Contacts of the helix formed by residues 254 - 271 (chain D) in PDB entry 3HUU
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 ASN 254 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252D ASN* 2.8 25.4 + - - -
253D ILE* 1.3 78.5 - - - +
255D PRO* 1.3 72.2 - - - +
256D ASP* 3.2 9.1 - - - +
257D VAL* 3.1 26.3 + - + +
258D LEU* 3.2 10.0 + - - +
282D ILE* 3.8 12.4 - - + +
283D SER* 2.8 28.5 + - - -
285D GLN* 3.1 24.2 + - - +
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Residues in contact with PRO 255 (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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39D PHE* 4.0 26.5 - - + -
42D ASP* 3.3 41.1 - - + +
43D VAL* 3.6 11.7 - - - +
236D ASN* 4.2 8.5 - - - +
237D THR 5.5 2.2 - - - +
252D ASN* 4.4 6.3 - - - +
253D ILE* 3.3 10.7 - - + -
254D ASN* 1.3 88.0 - - - +
256D ASP* 1.3 63.1 + - - +
257D VAL 3.2 0.2 - - - -
258D LEU* 3.2 14.8 + - + +
259D GLY 2.9 23.4 + - - -
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Residues in contact with ASP 256 (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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35C ARG* 5.0 8.5 - - - +
42D ASP* 3.8 19.2 + - + +
45D ASN* 5.0 9.9 - - - +
46D GLY* 3.6 9.6 - - - -
49D GLN* 5.1 4.8 - - - +
254D ASN* 3.5 16.3 - - - +
255D PRO* 1.3 78.7 - - - +
257D VAL* 1.3 67.1 + - - +
260D PHE* 3.0 29.5 + - - +
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Residues in contact with VAL 257 (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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254D ASN* 3.1 28.2 + - + +
256D ASP* 1.3 85.7 - - - +
258D LEU* 1.3 62.6 - - - +
260D PHE* 4.1 5.1 - - + +
261D THR* 2.6 38.9 + - - +
282D ILE* 3.6 27.8 - - + -
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Residues in contact with LEU 258 (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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39D PHE* 4.1 21.5 - - + -
43D VAL* 4.6 3.8 - - + -
110D VAL* 4.5 14.0 - - + +
122D ILE* 3.9 16.8 - - + +
123D ASP* 3.8 28.0 - - - +
124D ASN* 3.5 21.8 - - - +
253D ILE* 3.9 4.3 - - + +
254D ASN 3.2 8.0 + - - +
255D PRO* 3.2 21.8 + - + +
257D VAL* 1.3 77.4 - - - +
259D GLY* 1.3 57.8 + - - +
261D THR* 3.9 1.7 - - - -
262D ALA* 3.0 30.2 + - - +
282D ILE* 3.4 27.4 - - + -
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Residues in contact with GLY 259 (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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43D VAL* 3.4 33.6 - - - +
46D GLY 3.5 6.7 - - - -
47D ILE* 3.4 13.2 - - - +
255D PRO 2.9 12.0 + - - -
256D ASP 3.9 1.6 - - - -
258D LEU* 1.3 75.8 - - - +
260D PHE* 1.3 59.0 + - - +
262D ALA* 3.3 1.8 + - - +
263D GLY 2.8 25.6 + - - -
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Residues in contact with PHE 260 (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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46D GLY* 3.3 22.7 - - - +
49D GLN* 3.8 22.7 - - + +
50D ALA* 3.7 21.6 - - + +
53D VAL* 5.4 4.0 - - + -
256D ASP 3.0 18.1 + - - +
257D VAL* 4.1 5.8 - - + +
259D GLY* 1.3 72.1 - - - +
261D THR* 1.3 69.0 + - - +
263D GLY 3.5 0.3 + - - -
264D ASN* 3.1 57.5 + - - -
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Residues in contact with THR 261 (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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122D ILE* 3.7 16.4 - - + -
257D VAL* 2.6 34.2 + - - +
258D LEU 3.9 3.1 - - - -
260D PHE* 1.3 82.0 - - - +
262D ALA* 1.3 54.9 + - - +
264D ASN* 4.0 3.3 - - - +
265D THR* 2.7 38.3 + - - +
280D LYS* 3.8 31.0 - - + -
282D ILE* 4.1 7.9 - - + +
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Residues in contact with ALA 262 (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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47D ILE* 4.9 1.3 - - + -
86D ILE* 3.8 12.1 - - + +
108D LEU* 3.6 15.5 - - + +
110D VAL* 3.8 25.4 - - + -
122D ILE* 3.3 13.6 - - + +
258D LEU 3.0 19.0 + - - +
259D GLY* 3.6 6.3 - - - +
261D THR* 1.3 74.0 - - - +
263D GLY* 1.3 66.0 + - - +
266D ILE* 3.1 25.1 + - - +
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Residues in contact with GLY 263 (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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47D ILE* 4.5 10.5 - - - -
50D ALA* 3.9 13.5 - - - -
51D CYS* 4.8 3.1 - - - -
86D ILE* 4.1 12.1 - - - +
259D GLY 2.8 20.0 + - - -
260D PHE 3.9 0.9 - - - -
261D THR 3.3 0.2 - - - -
262D ALA* 1.3 73.8 - - - +
264D ASN* 1.3 60.1 + - - +
266D ILE* 3.4 3.9 - - - +
267D ILE* 3.2 30.1 + - - +
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Residues in contact with ASN 264 (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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50D ALA* 3.6 13.6 - - - +
53D VAL* 5.3 1.4 - - - +
54D ARG* 3.0 47.2 + - - +
260D PHE* 3.1 60.2 + - - +
261D THR* 4.1 3.8 - - - +
263D GLY* 1.3 75.5 - - - +
265D THR* 1.3 58.6 + - - +
267D ILE* 3.5 1.8 + - - +
268D ASP* 3.0 25.6 + - - +
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Residues in contact with THR 265 (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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108D LEU* 3.7 20.0 - - + -
120D ILE* 3.9 26.9 - - + -
122D ILE* 3.9 2.8 - - + +
261D THR* 2.7 25.1 + - - +
264D ASN* 1.3 75.5 - - - +
266D ILE* 1.3 64.5 + - - +
268D ASP* 3.2 12.0 + - + +
269D VAL* 3.0 22.0 + - + +
280D LYS* 3.6 26.9 - - - +
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Residues in contact with ILE 266 (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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23D ILE* 3.8 24.7 - - + -
84D GLY* 3.5 9.6 - - - -
85D PHE 2.8 50.3 - - - +
86D ILE* 3.9 11.4 - - + -
106D PRO* 4.6 3.4 - - + +
107D TYR* 5.1 3.6 - - - -
108D LEU* 3.7 15.0 - - + +
262D ALA 3.1 14.9 + - - +
263D GLY* 3.4 14.1 - - - +
265D THR* 1.3 73.4 - - - +
267D ILE* 1.3 67.8 + - + +
269D VAL* 3.3 10.0 + - + +
270D LEU* 3.0 30.2 + - + +
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Residues in contact with ILE 267 (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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23D ILE* 4.7 4.3 - - + -
50D ALA 4.3 1.8 - - - +
51D CYS* 4.1 20.9 - - - -
54D ARG* 3.3 49.8 - - + +
56D TYR* 3.5 41.1 - - + -
263D GLY 3.2 21.4 + - - +
264D ASN* 3.7 4.5 - - - +
265D THR 3.2 0.6 - - - -
266D ILE* 1.3 83.1 - - + +
268D ASP* 1.3 63.1 + - - +
270D LEU* 3.1 8.1 + - - +
271D ARG* 2.9 33.8 + - - +
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Residues in contact with ASP 268 (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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54D ARG* 2.6 40.0 + - - +
264D ASN* 3.0 22.3 + - - +
265D THR* 3.3 14.7 + - + +
267D ILE* 1.3 77.8 - - - +
269D VAL* 1.3 61.7 + - + +
271D ARG* 3.2 21.1 + - - +
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Residues in contact with VAL 269 (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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106D PRO* 4.4 17.7 - - + -
107D TYR 6.0 0.2 - - - +
108D LEU* 5.8 1.6 - - + -
120D ILE* 3.5 31.0 - - + -
265D THR* 3.0 16.4 + - + +
266D ILE* 3.6 12.3 - - + +
267D ILE 3.2 0.2 - - - -
268D ASP* 1.3 77.7 - - + +
270D LEU* 1.3 62.2 + - + +
271D ARG 3.2 8.0 - - - +
275D ILE* 3.5 38.6 - - - +
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Residues in contact with LEU 270 (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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23D ILE* 3.5 32.8 - - + -
56D TYR* 4.0 18.7 + - + +
83D ASP* 3.3 41.7 - - + +
84D GLY* 4.1 5.6 - - - +
106D PRO* 3.8 26.2 - - + -
266D ILE* 3.0 22.1 + - + +
267D ILE 3.1 4.7 + - - +
269D VAL* 1.3 75.4 - - - +
271D ARG* 1.3 60.0 + - - +
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Residues in contact with ARG 271 (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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21D LEU* 5.6 3.6 - - - +
54D ARG* 3.7 37.8 + - - +
56D TYR* 4.0 19.7 - - - +
267D ILE* 2.9 36.3 + - - +
268D ASP* 3.2 13.7 - - - +
269D VAL 3.1 13.2 - - - +
270D LEU* 1.3 80.6 - - - +
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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