Contacts of the helix formed by residues 301 - 312 (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 GLY 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A ALA* 2.8 24.7 + - - +
291A TYR* 3.5 9.7 - - - -
300A GLN* 1.3 73.5 - - - +
302A LYS* 1.3 66.6 + - - -
303A ALA* 3.1 4.5 - - - -
304A ASN 3.0 14.4 + - - -
305A ALA 3.3 7.1 + - - -
4233D GLU 5.5 0.7 - - - -
4234D GLY* 5.0 15.5 - - - -
4235D GLU* 5.5 3.4 - - - -
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Residues in contact with LYS 302 (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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261A GLN* 5.2 16.4 + - - +
269A ASN* 5.0 3.2 - - - +
272A GLY* 2.9 40.8 + - - -
275A VAL* 4.2 9.4 - - + -
276A ASP* 3.2 31.9 + - - +
291A TYR* 3.3 24.9 + - - +
301A GLY* 1.3 69.7 - - - -
303A ALA* 1.3 58.6 + - - +
305A ALA* 3.4 3.3 + - - +
306A THR* 2.7 38.6 + - - +
4234D GLY* 5.7 2.4 - - - -
4235D GLU* 5.9 3.3 - - + +
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Residues in contact with ALA 303 (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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300A GLN 5.5 0.2 - - - +
301A GLY* 3.0 2.6 + - - +
302A LYS* 1.3 78.1 - - - +
304A ASN* 1.3 65.1 + - - +
306A THR* 3.5 6.5 - - - -
307A ALA* 3.3 20.1 + - - +
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Residues in contact with ASN 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ILE 4.1 1.0 - - - +
299A GLY* 4.0 5.6 - - - -
300A GLN* 2.9 37.4 + - - +
301A GLY 3.0 2.6 + - - -
303A ALA* 1.3 81.1 - - - +
305A ALA* 1.3 60.7 + - - +
307A ALA* 3.1 12.5 + - - +
308A TRP* 2.9 28.1 + - - +
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Residues in contact with ALA 305 (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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275A VAL* 3.9 17.7 - - + +
291A TYR* 3.8 39.0 - - + -
298A ILE* 4.1 19.8 - - + +
299A GLY* 4.2 1.9 - - - -
301A GLY 3.3 3.6 + - - -
302A LYS 3.8 6.5 - - - +
304A ASN* 1.3 77.8 - - - +
306A THR* 1.3 62.5 + - - +
308A TRP* 3.3 4.0 + - - +
309A LEU* 3.3 26.2 + - - +
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Residues in contact with THR 306 (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* 3.7 14.1 + - - +
271A TYR* 3.6 11.2 - - + +
272A GLY* 3.6 35.8 - - - +
275A VAL* 3.8 11.4 - - - +
302A LYS* 2.7 26.6 + - - +
303A ALA* 3.5 8.0 - - - -
305A ALA* 1.3 77.0 - - - +
307A ALA* 1.3 61.9 + - - +
309A LEU* 3.2 5.8 + - - +
310A LYS* 3.2 31.6 + - - +
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Residues in contact with ALA 307 (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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303A ALA 3.3 10.3 + - - +
304A ASN* 3.1 16.9 + - - +
306A THR* 1.3 79.3 - - - +
308A TRP* 1.3 63.0 + - - +
310A LYS* 3.4 14.6 + - + +
311A ASP* 3.1 30.0 + - - +
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Residues in contact with TRP 308 (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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293A TYR* 4.7 8.3 - + + -
296A GLU* 3.8 26.4 + - - -
297A LYS 5.1 1.0 + - - -
298A ILE* 3.2 66.1 - - + +
304A ASN 2.9 7.6 + - - +
305A ALA 3.5 8.3 - - - +
306A THR 3.2 0.2 - - - -
307A ALA* 1.3 78.1 - - - +
309A LEU* 1.3 81.0 + - + +
311A ASP* 3.1 7.2 + - + +
312A ASN* 2.8 65.2 + - + +
315A THR* 4.0 27.8 - - + -
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Residues in contact with LEU 309 (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* 3.8 23.5 - - + +
274A LEU* 4.0 22.2 - - + -
275A VAL* 3.7 31.9 - - + +
284A ILE* 4.7 7.9 - - + -
298A ILE* 5.0 3.4 - - + -
305A ALA 3.3 6.0 + - - +
306A THR 3.2 8.7 + - - +
308A TRP* 1.3 92.9 - - + +
310A LYS* 1.3 66.6 + - - +
312A ASN 3.3 19.8 - - - +
313A PRO* 3.7 1.9 - - - +
316A ALA* 3.8 27.3 - - + +
319A ILE* 3.9 24.7 - - + -
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Residues in contact with LYS 310 (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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266A GLU* 2.9 30.2 + - - +
269A ASN* 5.7 2.1 + - - -
271A TYR* 3.5 38.3 + - + -
306A THR* 3.2 25.7 + - - +
307A ALA* 3.4 17.3 - - + +
309A LEU* 1.3 76.0 - - - +
311A ASP* 1.3 64.9 + - - +
312A ASN 3.5 0.2 + - - -
313A PRO* 3.6 15.1 - - - +
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Residues in contact with ASP 311 (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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307A ALA* 3.1 16.6 + - - +
308A TRP* 3.1 13.9 + - + +
310A LYS* 1.3 84.7 - - - +
312A ASN* 1.3 63.7 + - - +
313A PRO* 3.2 9.4 - - - +
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Residues in contact with ASN 312 (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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308A TRP* 2.8 56.1 + - + +
309A LEU* 3.3 8.2 - - - +
311A ASP* 1.3 86.8 - - - +
313A PRO* 1.3 61.0 - - - +
314A GLU* 3.2 6.0 + - + -
315A THR* 3.2 20.9 + - - +
316A ALA* 3.0 22.2 + - - +
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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