Contacts of the helix formed by residues 288 - 299 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET 4.0 8.5 - - - +
283B VAL 2.8 24.5 + - - -
284B VAL* 3.4 6.1 - - - +
285B THR* 2.6 41.5 + - - +
287B GLU* 1.3 76.1 - - + +
289B LEU* 1.3 63.2 + - - +
290B ASP 3.4 2.0 - - - -
291B GLU* 3.3 12.7 + - + +
292B TYR* 3.1 20.9 + - - +
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B LEU* 3.9 35.4 - - + +
225B VAL* 4.1 7.2 - - + -
226B LYS* 3.7 43.7 - - + +
284B VAL* 3.9 19.3 - - + -
285B THR 3.0 15.3 + - - +
286B PRO 4.0 9.4 - - - +
287B GLU 3.5 2.4 - - - -
288B ASN* 1.3 76.7 - - - +
290B ASP* 1.3 70.4 + - - +
292B TYR* 3.1 3.0 + - + +
293B LEU* 3.0 34.0 + - + +
305B PHE* 4.5 7.4 - - + -
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Residues in contact with ASP 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 5.3 13.5 - - - +
2A LEU* 5.5 10.3 - - + +
254A LYS* 4.6 13.2 + - - -
286B PRO 5.2 0.8 + - - -
287B GLU 5.0 1.7 + - - +
288B ASN 3.4 0.4 - - - -
289B LEU* 1.3 82.2 - - - +
291B GLU* 1.3 62.8 + - - +
293B LEU* 3.2 17.9 + - - +
294B LYS* 3.2 21.7 + - - +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET 4.4 20.8 + - - +
57A GLY 5.6 1.7 - - - +
288B ASN* 3.3 17.8 + - + +
289B LEU 3.2 0.2 - - - -
290B ASP* 1.3 78.2 - - - +
292B TYR* 1.3 65.0 + - - +
294B LYS* 3.2 16.4 + - - +
295B LYS* 3.0 27.7 + - + +
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Residues in contact with TYR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN* 5.7 0.3 + - - -
217B THR* 3.4 37.6 + - + +
222B LEU* 4.6 10.3 - - + -
235B GLY* 4.7 0.7 - - - -
236B GLN 4.5 6.8 + - - -
282B ASP* 3.6 36.9 + - + -
284B VAL* 3.6 30.7 - - + -
288B ASN* 3.1 13.3 + - - +
289B LEU* 3.1 7.6 + - + +
291B GLU* 1.3 77.7 - - - +
293B LEU* 1.3 74.1 + - + +
295B LYS* 3.5 12.7 + - + +
296B MET* 3.1 64.7 + - + +
303B ILE* 6.3 0.9 - - + -
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 3.5 31.4 - - + -
289B LEU* 3.0 27.1 + - + +
290B ASP* 3.5 18.2 - - - +
291B GLU 3.2 0.2 - - - -
292B TYR* 1.3 80.4 - - + +
294B LYS* 1.3 50.5 + - - +
296B MET* 3.1 7.2 + - + +
297B GLU* 2.8 39.0 + - + +
303B ILE* 3.9 28.7 - - + +
305B PHE* 4.0 25.1 - - + -
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLY* 2.7 42.1 + - - +
58A VAL 3.5 8.5 + - - -
59A ASN* 4.2 17.9 - - - +
81A MET 5.5 7.3 + - - -
83A ILE* 5.1 6.0 - - - +
290B ASP 3.2 9.9 + - - +
291B GLU* 3.5 17.9 - - - +
293B LEU* 1.3 76.6 - - - +
295B LYS* 1.3 66.0 + - - +
296B MET 3.0 0.3 + - - -
297B GLU* 3.0 13.4 + - + +
298B GLU* 2.8 49.2 + - + +
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Residues in contact with LYS 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B ARG* 4.5 9.1 - - - +
282B ASP* 3.0 28.2 + - - +
291B GLU* 3.0 20.2 + - + +
292B TYR* 3.6 17.3 - - + +
294B LYS* 1.3 75.9 - - - +
296B MET* 1.3 80.1 + - + +
298B GLU* 3.6 10.0 + - - +
299B LEU* 3.3 32.1 + - + +
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Residues in contact with MET 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLN* 5.1 6.5 - - - +
236B GLN 6.0 1.1 - - - +
237B ARG* 6.0 2.7 - - + -
239B TYR* 6.3 0.7 - - + -
282B ASP* 4.6 4.5 - - - +
292B TYR* 3.1 56.0 + - + +
293B LEU* 3.1 10.7 + - + +
294B LYS 3.0 0.8 - - - -
295B LYS* 1.3 93.8 - - + +
297B GLU* 1.3 66.6 + - - +
299B LEU* 3.1 26.1 + - + +
301B ILE* 2.9 61.0 + - + +
303B ILE* 5.7 7.4 - - + -
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293B LEU* 2.8 18.8 + - + +
294B LYS* 3.2 16.2 - - + +
296B MET* 1.3 71.4 - - - +
298B GLU* 1.3 54.6 + - + +
300B GLY* 2.5 30.0 + - - -
301B ILE 3.5 12.0 + - - +
302B PRO* 6.0 2.0 - - + -
303B ILE* 5.9 7.2 - - + +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ALA 5.8 0.3 - - - +
57A GLY* 4.7 6.5 - - - -
294B LYS* 2.8 59.0 + - + +
295B LYS* 3.7 9.1 - - - +
297B GLU* 1.3 74.9 - - + +
299B LEU* 1.3 61.7 + - + +
300B GLY* 3.0 4.5 + - - -
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN* 3.0 18.9 + - - -
239B TYR* 3.9 54.2 + - + +
240B MET* 6.2 1.1 - - + -
295B LYS* 3.3 20.6 + - + +
296B MET* 3.1 34.7 + - + +
298B GLU* 1.3 79.5 - - + +
300B GLY* 1.3 57.3 + - - +
301B ILE* 3.2 12.2 - - + +
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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