Contacts of the helix formed by residues 344 - 354 (chain C) in PDB entry 3CMM
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 344 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287C ASP* 4.7 12.3 + - - -
288C ARG* 5.1 4.6 - - - +
291C GLN* 2.7 30.5 + - + +
342C ASP 3.4 1.4 + - - +
343C VAL* 1.3 72.4 - - - +
345C GLU* 1.3 63.1 + - - +
346C ASP* 3.7 9.0 + - - +
347C LEU* 2.9 46.4 + - + +
348C ILE* 3.1 12.6 + - - +
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Residues in contact with GLU 345 (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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323C ILE* 3.8 42.5 - - + +
327C THR* 4.8 3.8 + - - -
343C VAL* 3.1 22.6 + - + +
344C ASN* 1.3 71.1 + - - +
346C ASP* 1.3 53.2 + - - +
348C ILE* 3.3 1.3 + - - +
349C LYS* 2.7 38.6 + - - +
5129C PRO* 5.6 6.1 - - - -
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Residues in contact with ASP 346 (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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344C ASN* 3.7 7.6 + - - +
345C GLU* 1.3 79.8 - - - +
347C LEU* 1.3 60.2 + - - +
349C LYS* 3.7 25.6 - - - +
350C GLU* 3.3 27.2 + - - +
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Residues in contact with LEU 347 (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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160C PHE* 4.1 11.8 - - + -
288C ARG* 4.0 32.8 - - + +
291C GLN* 3.6 31.6 - - + -
292C LEU* 4.0 17.0 - - + -
344C ASN* 2.9 31.1 + - - +
346C ASP* 1.3 76.2 - - - +
348C ILE* 1.3 68.4 + - + +
350C GLU* 3.2 7.2 + - - +
351C LEU* 3.1 21.0 + - - +
392C ASP* 4.9 0.7 - - - +
394C LEU* 3.7 28.5 - - + -
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Residues in contact with ILE 348 (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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291C GLN* 3.9 24.9 - - + +
292C LEU* 5.0 1.8 - - + +
295C GLY* 3.9 26.2 - - - -
322C LEU* 3.9 13.1 - - + +
323C ILE* 3.8 29.2 - - + +
326C VAL* 3.8 27.8 - - + -
343C VAL* 4.0 14.6 - - + -
344C ASN 3.1 11.0 + - - +
345C GLU* 3.8 5.6 - - - +
347C LEU* 1.3 79.5 - - + +
349C LYS* 1.3 65.8 + - - +
351C LEU* 3.1 10.5 + - + +
352C SER* 3.0 21.2 + - - -
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Residues in contact with LYS 349 (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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319C ALA* 4.4 3.1 - - + -
323C ILE* 4.2 14.7 - - + +
345C GLU 2.7 19.9 + - - +
346C ASP* 3.7 31.4 + - - +
347C LEU 3.3 0.2 - - - -
348C ILE* 1.3 72.9 - - - +
350C GLU* 1.3 74.3 + - - +
352C SER* 3.2 9.7 + - - -
353C TYR* 3.0 63.8 + - + +
5129C PRO* 3.6 26.5 - - + -
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Residues in contact with GLU 350 (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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160C PHE* 3.8 14.4 - - + -
346C ASP 3.3 12.9 + - - +
347C LEU 3.2 10.1 + - - +
349C LYS* 1.3 91.5 + - - +
351C LEU* 1.3 66.9 + - - +
353C TYR* 3.2 10.6 + - - +
354C GLN* 2.8 54.6 + - - +
394C LEU* 4.5 13.2 - - + -
397C LEU* 4.1 8.3 - - + +
405C ARG* 2.7 34.1 + - - -
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Residues in contact with LEU 351 (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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157C ARG* 4.7 4.5 - - + -
160C PHE* 3.5 45.0 - - + -
292C LEU* 5.1 4.3 - - + -
295C GLY* 3.5 42.0 - - - +
296C PHE* 4.0 19.3 - - + +
299C LEU* 4.1 20.6 - - + -
322C LEU* 4.3 6.5 - - + -
347C LEU 3.1 12.0 + - - +
348C ILE* 3.1 14.3 + - + +
350C GLU* 1.3 75.8 - - - +
352C SER* 1.3 61.3 + - - +
354C GLN* 3.8 1.2 - - - +
355C ALA* 3.2 24.6 + - - +
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Residues in contact with SER 352 (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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311C PRO* 3.4 29.3 - - - +
312C ARG 4.3 5.2 + - - +
315C ASN 4.7 1.0 + - - -
318C ASP* 3.7 3.1 + - - +
319C ALA* 3.3 33.6 + - - +
322C LEU* 3.7 20.9 - - - +
348C ILE 3.0 8.2 + - - -
349C LYS 3.3 9.4 - - - -
351C LEU* 1.3 74.5 - - - +
353C TYR* 1.3 65.3 + - - +
354C GLN 3.2 0.7 + - - -
355C ALA* 3.3 16.2 + - - +
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Residues in contact with TYR 353 (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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312C ARG 4.8 0.7 - - - -
313C THR* 3.6 15.4 - - - +
314C MET* 3.3 82.6 + - + +
315C ASN 3.6 3.1 - - - -
316C ASP* 2.6 25.3 + - - -
319C ALA* 3.7 22.2 - - + -
349C LYS* 3.0 52.7 + - + +
350C GLU* 3.2 24.7 + - - +
352C SER* 1.3 76.2 - - - +
354C GLN* 1.3 59.8 + - + +
355C ALA 3.4 0.9 + - - -
356C ARG 5.0 0.9 + - - -
422C ALA* 4.5 2.6 - - - +
5129C PRO* 3.9 4.7 - - - +
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Residues in contact with GLN 354 (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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157C ARG 3.4 1.9 - - - +
158C GLY* 3.2 16.9 + - - -
159C LEU* 3.0 34.6 + - - +
160C PHE* 4.0 7.4 - - + -
350C GLU* 2.8 43.3 + - - +
351C LEU 3.8 2.5 - - - +
353C TYR* 1.3 77.4 - - - +
355C ALA* 1.3 63.4 + - - +
356C ARG 3.2 3.1 - - - -
357C GLY 3.1 12.1 + - - -
394C LEU* 3.5 23.2 - - - +
397C LEU* 3.9 11.7 - - - +
405C ARG* 4.0 11.7 - - - +
422C ALA* 5.4 1.8 - - - -
423C VAL* 3.9 25.9 - - + +
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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