Contacts of the helix formed by residues 269 - 281 (chain A) in PDB entry 3CMT
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 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A GLN* 2.7 51.3 + - + +
263A LEU* 3.7 27.6 - - + +
266A GLU* 5.2 5.6 - - - +
267A GLY 3.3 3.7 + - - -
268A ILE* 1.4 67.0 - - - +
270A PHE* 1.3 62.8 + - - +
271A TYR* 3.7 2.3 + - - +
272A GLY* 2.9 33.9 + - - -
273A GLU* 3.3 21.1 + - - +
302A LYS* 5.0 3.0 - - - +
306A THR* 3.7 14.5 + - - +
310A LYS* 5.7 2.1 + - - -
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Residues in contact with PHE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY* 3.6 23.6 - - - +
44A SER 4.8 0.4 - - - -
45A LEU* 3.7 27.1 - - + +
48A ASP* 6.2 0.2 - - - -
268A ILE 2.8 13.1 + - - +
269A ASN* 1.3 69.7 + - - +
271A TYR* 1.3 92.6 + + + +
273A GLU* 3.2 21.1 + - - +
274A LEU* 3.0 32.9 + - + +
317A LYS* 4.8 7.4 - - - -
320A GLU* 3.7 37.9 - - + -
324A ARG* 5.5 2.0 - - - -
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Residues in contact with TYR 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ASN* 3.5 1.9 + - - +
270A PHE* 1.3 95.2 - + + +
272A GLY* 1.3 64.8 + - - +
274A LEU* 3.2 14.3 + - + +
275A VAL* 3.0 27.5 + - - +
306A THR* 3.6 25.1 - - + +
309A LEU* 3.8 28.0 + - + +
310A LYS* 3.5 40.2 + - + -
313A PRO* 4.8 10.0 - - - +
316A ALA* 3.7 24.4 - - + +
317A LYS* 5.3 8.5 + - - -
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Residues in contact with GLY 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ASN* 2.9 29.1 + - - -
270A PHE 3.2 0.2 - - - -
271A TYR* 1.3 76.4 - - - +
273A GLU* 1.3 60.9 + - - +
275A VAL* 3.3 3.6 + - - +
276A ASP* 3.2 13.2 + - - -
302A LYS* 2.9 32.3 + - - -
306A THR* 3.6 11.3 - - - +
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A SER* 2.8 30.3 + - - -
45A LEU* 3.4 23.7 + - + -
46A SER* 2.9 21.2 + - - +
259A GLU 4.7 2.7 - - - +
260A PHE* 3.4 24.3 - - + +
261A GLN 5.5 0.2 - - - +
268A ILE* 3.8 3.4 - - - +
269A ASN 3.3 10.0 + - - +
270A PHE* 3.2 23.9 + - - +
272A GLY* 1.3 74.4 - - - +
274A LEU* 1.3 54.9 + - - +
276A ASP* 3.0 7.3 + - - +
277A LEU* 2.8 49.7 + - + +
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.1 17.7 - - + +
270A PHE* 3.0 17.0 + - + +
271A TYR* 3.2 19.9 + - + +
273A GLU* 1.3 79.8 - - - +
275A VAL* 1.3 56.1 + - - +
277A LEU* 4.0 2.9 - - - -
278A GLY* 2.8 28.4 + - - -
284A ILE* 4.3 2.1 - - - +
309A LEU* 4.0 18.4 - - + -
316A ALA* 3.7 38.4 - - + +
319A ILE* 4.3 12.6 - - + -
320A GLU* 3.7 33.2 - - + +
323A VAL* 4.6 4.3 - - + -
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A TYR 3.0 18.4 + - - +
272A GLY 3.5 7.4 - - - +
273A GLU 3.2 0.2 - - - -
274A LEU* 1.3 74.2 - - - +
276A ASP* 1.3 66.5 + - - +
278A GLY* 3.1 2.3 + - - -
279A VAL* 2.8 30.6 + - + +
284A ILE* 4.1 10.4 - - + +
291A TYR* 3.7 34.3 - - + -
302A LYS* 4.2 11.4 - - + -
305A ALA* 3.9 9.4 - - + -
306A THR* 3.8 27.8 - - - +
309A LEU* 3.7 18.2 - - + -
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Residues in contact with ASP 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A GLY 3.2 2.0 + - - +
273A GLU* 3.0 9.9 + - - +
275A VAL* 1.3 77.8 - - - +
277A LEU* 1.3 61.4 + - + +
279A VAL* 3.5 6.1 + - - +
280A LYS* 3.0 30.0 + - - +
291A TYR* 5.2 1.9 + - - -
302A LYS* 3.2 43.0 + - - +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 4.4 9.4 - - + -
46A SER* 4.4 18.4 - - - -
49A ILE* 4.5 8.3 - - + -
273A GLU* 2.8 45.0 + - + +
274A LEU* 4.0 4.0 - - - +
276A ASP* 1.3 73.4 - - + +
278A GLY* 1.3 59.3 + - - +
280A LYS* 3.5 17.0 + - + +
281A GLU* 3.0 35.2 + - - +
323A VAL* 4.0 22.9 - - + -
327A LEU* 3.8 27.1 - - + -
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Residues in contact with GLY 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU 2.8 22.4 + - - -
275A VAL 3.6 1.1 - - - -
277A LEU* 1.3 71.3 - - - +
279A VAL* 1.3 62.1 + - - +
281A GLU 3.3 1.6 + - - -
282A LYS 3.2 3.5 + - - -
283A LEU* 2.9 37.1 + - - -
284A ILE* 3.7 17.7 - - - -
319A ILE* 4.6 2.5 - - - -
323A VAL* 4.4 9.8 - - - +
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A VAL* 2.8 19.7 + - + +
276A ASP* 3.9 6.1 - - - +
278A GLY* 1.3 74.4 - - - +
280A LYS* 1.3 63.6 + - - +
282A LYS* 3.2 20.1 + - - +
284A ILE* 3.5 25.5 - - + +
286A LYS* 4.2 24.9 - - + -
291A TYR* 3.6 35.2 - - + -
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Residues in contact with LYS 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A ASP 3.0 19.1 + - - +
277A LEU* 3.6 20.3 - - + +
278A GLY 3.3 0.2 - - - -
279A VAL* 1.3 77.8 - - - +
281A GLU* 1.3 75.5 + - - +
282A LYS* 3.3 13.9 + - - +
327A LEU* 5.2 9.3 - - - +
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A LEU 3.0 20.3 + - - +
278A GLY 4.1 2.2 - - - +
279A VAL 3.2 0.4 - - - -
280A LYS* 1.3 94.6 - - + +
282A LYS* 1.3 70.4 + - - +
283A LEU* 3.2 17.0 + - + +
323A VAL* 5.0 4.9 - - + -
326A LEU* 3.9 35.6 - - + +
327A LEU* 3.6 43.4 - - + +
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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