Contacts of the helix formed by residues 287 - 301 (chain C) in PDB entry 3L73
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 287 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285C ILE* 3.0 9.5 + - + +
286C PRO* 1.3 78.1 - - - +
288C LYS* 1.3 65.7 + - - +
289C LEU* 2.8 13.6 + - - +
290C GLY* 2.7 27.6 + - - +
291C GLY* 3.1 9.4 + - - -
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ASN* 3.5 38.1 + - - +
150C LEU* 4.0 27.3 - - + +
152C SER* 3.6 10.5 + - - +
153C ALA* 3.5 20.4 - - + -
282C LEU* 5.4 0.9 - - - +
287C ASN* 1.3 71.8 + - - +
289C LEU* 1.3 61.0 + - - +
291C GLY* 3.7 1.7 + - - -
292C VAL* 3.3 26.5 + - - +
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Residues in contact with LEU 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ALA* 3.8 30.2 - - + +
154C ILE* 4.8 9.0 - - + -
155C PRO* 4.2 20.9 - - + -
287C ASN* 2.8 14.6 + - - +
288C LYS* 1.3 72.4 - - - +
290C GLY* 1.3 65.9 + - - +
292C VAL* 3.3 11.8 + - + -
293C LEU* 3.1 39.3 + - + +
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Residues in contact with GLY 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ILE* 3.8 17.0 - - - +
287C ASN* 2.7 20.2 + - - -
289C LEU* 1.3 72.5 - - - +
291C GLY* 1.3 63.9 + - - +
293C LEU* 3.1 13.1 + - - +
294C ALA* 2.8 22.9 + - - +
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Residues in contact with GLY 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C LEU* 3.4 38.2 - - - +
285C ILE* 3.7 18.1 - - - +
287C ASN 3.1 10.7 + - - -
288C LYS* 4.1 1.8 - - - -
290C GLY* 1.3 76.3 - - - +
292C VAL* 1.3 61.5 + - - +
294C ALA* 3.3 4.7 + - - +
295C LEU* 2.9 17.7 + - - +
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Residues in contact with VAL 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150C LEU* 4.0 43.3 - - + +
151C PHE* 5.8 9.2 - - + -
153C ALA* 4.7 2.5 - - + -
154C ILE* 5.8 7.4 - - + -
282C LEU* 4.2 5.2 - - + -
288C LYS 3.3 17.7 + - - +
289C LEU* 3.3 17.6 + - + +
290C GLY 3.1 0.6 - - - -
291C GLY* 1.3 74.4 - - - +
293C LEU* 1.3 71.6 + - + +
295C LEU* 2.7 18.8 + - + +
296C ALA* 2.9 14.9 + - + +
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Residues in contact with LEU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C LEU* 3.1 33.5 + - + +
290C GLY* 3.5 11.2 - - - +
292C VAL* 1.3 82.0 - - + +
294C ALA* 1.3 58.1 + - - +
296C ALA* 3.0 10.2 + - + +
297C ALA* 2.7 32.7 + - - +
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Residues in contact with ALA 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C ILE* 3.6 20.7 - - + +
284C SER* 4.9 0.2 - - - +
285C ILE* 3.8 23.6 - - + -
290C GLY 2.8 16.1 + - - +
291C GLY* 3.5 8.3 - - - +
292C VAL 3.0 0.2 + - - -
293C LEU* 1.3 71.5 - - - +
295C LEU* 1.3 57.1 + - - +
297C ALA* 3.6 6.5 + - - +
298C SER* 2.9 28.6 + - - -
360C PHE* 3.8 8.3 - - + -
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Residues in contact with LEU 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ILE* 5.7 1.6 - - + -
150C LEU* 4.8 9.0 - - + -
278C ALA* 3.5 40.2 - - + +
279C TYR* 6.3 0.2 - - - -
281C ILE* 4.2 4.9 - - - +
282C LEU* 4.2 26.7 - - + -
291C GLY 2.9 12.0 + - - +
292C VAL* 2.7 17.8 + - + +
294C ALA* 1.3 68.8 - - - +
296C ALA* 1.3 67.9 + - - +
298C SER* 2.4 29.0 + - - +
299C VAL* 3.6 6.2 + - + +
2001C JZZ 3.6 29.2 - - + -
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Residues in contact with ALA 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C VAL* 2.9 13.9 + - + +
293C LEU* 3.3 15.3 - - + +
295C LEU* 1.3 80.4 - - - +
297C ALA* 1.3 65.9 + - - +
299C VAL* 3.0 3.3 + - - +
300C LEU* 2.9 39.2 + - + +
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C LEU 2.7 21.1 + - - +
294C ALA* 3.7 6.1 - - - +
296C ALA* 1.3 73.9 - - - +
298C SER* 1.3 56.4 + - - +
300C LEU* 4.3 8.5 - - - +
301C ILE* 2.7 37.7 + - + +
360C PHE* 4.0 15.3 - - + -
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Residues in contact with SER 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C PHE* 4.5 8.8 - - - -
281C ILE* 3.6 30.7 - - - -
294C ALA 2.9 15.7 + - - -
295C LEU* 2.4 29.0 + - - +
296C ALA 2.9 0.6 + - - -
297C ALA* 1.3 74.1 - - - +
299C VAL* 1.3 67.6 + - - +
301C ILE* 3.0 19.8 - - - +
302C LEU* 5.3 0.5 - - - +
359C TYR* 3.1 14.9 + - - -
360C PHE* 3.8 11.0 - - - -
2007C PEE 5.4 1.7 - - - +
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Residues in contact with VAL 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C VAL* 4.6 3.1 - - + +
121C LEU* 4.0 23.8 - - + -
122C LEU* 3.5 32.5 - - + -
125C MET* 4.2 23.6 - - + -
277C PHE* 4.4 16.4 - - + -
295C LEU* 4.6 6.7 - - + +
296C ALA 3.0 4.7 + - - +
298C SER* 1.3 88.6 + - - +
300C LEU* 1.3 69.2 + - + +
301C ILE 3.0 2.7 + - - -
302C LEU* 3.2 26.1 + - + +
2007C PEE 5.5 3.1 - - + -
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C VAL* 5.5 0.9 - - + -
122C LEU* 4.2 29.2 - - + -
296C ALA* 2.9 36.6 + - + +
297C ALA* 4.2 3.6 - - - +
299C VAL* 1.3 73.1 - - + +
301C ILE* 1.3 63.2 + - - +
302C LEU 2.8 7.2 + - - -
303C PHE* 2.9 41.4 + - + +
304C LEU* 4.3 2.1 + - - +
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Residues in contact with ILE 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C ALA* 2.7 21.8 + - + +
298C SER 3.0 25.4 - - - +
299C VAL 4.2 0.9 - - - +
300C LEU* 1.3 71.9 - - - +
302C LEU* 1.3 66.9 + - + +
304C LEU* 3.0 37.8 + - + +
305C ILE* 3.8 8.1 + - + +
308C LEU* 5.7 1.3 - - + -
359C TYR* 3.6 14.8 - - + +
360C PHE* 4.4 17.0 - - + -
363C LEU* 4.0 25.8 - - + -
364C LEU* 3.6 36.1 - - + -
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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