Contacts of the helix formed by residues 344 - 354 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A ASP* 5.2 7.5 + - - -
288A ARG* 5.5 6.5 - - - +
291A GLN* 2.8 30.7 + - + +
342A ASP 3.5 2.2 + - - +
343A VAL* 1.3 71.1 - - - +
345A GLU* 1.3 62.4 + - - +
346A ASP* 3.5 7.1 + - - +
347A LEU* 3.2 33.7 + - + +
348A ILE* 3.1 23.6 + - - +
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Residues in contact with GLU 345 (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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323A ILE* 3.7 41.0 - - + +
327A THR* 5.2 1.7 + - - -
343A VAL* 3.0 21.0 + - + +
344A ASN* 1.3 72.0 + - - +
346A ASP* 1.3 59.2 + - - +
348A ILE* 4.6 0.4 - - - +
349A LYS* 2.8 33.2 + - - +
5119A PRO* 4.9 13.3 - - + +
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Residues in contact with ASP 346 (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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344A ASN* 3.4 7.1 + - - +
345A GLU* 1.3 79.5 - - - +
347A LEU* 1.3 59.1 + - - +
349A LYS* 3.2 30.2 + - - +
350A GLU* 3.3 28.2 + - - +
394A LEU* 5.8 0.2 - - - +
5119A PRO* 4.5 9.9 - - - -
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Residues in contact with LEU 347 (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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160A PHE* 4.0 10.8 - - + -
288A ARG* 3.9 39.3 - - + +
291A GLN* 3.8 27.8 - - + -
292A LEU* 3.9 22.4 - - + -
344A ASN* 3.2 29.5 + - - +
346A ASP* 1.3 76.7 - - - +
348A ILE* 1.3 60.8 + - + +
350A GLU* 3.2 6.1 + - - +
351A LEU* 3.0 25.6 + - - +
392A ASP* 4.4 1.1 - - - +
394A LEU* 3.8 27.6 - - + -
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Residues in contact with ILE 348 (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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291A GLN* 3.7 32.1 - - - +
292A LEU* 4.9 2.0 - - + -
295A GLY* 4.0 15.3 - - - -
322A LEU* 3.7 16.0 - - + +
323A ILE* 3.8 28.3 - - + +
326A VAL* 3.7 33.9 - - + -
343A VAL* 4.4 4.3 - - + -
344A ASN 3.1 17.8 + - - +
345A GLU* 4.0 2.7 - - - +
347A LEU* 1.3 82.6 - - + +
349A LYS* 1.3 64.9 + - - +
351A LEU* 3.2 11.6 + - + +
352A SER* 3.1 18.2 + - - -
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Residues in contact with LYS 349 (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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319A ALA* 4.1 18.6 - - + +
323A ILE* 4.2 9.3 - - + +
345A GLU 2.8 19.8 + - - +
346A ASP* 3.2 37.7 + - - +
348A ILE* 1.3 74.5 - - - +
350A GLU* 1.3 71.5 + - - +
352A SER* 2.9 6.9 + - - -
353A TYR* 2.9 70.3 + - + +
5119A PRO* 4.2 22.2 - - + -
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Residues in contact with GLU 350 (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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160A PHE* 3.7 14.8 - - + -
346A ASP 3.3 13.8 + - - +
347A LEU 3.2 9.7 + - - +
349A LYS* 1.3 92.4 + - - +
351A LEU* 1.3 61.7 + - - +
353A TYR* 3.3 12.3 + - - +
354A GLN* 2.8 46.3 + - - +
394A LEU* 4.5 14.1 - - + -
397A LEU* 4.2 11.2 - - + +
405A ARG* 2.4 37.3 + - - -
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Residues in contact with LEU 351 (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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157A ARG* 4.4 11.2 - - + -
160A PHE* 3.6 39.2 - - + -
292A LEU* 4.6 9.2 - - + -
295A GLY* 3.6 38.8 - - - +
296A PHE* 4.0 18.8 - - + +
299A LEU* 3.8 21.8 - - + -
322A LEU* 4.5 5.4 - - + -
347A LEU 3.0 12.4 + - - +
348A ILE* 3.2 12.7 + - + +
350A GLU* 1.3 74.5 - - - +
352A SER* 1.3 61.7 + - - +
354A GLN 3.7 0.5 - - - -
355A ALA* 3.0 22.6 + - - +
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Residues in contact with SER 352 (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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311A PRO* 3.3 32.7 - - - +
312A ARG 4.1 6.1 + - - +
315A ASN 4.7 1.0 + - - -
318A ASP* 3.4 3.3 + - - +
319A ALA* 3.2 34.0 + - - +
322A LEU* 3.6 19.9 - - - +
348A ILE 3.1 7.0 + - - -
349A LYS 2.9 9.5 + - - -
351A LEU* 1.3 76.5 - - - +
353A TYR* 1.3 64.3 - - - +
354A GLN 3.1 1.0 + - - -
355A ALA* 3.2 15.2 + - - +
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Residues in contact with TYR 353 (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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312A ARG 4.7 0.2 - - - -
313A THR* 3.7 14.4 + - - +
314A MET* 3.3 80.8 + - + +
315A ASN 3.8 12.3 - - - -
316A ASP* 2.6 29.0 + - - -
319A ALA* 4.0 11.9 - - + -
349A LYS* 2.9 47.9 + - + +
350A GLU* 3.5 20.2 - - - +
352A SER* 1.3 76.8 - - - +
354A GLN* 1.3 58.7 + - - +
355A ALA 3.9 0.2 + - - -
356A ARG 5.1 0.7 + - - -
405A ARG* 3.8 10.1 - - - +
422A ALA 4.5 2.4 - - - +
5119A PRO* 4.5 4.0 - - - -
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Residues in contact with GLN 354 (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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157A ARG 4.5 0.9 - - - -
158A GLY* 3.1 19.7 + - - -
159A LEU* 3.0 35.2 + - - +
160A PHE* 3.8 9.3 - - + -
350A GLU* 2.8 39.6 + - - +
351A LEU 3.7 1.8 - - - +
353A TYR* 1.3 76.6 - - - +
355A ALA* 1.3 64.8 + - - +
356A ARG 3.2 3.8 - - - -
357A GLY 2.9 15.0 + - - +
394A LEU* 3.5 21.8 - - - +
397A LEU* 3.9 9.9 - - - +
405A ARG* 3.7 16.8 - - - +
422A ALA* 5.4 2.2 - - - -
423A VAL* 4.0 16.6 - - + +
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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