Contacts of the helix formed by residues 301 - 312 (chain D) 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 GLY 301 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4233A GLU* 3.8 24.2 - - - -
289D ALA* 2.8 18.1 + - - +
291D TYR* 3.5 9.5 - - - -
300D GLN* 1.3 74.9 - - - +
302D LYS* 1.3 66.1 + - - -
303D ALA* 3.1 4.7 - - - -
304D ASN 3.0 14.4 + - - -
305D ALA 3.2 7.3 + - - -
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Residues in contact with LYS 302 (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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4233A GLU* 4.5 5.8 + - - +
4234A GLY* 4.8 23.1 - - - +
4235A GLU* 5.8 2.2 - - + +
261D GLN* 5.6 9.6 - - - +
269D ASN* 5.0 5.0 - - - +
272D GLY* 2.9 41.0 + - - -
275D VAL* 4.2 9.6 - - + -
276D ASP* 3.2 32.7 + - - +
291D TYR* 3.3 24.5 + - - +
301D GLY* 1.3 70.3 - - - -
303D ALA* 1.3 57.8 + - - +
305D ALA* 3.4 3.3 + - - +
306D THR* 2.7 38.9 + - - +
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Residues in contact with ALA 303 (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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4303A ALA* 6.0 6.5 - - + -
4304A ASN* 6.1 0.4 - - - +
300D GLN 5.5 0.2 - - - +
301D GLY* 3.0 2.0 + - - -
302D LYS* 1.3 78.5 - - - +
304D ASN* 1.3 65.6 + - - +
306D THR* 3.5 7.2 - - - -
307D ALA* 3.3 19.1 + - - +
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Residues in contact with ASN 304 (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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4303A ALA* 6.2 0.2 - - - +
4304A ASN* 3.2 38.8 + - - +
298D ILE 4.1 1.0 - - - +
299D GLY* 4.0 6.3 - - - -
300D GLN* 2.9 37.3 + - - +
301D GLY 3.0 2.8 + - - +
303D ALA* 1.3 80.1 - - - +
305D ALA* 1.3 60.0 + - - +
307D ALA* 3.1 11.9 + - - +
308D TRP* 3.0 27.7 + - - +
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Residues in contact with ALA 305 (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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275D VAL* 3.9 16.6 - - + -
291D TYR* 3.8 39.9 - - + -
298D ILE* 4.1 19.8 - - + +
299D GLY* 4.3 2.5 - - - -
301D GLY 3.2 3.0 + - - -
302D LYS 3.8 6.7 - - - +
304D ASN* 1.3 77.1 - - - +
306D THR* 1.3 62.6 + - - +
308D TRP* 3.3 4.3 + - - +
309D LEU* 3.3 25.5 + - - +
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Residues in contact with THR 306 (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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269D ASN* 3.8 14.1 + - - +
271D TYR* 3.6 11.9 - - + +
272D GLY* 3.6 35.7 - - - +
275D VAL* 3.8 10.2 - - - +
302D LYS* 2.7 26.2 + - - +
303D ALA* 3.5 7.5 - - - -
305D ALA* 1.3 77.3 - - - +
307D ALA* 1.3 62.2 + - - +
309D LEU* 3.2 6.3 + - - +
310D LYS* 3.2 31.3 + - - +
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Residues in contact with ALA 307 (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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4300A GLN* 5.3 10.3 - - - +
303D ALA 3.3 10.3 + - - +
304D ASN* 3.1 17.3 + - - +
306D THR* 1.3 78.6 - - - +
308D TRP* 1.3 61.7 + - - +
310D LYS* 3.4 15.0 + - + +
311D ASP* 3.1 29.7 + - - +
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Residues in contact with TRP 308 (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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293D TYR* 4.7 7.9 - + + -
296D GLU* 3.8 26.4 + - - -
297D LYS 5.1 1.0 + - - -
298D ILE* 3.2 66.8 - - + +
304D ASN 3.0 7.6 + - - +
305D ALA 3.5 7.9 - - - +
306D THR 3.2 0.2 - - - -
307D ALA* 1.3 77.9 - - - +
309D LEU* 1.3 81.4 + - + +
311D ASP* 3.1 7.8 + - + +
312D ASN* 2.8 68.2 + - + +
315D THR* 4.0 24.7 - - + -
319D ILE* 5.3 0.2 - - + -
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Residues in contact with LEU 309 (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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271D TYR* 3.8 22.8 - - + +
274D LEU* 4.0 22.2 - - + -
275D VAL* 3.7 31.2 - - + +
284D ILE* 4.8 8.3 - - + -
298D ILE* 5.0 3.8 - - + -
305D ALA 3.3 5.5 + - - +
306D THR 3.2 8.3 + - - +
308D TRP* 1.3 94.4 - - + +
310D LYS* 1.3 65.6 + - - +
312D ASN 3.4 19.6 - - - +
313D PRO* 3.7 1.9 - - - +
316D ALA* 3.8 26.5 - - - +
319D ILE* 3.9 25.1 - - + -
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Residues in contact with LYS 310 (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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266D GLU* 3.1 28.0 + - - +
269D ASN* 5.7 2.8 + - - -
271D TYR* 3.5 36.7 + - + -
306D THR* 3.2 26.1 + - - +
307D ALA* 3.4 15.0 - - + +
308D TRP 3.3 0.2 - - - -
309D LEU* 1.3 76.0 - - - +
311D ASP* 1.3 65.6 + - - +
312D ASN 3.5 0.2 + - - -
313D PRO* 3.6 15.1 - - - +
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Residues in contact with ASP 311 (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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307D ALA* 3.1 15.0 + - - +
308D TRP* 3.1 14.9 + - + +
310D LYS* 1.3 84.6 - - - +
312D ASN* 1.3 65.3 + - - +
313D PRO* 3.2 9.3 - - - +
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Residues in contact with ASN 312 (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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308D TRP* 2.8 53.7 + - + +
309D LEU* 3.4 8.6 - - - +
311D ASP* 1.3 87.4 - - - +
313D PRO* 1.3 60.2 - - - +
314D GLU* 3.2 7.0 + - + -
315D THR* 3.2 20.1 + - - +
316D ALA* 3.0 22.3 + - - +
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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