Contacts of the helix formed by residues 283 - 296 (chain D) in PDB entry 4XH9
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 ASP 283 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209D ILE 4.3 6.6 - - - +
280D LYS* 3.0 32.0 + - + +
281D LYS 3.3 0.4 - - - -
282D GLN* 1.3 78.1 - - - +
284D PRO* 1.3 67.4 - - - +
285D ARG* 3.1 23.5 + - - +
286D VAL* 3.2 25.0 + - + +
287D GLN* 3.0 26.3 + - - +
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Residues in contact with PRO 284 (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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282D GLN 3.2 10.7 - - - +
283D ASP* 1.3 90.4 - - - +
285D ARG* 1.3 58.5 + - + +
287D GLN* 3.4 5.6 + - + +
288D ASP* 2.9 32.6 + - - +
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Residues in contact with ARG 285 (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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207D LEU* 3.1 17.4 + - - +
208D SER* 2.4 41.9 + - - -
209D ILE* 3.8 25.4 + - + +
283D ASP* 3.1 11.6 + - - +
284D PRO* 1.3 75.6 - - + +
286D VAL* 1.3 67.0 + - + +
288D ASP* 4.0 4.9 - - - +
289D PHE* 3.2 23.2 + - - +
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Residues in contact with VAL 286 (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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204D MET* 5.1 4.5 - - - -
209D ILE* 3.7 31.6 - - + +
210D MET* 3.9 18.8 - - + -
277D LEU* 5.6 3.6 - - + -
280D LYS* 3.9 20.2 - - + +
283D ASP* 3.2 32.3 + - + +
285D ARG* 1.3 77.2 - - - +
287D GLN* 1.3 75.7 + - - +
289D PHE* 3.2 4.9 + - - +
290D LEU* 3.1 35.5 + - + +
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Residues in contact with GLN 287 (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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277D LEU 4.8 1.4 - - - +
280D LYS* 2.8 20.8 - - - +
281D LYS* 3.4 38.0 - - - +
283D ASP 3.0 16.7 + - - +
284D PRO* 3.9 5.6 - - + +
286D VAL* 1.3 83.5 - - - +
288D ASP* 1.3 57.9 + - - +
290D LEU* 3.4 18.2 + - - +
291D GLN* 3.0 37.5 + - + +
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Residues in contact with ASP 288 (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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284D PRO 2.9 19.7 + - - +
285D ARG* 4.0 5.2 - - - +
287D GLN* 1.3 75.2 - - - +
289D PHE* 1.3 60.0 + - - +
291D GLN* 3.3 10.4 + - - +
292D ARG* 3.0 27.3 + - - +
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Residues in contact with PHE 289 (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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199D ALA 3.5 22.0 - - - -
200D TYR* 4.0 11.4 - + - -
203D PRO* 3.8 21.8 - - + -
204D MET* 3.4 33.0 - - + -
207D LEU* 4.6 0.9 - - + -
209D ILE* 3.6 26.9 - - + -
285D ARG 3.2 17.9 + - - +
286D VAL 3.2 4.2 + - - +
288D ASP* 1.3 77.3 + - - +
290D LEU* 1.3 64.7 + - + +
292D ARG* 3.2 42.2 + - - +
293D CYS* 3.0 46.1 + - - -
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Residues in contact with LEU 290 (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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200D TYR* 4.6 9.4 - - + -
204D MET* 4.8 5.4 - - - -
277D LEU* 5.2 8.1 - - + -
286D VAL* 3.1 35.6 + - + +
287D GLN* 3.7 23.3 - - - +
288D ASP 3.3 0.2 - - - -
289D PHE* 1.3 87.1 - - + +
291D GLN* 1.3 67.0 + - - +
293D CYS* 3.3 5.8 + - - +
294D LEU* 3.1 31.7 + - + +
304D LEU* 4.0 38.1 - - + +
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Residues in contact with GLN 291 (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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287D GLN* 3.0 23.4 + - + +
288D ASP* 3.4 15.0 - - - +
289D PHE 3.3 0.2 - - - -
290D LEU* 1.3 77.6 - - - +
292D ARG* 1.3 62.2 + - - +
294D LEU* 3.1 16.5 + - - +
295D GLU* 3.1 38.1 + - - +
5E ARG* 2.8 33.3 + - - +
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Residues in contact with ARG 292 (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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203D PRO* 5.2 4.4 - - - +
207D LEU* 3.9 23.2 - - - +
288D ASP* 3.0 14.5 + - - +
289D PHE* 3.2 37.6 + - - +
291D GLN* 1.3 77.5 - - - +
293D CYS* 1.3 66.6 + - - +
295D GLU* 3.1 26.7 + - + +
296D SER* 3.4 17.4 + - - +
298D PHE* 6.2 2.2 - - - -
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Residues in contact with CYS 293 (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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199D ALA 4.2 1.6 - - - -
200D TYR* 3.6 32.5 - - + +
289D PHE* 3.0 53.3 + - - -
290D LEU* 3.6 7.9 - - - +
291D GLN 3.3 0.2 - - - -
292D ARG* 1.3 79.2 - - - +
294D LEU* 1.3 60.8 + - + +
296D SER* 3.2 12.8 + - - +
298D PHE* 3.8 22.8 - - + -
299D SER* 2.8 22.0 + - - -
302D LEU 6.0 0.2 - - - +
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Residues in contact with LEU 294 (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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290D LEU* 3.1 22.3 + - + +
291D GLN* 3.1 21.4 + - - +
293D CYS* 1.3 76.7 - - + +
295D GLU* 1.3 59.2 + - - +
296D SER 3.3 2.0 + - - +
299D SER* 3.6 9.0 + - - -
301D LYS* 3.5 42.0 - - - +
302D LEU 3.5 22.7 - - - +
303D ASP* 3.8 15.7 - - + +
5E ARG* 3.6 45.5 + - - +
54E GLU* 5.1 1.2 - - - +
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Residues in contact with GLU 295 (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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291D GLN* 3.1 29.1 + - - +
292D ARG* 3.1 17.0 + - - +
294D LEU* 1.3 77.9 - - - +
296D SER* 1.3 59.7 + - - +
297D PRO* 4.3 1.7 - - - +
5E ARG* 4.1 13.8 + - - +
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Residues in contact with SER 296 (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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292D ARG* 3.4 13.5 + - - +
293D CYS 3.2 3.8 + - - +
294D LEU 4.1 1.7 - - - +
295D GLU* 1.3 82.7 + - - +
297D PRO* 1.3 72.1 - - - +
298D PHE* 3.3 29.9 + - - -
299D SER* 3.0 22.9 + - - -
300D ARG 4.3 0.9 + - - -
301D LYS* 4.8 1.4 + - - +
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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