2.2 - - - +
348D ILE* 1.3 83.4 - - - +
350D ALA* 1.3 56.4 + - - +
352D SER* 3.6 5.4 + - - -
353D GLY 3.2 3.1 + - - -
354D ARG* 3.0 59.8 + - + +
355D GLN* 2.8 42.0 + - + +
1357D LEU* 4.1 10.7 - - - +
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Residues in contact with ALA 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D LEU* 4.1 17.7 - - + -
196D VAL* 3.7 33.9 - - + +
346D ALA 2.9 18.3 + - - +
347D VAL 3.8 2.7 - - - +
349D ASN* 1.3 73.3 - - - +
351D ALA* 1.3 65.5 + - - +
353D GLY* 3.5 10.0 + - - -
355D GLN 3.6 15.1 - - - +
357D VAL* 4.3 9.8 - - + +
360D ALA* 4.3 8.7 - - + +
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Residues in contact with ALA 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D LEU* 5.4 7.0 - - + -
195D LEU* 5.8 5.4 - - + -
196D VAL* 4.5 10.1 - - + +
199D ILE* 3.9 25.3 - - + +
206D ALA* 3.8 29.3 - - + +
347D VAL* 2.9 23.1 + - + +
348D ILE* 3.7 5.8 - - - +
350D ALA* 1.3 78.2 - - - +
352D SER* 1.3 60.9 + - - +
353D GLY* 3.3 1.2 + - - -
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Residues in contact with SER 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D ALA* 4.6 8.3 - - - -
348D ILE* 2.8 29.6 + - - +
349D ASN* 3.5 11.3 + - - -
351D ALA* 1.3 72.8 - - - +
353D GLY* 1.3 57.2 + - - +
354D ARG* 3.2 18.7 + - - +
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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