Contacts of the helix formed by residues 344 - 353 (chain A) in PDB entry 3CPE
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 SER 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A ILE* 3.3 7.6 + - - -
343A SER* 1.3 86.9 + - - +
345A LEU* 1.3 59.3 + - - +
346A ALA* 4.0 8.3 - - - -
347A GLN* 3.1 25.2 + - - +
348A PHE* 2.8 29.4 + - - +
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Residues in contact with LEU 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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11A PHE* 5.9 3.6 - - + -
13A PRO* 3.2 32.5 - - + +
14A LEU* 4.4 8.3 - - + -
16A GLU* 4.3 12.6 - - + +
340A ILE* 3.7 39.4 - - + +
344A SER* 1.3 69.3 - - - +
346A ALA* 1.3 65.4 + - - +
348A PHE* 3.7 1.2 - - - +
349A ARG* 3.1 59.3 + - - +
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Residues in contact with ALA 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 SER* 4.0 7.3 - - - -
345A LEU* 1.3 79.7 - - - +
347A GLN* 1.3 59.5 + - - +
349A ARG* 3.8 15.3 + - - +
350A GLN* 3.3 24.5 + - - +
357A GLU* 5.6 1.6 - - - +
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Residues in contact with GLN 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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343A SER* 4.3 18.8 - - - +
344A SER* 3.1 27.7 + - - +
346A ALA* 1.3 79.5 - - - +
348A PHE* 1.3 53.9 + - - +
350A GLN* 3.1 16.9 + - + +
351A GLU* 2.7 48.3 + - + +
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Residues in contact with PHE 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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14A LEU* 3.9 20.6 - - + -
315A TRP* 3.8 39.3 - + - -
335A TRP* 3.7 21.1 - + - -
336A SER* 4.2 14.6 - - - -
339A THR* 3.7 23.8 - - + +
340A ILE* 3.6 25.8 - - + -
343A SER* 5.3 1.3 + - - +
344A SER 2.8 15.4 + - - +
345A LEU 3.2 5.4 + - - +
347A GLN* 1.3 73.8 - - - +
349A ARG* 1.3 57.4 + - - +
352A HIS* 2.6 64.5 + + + +
353A THR* 3.5 14.0 + - + -
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Residues in contact with ARG 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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14A LEU* 5.1 11.6 + - + +
16A GLU* 3.0 43.6 + - - +
21A LEU* 6.1 2.6 - - - +
288A PRO* 6.0 0.2 - - - +
345A LEU* 3.1 39.1 + - - +
346A ALA* 3.9 14.2 - - - +
348A PHE* 1.3 79.0 - - + +
350A GLN* 1.3 61.7 + - - +
353A THR* 2.7 40.7 + - + +
354A ALA* 3.8 5.7 + - - -
355A ALA* 4.2 14.5 + - + +
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Residues in contact with GLN 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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162A ARG* 5.1 7.4 + - - +
259A PHE* 6.3 4.0 - - + -
287A THR* 5.1 9.5 - - - -
288A PRO* 5.5 5.7 - - - +
346A ALA 3.3 13.8 + - - +
347A GLN* 3.1 21.4 + - + +
349A ARG* 1.3 81.5 - - - +
351A GLU* 1.3 59.2 + - + +
353A THR 5.1 0.2 - - - -
354A ALA 5.5 1.6 + - - -
355A ALA 5.9 1.1 - - - -
357A GLU* 3.3 25.4 - - + +
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Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A SER* 3.7 0.6 - - - -
162A ARG* 2.7 63.7 + - - +
163A GLN* 3.3 28.4 - - + +
347A GLN* 2.7 29.5 + - + +
350A GLN* 1.3 76.1 - - + +
352A HIS* 1.3 81.1 + - + +
353A THR 3.8 0.9 - - - -
354A ALA 5.5 0.2 - - - -
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Residues in contact with HIS 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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161A SER* 3.4 11.0 - - - -
162A ARG 4.2 3.8 + - - -
163A GLN* 3.6 35.2 + - + -
314A ILE* 3.2 5.4 - - - +
315A TRP* 3.1 37.6 + - + +
321A ARG* 3.8 13.1 + - - -
335A TRP* 3.6 22.8 - + - -
339A THR* 3.6 15.1 - - + +
348A PHE* 2.6 55.6 + + + +
351A GLU* 1.3 91.6 + - + +
353A THR* 1.3 56.5 + - - +
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Residues in contact with THR 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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14A LEU* 5.1 5.8 - - + -
21A LEU* 6.0 3.8 - - + -
314A ILE* 3.4 22.5 - - + +
315A TRP* 4.6 4.9 - - + +
348A PHE* 3.7 32.5 - - + +
349A ARG* 2.7 38.6 + - + +
352A HIS* 1.3 83.1 - - - +
354A ALA* 1.3 70.6 + - - +
355A ALA* 3.0 14.2 + - - +
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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