Contacts of the helix formed by residues 244 - 257 (chain D) in PDB entry 3AP3
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 HIS 244 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240D GLN* 2.9 43.4 + - - +
241D LEU 3.5 2.7 - - - -
243D LEU* 1.3 81.9 - - + +
245D PRO* 1.3 60.6 - - - +
246D ARG 3.1 2.8 + - - -
247D ARG* 3.8 21.4 - - + +
248D SER* 2.8 28.8 + - - +
335D GLY* 5.6 1.4 - - - -
336D ASN* 3.4 28.9 + - + -
338D ASP* 3.2 21.2 + - - +
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Residues in contact with PRO 245 (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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87D MET* 5.4 0.2 - - - -
241D LEU* 3.2 24.4 - - + +
243D LEU 3.2 14.6 - - - +
244D HIS* 1.3 84.4 - - - +
246D ARG* 1.3 62.5 + - + +
249D LEU* 3.2 30.7 + - + +
265D LEU* 3.8 15.2 - - + +
293D VAL* 4.4 18.8 - - + -
338D ASP* 3.3 11.2 - - - +
340D PHE* 3.5 31.9 - - + -
341D VAL* 3.6 10.3 - - + -
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Residues in contact with ARG 246 (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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244D HIS 3.1 0.6 - - - -
245D PRO* 1.3 82.5 - - + +
247D ARG* 1.3 66.6 + - - +
248D SER 3.3 0.2 + - - -
249D LEU* 4.6 0.5 - - - +
250D LYS* 3.4 52.6 + - - +
260D TRP* 4.6 19.6 - - + +
262D ASP* 3.3 24.8 + - - -
265D LEU* 3.7 24.3 - - + +
338D ASP* 4.6 7.9 - - - +
340D PHE* 6.1 1.6 - - + -
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Residues in contact with ARG 247 (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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244D HIS* 3.2 24.8 + - + +
246D ARG* 1.3 79.2 - - - +
248D SER* 1.3 66.5 + - - +
250D LYS* 3.6 8.7 + - - +
251D LEU* 3.3 54.5 + - + +
338D ASP* 5.0 0.6 + - - -
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Residues in contact with SER 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236D VAL* 6.2 1.1 - - - -
240D GLN* 3.1 22.3 + - - +
241D LEU* 3.4 23.6 - - - -
244D HIS* 2.8 24.1 + - - +
245D PRO 4.0 2.7 - - - -
247D ARG* 1.3 75.6 - - - +
249D LEU* 1.4 57.9 + - - +
251D LEU* 2.7 36.9 + - - +
252D ILE* 3.0 16.9 + - - +
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Residues in contact with LEU 249 (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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84D MET* 3.8 14.8 - - + -
87D MET* 3.6 23.6 - - + -
88D LEU* 4.5 7.6 - - + -
241D LEU* 3.5 25.8 - - + -
245D PRO* 3.2 20.8 + - + +
248D SER* 1.4 77.6 - - - +
250D LYS* 1.3 53.6 + - - +
252D ILE* 2.9 28.5 + - + +
253D LEU* 2.7 44.3 + - + +
260D TRP* 4.3 7.4 - - + -
264D VAL* 3.3 35.2 - - + -
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Residues in contact with LYS 250 (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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246D ARG* 3.4 49.0 + - + +
247D ARG* 3.6 11.0 - - - +
248D SER 2.8 0.8 + - - -
249D LEU* 1.3 76.1 - - - +
251D LEU* 1.3 59.8 + - + +
253D LEU* 4.1 1.3 - - - +
254D ASP* 2.9 29.9 + - - +
260D TRP* 3.5 44.3 - - + +
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Residues in contact with LEU 251 (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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234D LEU* 5.2 4.7 - - + -
247D ARG* 3.3 52.7 - - + +
248D SER* 2.7 12.4 + - - +
250D LYS* 1.3 73.9 - - + +
252D ILE* 1.3 53.7 + - + +
254D ASP* 3.1 8.3 - - + +
255D PHE* 2.8 36.0 + - - +
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Residues in contact with ILE 252 (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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84D MET* 3.7 22.9 - - + -
88D LEU* 4.4 3.4 - - + -
179D LEU* 4.3 14.8 - - + -
234D LEU* 4.4 19.7 - - + -
236D VAL* 4.6 16.4 - - + -
241D LEU* 5.1 1.3 - - + -
248D SER* 3.0 16.0 + - - +
249D LEU* 2.9 49.3 + - + +
251D LEU* 1.3 75.8 - - + +
253D LEU* 1.3 67.6 + - + +
255D PHE* 2.9 7.3 + - - +
256D LEU* 2.9 43.3 + - + +
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Residues in contact with LEU 253 (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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88D LEU* 4.5 14.8 - - + -
91D HIS* 4.2 20.2 - - + -
94D VAL* 6.1 0.7 - - + -
249D LEU* 2.7 25.1 + - + +
250D LYS* 4.2 2.2 - - - +
252D ILE* 1.3 76.3 - - + +
254D ASP* 1.3 55.9 + - - +
256D LEU* 3.4 19.8 + - + +
257D GLY 2.9 23.0 + - - -
258D ILE* 2.9 37.2 + - + +
259D ALA 5.3 0.4 - - - -
260D TRP* 3.8 30.3 - - + -
261D SER 4.5 8.3 - - - +
264D VAL* 3.9 23.8 - - + -
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Residues in contact with ASP 254 (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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250D LYS 2.9 20.8 + - - +
251D LEU* 3.1 11.9 - - - +
253D LEU* 1.3 75.5 - - - +
255D PHE* 1.3 57.2 + - - +
257D GLY* 2.8 25.2 + - - -
258D ILE 5.0 1.8 - - - -
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Residues in contact with PHE 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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177D LYS* 3.4 23.6 + - + -
178D PHE 3.9 3.4 - - - -
179D LEU* 3.7 19.5 - - + -
230D LYS 3.0 26.7 - - - -
231D GLU* 3.2 15.9 - - - -
232D LYS 3.4 26.9 - - - -
234D LEU* 3.4 46.7 - - + -
251D LEU 2.8 16.2 + - - +
252D ILE 3.3 7.4 - - - +
254D ASP* 1.3 76.6 + - - +
256D LEU* 1.3 71.5 + - + +
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Residues in contact with LEU 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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71D ILE* 4.1 33.4 - - + -
88D LEU* 4.4 7.9 - - + -
177D LYS* 4.1 37.4 + - + +
179D LEU* 4.2 18.4 - - + -
252D ILE* 2.9 38.1 + - + +
253D LEU* 3.6 22.4 - - + +
255D PHE* 1.3 80.5 - - + +
257D GLY* 1.3 60.1 + - - +
258D ILE* 4.2 21.1 - - + +
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Residues in contact with GLY 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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153D ARG* 5.7 0.9 + - - -
253D LEU 2.9 0.6 + - - -
254D ASP* 2.8 17.9 + - - -
255D PHE 3.3 0.4 - - - -
256D LEU* 1.3 79.5 - - - +
258D ILE* 1.3 61.0 - - - +
259D ALA 4.4 0.3 + - - -
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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