Contacts of the helix formed by residues 285 - 293 (chain D) in PDB entry 6CP3
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 LEU 285 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A VAL* 5.7 4.9 - - + -
281A ARG* 5.4 11.7 - - - +
262D THR* 3.8 23.5 - - + +
281D TYR* 3.7 32.8 - - + -
282D GLN* 4.1 15.3 - - + +
283D PRO 2.9 8.9 + - - +
284D THR* 1.3 74.0 - - - +
286D ALA* 1.3 65.1 + - + +
287D THR 3.2 1.5 - - - +
288D ASP* 3.8 0.8 - - - -
289D MET* 2.8 38.1 + - + +
320D PRO* 3.9 16.6 - - + +
321D ALA* 4.7 5.6 - - - +
324D THR* 3.3 32.3 - - + +
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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
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238A ALA* 4.2 8.2 - - + +
245A GLN* 5.1 14.1 - - - +
275A LYS* 5.5 9.0 - - + +
278A VAL* 3.8 28.7 - - + +
279A ALA* 5.7 0.7 - - - +
282A GLN* 5.0 4.9 + - - +
283D PRO 4.8 1.0 + - - -
285D LEU* 1.3 83.4 - - + +
287D THR* 1.3 60.3 + - + +
289D MET* 4.4 0.4 - - - +
290D GLY* 2.9 24.6 + - - -
324D THR* 4.5 16.4 - - + -
328D HIS* 5.2 1.9 + - - -
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Residues in contact with THR 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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238A ALA 4.4 5.2 - - - +
240A GLU 4.3 11.9 - - - +
241A ALA* 4.5 3.4 - - - -
242A ALA* 4.0 23.8 - - + +
245A GLN* 5.2 7.0 - - - +
282A GLN* 2.8 41.0 + - - +
284D THR* 3.9 8.3 - - - -
286D ALA* 1.3 80.6 - - + +
288D ASP* 1.3 61.3 + - - +
290D GLY* 3.6 0.7 - - - -
291D LEU* 2.9 37.1 + - - +
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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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261D PHE* 3.8 25.2 - - + -
274D ARG* 5.3 0.3 + - - -
282D GLN* 4.6 7.0 + - - +
284D THR* 2.8 41.3 + - - +
285D LEU* 3.2 3.0 + - - +
287D THR* 1.3 78.8 + - - +
289D MET* 1.3 62.1 + - - +
291D LEU* 3.3 11.8 + - - +
292D LEU* 3.0 29.5 + - - +
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Residues in contact with MET 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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258D ILE* 4.6 22.2 - - + +
259D PHE* 6.0 0.9 - - - -
261D PHE* 4.5 7.5 - - + -
262D THR* 3.3 28.9 + - + +
285D LEU* 2.8 26.1 + - + +
286D ALA 4.4 1.3 - - - +
288D ASP* 1.3 73.1 - - - +
290D GLY* 1.3 56.8 + - - +
292D LEU* 4.5 3.4 - - - +
293D GLN* 2.9 59.0 + - + +
321D ALA 4.5 9.4 - - - +
324D THR* 4.3 21.5 - - + -
325D THR* 3.6 26.2 - - - +
328D HIS* 4.6 8.3 - - + -
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Residues in contact with GLY 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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238A ALA* 3.3 24.5 - - - -
286D ALA 2.9 15.6 + - - -
287D THR 3.3 0.9 + - - -
288D ASP 3.1 0.2 - - - -
289D MET* 1.3 78.3 - - - +
291D LEU* 1.3 57.1 + - - +
293D GLN 3.1 1.4 + - - -
294D GLU* 3.0 35.1 + - - +
328D HIS* 4.0 15.7 - - - -
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Residues in contact with LEU 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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80A SER* 5.1 11.0 - - - +
238A ALA 4.2 0.2 + - - -
239A SER* 3.3 27.8 - - - +
119D ALA 5.9 0.4 - - - +
121D PRO* 4.0 27.4 - - + -
234D LEU* 5.0 3.5 - - - +
237D LEU* 4.8 0.7 - - - +
287D THR* 2.9 26.4 + - - +
288D ASP* 3.3 11.0 + - - +
290D GLY* 1.3 72.2 - - - +
292D LEU* 1.3 61.1 + - - +
294D GLU* 4.3 2.5 - - - +
295D ARG* 3.7 28.1 + - - +
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Residues in contact with LEU 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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233D ALA* 3.8 21.1 - - + +
234D LEU* 3.7 25.8 - - + -
237D LEU* 4.2 10.8 - - + -
255D ILE* 5.8 0.7 - - + -
258D ILE* 3.8 26.2 - - + -
261D PHE* 3.6 45.3 - - + -
288D ASP 3.0 15.4 + - - +
289D MET* 4.3 4.5 - - - +
291D LEU* 1.3 80.4 - - - +
293D GLN* 1.3 64.6 + - - +
294D GLU 3.4 1.6 + - - -
295D ARG* 4.3 1.5 + - - +
296D ILE* 3.7 27.3 + - + +
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Residues in contact with GLN 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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152D LYS* 3.0 36.5 + - - +
258D ILE* 4.0 20.8 - - - +
289D MET* 2.9 37.7 + - - +
290D GLY 3.1 2.0 + - - -
292D LEU* 1.3 83.0 + - - +
294D GLU* 1.3 65.1 + - - +
296D ILE* 4.5 4.7 - - - +
308D GLN* 2.6 45.8 + - - +
325D THR* 5.3 4.2 - - + +
328D HIS* 3.3 36.5 + - + +
329D LEU* 4.5 1.7 - - - +
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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