Contacts of the helix formed by residues 284 - 297 (chain D) in PDB entry 2C2L
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 284 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246C ILE* 3.9 8.0 - - - +
284C ASN* 2.6 39.7 + - - +
244D PRO* 3.0 26.2 + - + +
246D ILE* 3.7 23.7 - - + +
252D THR* 3.6 17.0 + - - +
282D ILE 3.0 5.1 + - - -
283D PRO* 1.3 67.1 - - - +
285D LEU* 1.3 62.0 + - - +
286D ALA 3.6 1.6 + - - -
287D MET* 2.8 43.0 + - + +
288D LYS* 3.4 14.2 + - - +
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Residues in contact with LEU 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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246C ILE* 4.1 0.4 - - - +
249C SER 4.9 2.5 - - - +
250C GLY* 3.0 35.0 + - - +
251C ILE* 4.4 11.7 - - + +
283D PRO* 2.9 27.8 + - + +
284D ASN* 1.3 69.1 - - - +
286D ALA* 1.3 69.8 + - - +
287D MET 3.1 1.6 - - - -
288D LYS* 2.8 26.7 + - + +
289D GLU* 3.0 12.9 + - - +
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Residues in contact with ALA 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C TYR* 4.7 3.4 - - + +
235C LYS* 6.3 0.7 - - - +
241C MET* 5.9 0.2 - - + -
250C GLY 4.7 2.0 + - - -
252C THR* 3.9 27.8 + - - +
287C MET* 3.5 30.9 - - + +
284D ASN* 3.6 2.4 + - - +
285D LEU* 1.3 77.2 - - - +
287D MET* 1.3 57.1 + - - +
289D GLU* 3.1 15.4 + - - +
290D VAL* 3.0 31.2 + - - +
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Residues in contact with MET 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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284C ASN* 3.7 4.3 - - - +
286C ALA* 3.2 48.9 - - + +
287C MET* 3.3 25.4 - - + +
290C VAL* 4.0 19.5 - - - -
231D TYR 4.5 8.1 - - - +
232D LEU* 5.2 3.4 - - - -
241D MET* 5.9 1.1 - - + -
244D PRO* 3.9 13.2 - - + -
252D THR* 4.5 4.7 - - + -
284D ASN* 2.8 33.2 + - - +
286D ALA* 1.3 70.1 - - - +
288D LYS* 1.3 60.4 + - - +
290D VAL* 3.4 9.7 - - - +
291D ILE* 2.7 48.8 + - + +
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Residues in contact with LYS 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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242D ARG 3.9 21.8 - - - +
243D GLU* 4.4 8.1 - - - +
244D PRO* 3.5 21.7 + - + +
283D PRO* 6.2 1.8 - - - +
284D ASN 3.4 10.1 + - - +
285D LEU* 2.8 17.8 + - - +
287D MET* 1.3 78.4 - - - +
289D GLU* 1.3 59.1 + - - +
291D ILE* 3.9 5.6 - - + +
292D ASP* 3.0 42.7 + - - +
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Residues in contact with GLU 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C TYR* 3.4 36.2 - - + +
235C LYS* 4.9 8.8 + - - -
285D LEU* 3.0 10.6 + - - +
286D ALA* 3.3 14.8 - - - +
288D LYS* 1.3 78.5 - - - +
290D VAL* 1.3 60.5 + - - +
292D ASP* 3.6 7.6 - - + +
293D ALA* 3.4 20.8 + - - +
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Residues in contact with VAL 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C TYR* 3.6 31.0 - - + -
287C MET* 4.0 22.2 - - + -
290C VAL* 3.9 30.3 - - + -
232D LEU* 4.4 15.3 - - + -
286D ALA 3.0 22.3 + - - +
287D MET* 3.0 11.2 + - - +
289D GLU* 1.3 74.9 - - - +
291D ILE* 1.3 66.1 + - - +
292D ASP 3.1 1.7 + - - -
293D ALA* 3.3 5.0 + - - +
294D PHE* 3.1 20.3 + - + +
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Residues in contact with ILE 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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232D LEU* 4.5 20.6 - - + +
240D LEU* 4.6 10.8 - - + -
241D MET* 3.1 56.3 - - + +
242D ARG* 5.0 5.2 - - - +
244D PRO* 3.7 19.5 - - + -
287D MET* 2.7 36.3 + - + +
288D LYS* 3.9 6.5 - - + +
290D VAL* 1.3 69.7 - - + +
292D ASP* 1.3 69.7 + - - +
294D PHE* 3.2 17.7 - - - +
295D ILE* 2.9 33.4 - - + +
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Residues in contact with ASP 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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288D LYS* 3.0 38.1 + - - +
289D GLU* 3.6 10.3 - - + +
291D ILE* 1.3 78.2 - - - +
293D ALA* 1.3 59.2 + - - +
295D ILE* 2.9 30.2 + - - +
296D SER* 3.2 13.5 + - - -
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Residues in contact with ALA 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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231C TYR* 3.5 30.7 - - + +
289D GLU 3.4 9.8 + - - +
290D VAL 3.3 8.0 + - - +
292D ASP* 1.3 79.0 - - - +
294D PHE* 1.3 60.7 + - - +
296D SER* 3.3 15.6 + - - -
297D GLU* 3.0 26.8 - - - +
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Residues in contact with PHE 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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227D ASP 4.7 3.1 - - - -
228D ILE* 3.3 35.2 - - + -
229D PRO* 3.8 26.0 - - + -
232D LEU* 3.5 25.1 - - + -
240D LEU* 3.9 18.6 - - + -
290D VAL* 3.1 13.5 + - + +
291D ILE 3.2 10.5 - - - +
293D ALA* 1.3 78.0 - - - +
295D ILE* 1.3 65.2 + - + +
297D GLU* 3.4 3.6 + - - +
298D ASN* 2.5 58.4 + - - +
300D TRP* 4.7 3.1 - + - -
301D VAL* 4.2 8.1 - - + -
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Residues in contact with ILE 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D LEU* 4.1 21.3 - - + -
242D ARG* 4.9 10.3 - - - +
291D ILE* 2.9 40.8 - - + +
292D ASP* 2.9 13.2 + - - +
294D PHE* 1.3 74.7 - - + +
296D SER* 1.3 58.0 + - - +
297D GLU 3.0 2.2 - - - -
298D ASN* 2.7 34.6 + - - +
299D GLY* 3.4 4.0 + - - -
301D VAL* 4.6 6.5 - - + -
302D GLU* 3.7 34.5 - - + +
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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
----------------------------------------------------------
292D ASP 3.2 14.5 + - - -
293D ALA* 3.4 15.9 + - - -
294D PHE 3.3 0.2 - - - -
295D ILE* 1.3 77.3 - - - +
297D GLU* 1.3 74.7 + - - +
299D GLY* 4.8 2.1 + - - -
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Residues in contact with GLU 297 (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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293D ALA* 3.0 23.9 - - - +
294D PHE* 3.4 6.7 + - - +
295D ILE 3.0 0.4 - - - -
296D SER* 1.3 93.5 - - - +
298D ASN* 1.3 76.7 + - - +
299D GLY 3.9 1.1 - - - -
300D TRP* 4.5 0.9 + - - -
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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