Contacts of the helix formed by residues 288 - 299 (chain D) in PDB entry 3C6Q
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 288 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283D VAL* 3.2 22.4 + - - +
284D VAL* 3.5 6.2 - - - +
285D THR* 2.6 43.5 + - - +
287D GLU* 1.3 77.0 - - + +
289D LEU* 1.3 64.5 + - - +
290D ASP 3.4 1.8 - - - -
291D GLU* 3.4 13.1 + - + +
292D TYR* 3.2 20.5 + - - +
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Residues in contact with LEU 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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222D LEU* 4.2 28.7 - - + +
225D VAL* 4.3 10.8 - - + -
226D LYS* 4.0 39.0 - - + +
284D VAL* 3.9 20.4 - - + -
285D THR 2.8 13.5 + - - +
286D PRO* 4.0 12.3 - - + +
287D GLU 3.3 2.8 - - - -
288D ASN* 1.3 79.1 - - - +
290D ASP* 1.3 69.1 + - - +
292D TYR* 2.9 27.8 + - + +
293D LEU* 3.2 23.3 + - + +
305D PHE* 5.7 5.6 - - + -
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Residues in contact with ASP 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D LYS* 5.6 5.5 + - - -
286D PRO 5.2 2.1 - - - +
287D GLU 4.6 4.3 + - - +
288D ASN 3.4 0.4 - - - -
289D LEU* 1.3 89.0 - - - +
291D GLU* 1.3 62.3 + - - +
292D TYR 3.3 0.3 + - - -
293D LEU* 3.6 16.0 + - - +
294D LYS* 3.4 20.1 + - - +
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Residues in contact with GLU 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287D GLU 5.5 0.2 + - - -
288D ASN* 3.4 16.2 + - + +
289D LEU 3.2 0.6 - - - -
290D ASP* 1.3 79.8 - - - +
292D TYR* 1.3 57.9 + - - +
294D LYS* 3.9 28.9 + - - +
295D LYS* 3.3 22.7 + - - +
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Residues in contact with TYR 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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217D THR* 3.1 40.1 + - + +
222D LEU* 5.0 4.3 - - + -
235D GLY* 4.9 0.6 - - - -
236D GLN 4.7 5.5 + - - -
282D ASP* 3.6 30.7 + - + -
283D VAL 5.6 0.9 - - - -
284D VAL* 3.6 31.9 - - + -
288D ASN* 3.2 14.0 + - - +
289D LEU* 2.9 16.5 + - + +
291D GLU* 1.3 76.4 - - - +
293D LEU* 1.3 81.3 + - + +
294D LYS 3.1 1.3 - - - -
295D LYS* 2.9 21.7 + - + +
296D MET* 2.9 46.3 + - + +
303D ILE* 4.5 8.9 - - + +
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Residues in contact with LEU 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D LEU* 4.3 17.3 - - + -
289D LEU* 3.2 29.6 + - + +
290D ASP* 3.6 19.0 + - - +
292D TYR* 1.3 84.2 - - + +
294D LYS* 1.3 63.2 + - - +
296D MET* 3.3 8.8 + - - +
297D GLU* 3.2 20.4 + - - +
303D ILE* 4.0 27.7 - - + +
305D PHE* 5.0 15.0 - - + -
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Residues in contact with LYS 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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143C GLN* 3.4 28.0 - - - +
146C LYS* 5.9 5.6 - - - +
290D ASP 3.4 14.4 + - - +
291D GLU* 3.9 30.4 + - - +
292D TYR 3.1 0.2 - - - -
293D LEU* 1.3 78.7 - - - +
295D LYS* 1.3 64.1 + - - +
297D GLU* 3.0 20.0 + - - +
298D GLU* 3.1 33.6 + - - +
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Residues in contact with LYS 295 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D ARG* 4.2 11.0 - - - +
282D ASP* 3.8 23.1 - - - +
291D GLU 3.3 13.6 + - - +
292D TYR* 2.9 16.2 + - + +
294D LYS* 1.3 80.2 - - - +
296D MET* 1.3 71.5 + - + +
298D GLU* 3.3 9.2 + - - +
299D LEU* 3.0 30.0 + - + +
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Residues in contact with MET 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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236D GLN 5.8 1.3 - - - +
237D ARG* 3.8 24.9 - - - +
282D ASP* 4.2 2.7 - - - +
292D TYR* 2.9 50.0 + - + +
293D LEU* 3.5 8.5 - - - +
295D LYS* 1.3 96.0 - - + +
297D GLU* 1.3 58.8 + - - +
299D LEU* 3.4 5.6 + - + +
300D GLY 3.2 2.6 + - - -
301D ILE* 2.9 63.5 + - + +
303D ILE* 3.6 32.1 - - + -
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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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150C LYS* 3.0 35.8 + - + +
293D LEU 3.2 8.5 + - - +
294D LYS* 3.0 13.7 + - + +
296D MET* 1.3 74.7 - - - +
298D GLU* 1.3 65.9 + - - +
299D LEU 3.0 4.5 - - - -
300D GLY* 2.8 22.1 + - - -
301D ILE 4.6 3.6 - - - +
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Residues in contact with GLU 298 (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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294D LYS* 3.1 43.9 + - - +
295D LYS* 3.3 9.8 + - - +
297D GLU* 1.3 84.5 - - - +
299D LEU* 1.3 63.8 - - + +
300D GLY 3.4 0.4 - - - -
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Residues in contact with LEU 299 (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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237D ARG* 4.0 27.6 - - - +
240D MET* 5.5 5.7 - - + +
295D LYS* 3.0 23.9 + - + +
296D MET* 3.7 10.3 - - + +
297D GLU 3.0 1.2 - - - -
298D GLU* 1.3 83.0 - - + +
300D GLY* 1.3 61.4 + - - +
301D ILE* 3.5 28.6 + - + +
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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