Contacts of the helix formed by residues 341 - 354 (chain A) in PDB entry 3CMQ
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 ALA 341 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLY* 5.6 7.0 - - - -
144A ARG* 5.6 0.9 - - - +
340A TYR* 1.3 88.8 - - - +
342A GLU* 1.3 66.6 + - - +
343A ASN* 4.4 3.4 - - + +
344A ASP* 3.0 48.5 + - - +
345A PHE 3.5 2.8 + - - -
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Residues in contact with GLU 342 (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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340A TYR* 3.8 12.4 - - + -
341A ALA* 1.3 70.5 - - - +
343A ASN* 1.3 65.0 + - - +
345A PHE* 3.1 15.6 + - - +
346A TYR* 2.5 53.5 + - + +
362A LEU* 3.7 25.9 - - + +
365A LYS* 4.8 4.9 + - - -
376A HIS* 5.0 3.4 + - + +
378A TYR* 3.7 14.1 - - + +
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Residues in contact with ASN 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLY* 2.7 32.2 + - - +
106A ASP* 3.4 10.3 + - - -
144A ARG* 3.0 41.3 + - + +
145A ASP* 3.6 13.5 + - - +
146A GLN 4.0 0.5 + - - -
341A ALA* 3.3 2.7 - - + +
342A GLU* 1.3 79.6 - - - +
344A ASP* 1.3 62.1 + - - +
345A PHE 3.3 0.2 - - - -
346A TYR* 3.0 27.6 + - + +
347A ASP* 3.0 20.1 + - - +
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Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ARG* 2.9 29.0 + - - +
340A TYR* 4.2 4.9 - - + -
341A ALA* 3.0 43.5 + - - +
343A ASN* 1.3 74.8 - - - +
345A PHE* 1.3 64.6 + - - +
347A ASP* 3.2 5.5 + - - +
348A LEU* 3.2 19.4 + - - +
409A LEU* 4.6 14.9 - - + +
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Residues in contact with PHE 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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331A ILE* 3.9 24.7 - - + -
333A PHE* 3.8 17.0 - + - -
340A TYR* 3.3 21.5 - - + +
341A ALA 3.5 1.0 + - - -
342A GLU 3.1 6.1 + - - +
344A ASP* 1.3 78.6 - - - +
346A TYR* 1.3 70.4 + + - +
348A LEU* 3.1 5.2 + - + +
349A VAL* 3.0 40.6 + - + +
360A VAL* 4.2 7.0 - - + -
378A TYR* 3.5 43.7 - + + +
380A ILE* 4.3 1.1 - - + -
401A LEU* 3.9 26.5 - - + -
405A ALA* 4.6 2.9 - - + -
409A LEU* 3.5 26.2 - - + +
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Residues in contact with TYR 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ASP 4.1 17.3 - - - +
146A GLN* 4.2 15.1 - - + +
147A ILE* 3.4 21.2 - - + +
342A GLU* 2.5 56.5 + - + +
343A ASN* 3.0 31.4 - - - +
344A ASP 3.2 0.2 - - - -
345A PHE* 1.3 85.4 - + - +
347A ASP* 1.3 60.1 + - - +
349A VAL* 3.4 1.5 + - - -
350A ARG* 3.1 28.4 + - - +
360A VAL* 3.7 38.5 + - + -
362A LEU* 4.3 6.6 + - - +
378A TYR* 3.7 17.2 - + - -
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Residues in contact with ASP 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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29A ASN 5.3 0.3 - - - +
31A THR* 4.1 25.9 + - + +
34A VAL* 4.9 0.5 - - - +
108A TYR* 2.8 28.4 + - - -
144A ARG* 2.7 42.3 + - - +
153A PRO* 5.4 0.3 - - - +
343A ASN 3.0 8.3 + - - +
344A ASP* 3.5 9.0 - - - +
345A PHE 3.2 0.2 - - - -
346A TYR* 1.3 73.9 - - - +
348A LEU* 1.3 62.4 + - - +
350A ARG* 3.2 11.6 + - - +
351A THR* 2.9 32.3 + - - -
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Residues in contact with LEU 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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344A ASP 3.2 8.9 + - - +
345A PHE* 3.1 10.2 + - + +
347A ASP* 1.3 76.7 - - - +
349A VAL* 1.3 60.2 + - - +
351A THR* 3.3 9.3 + - + -
352A ILE* 2.9 37.6 + - + +
401A LEU* 4.1 13.7 - - + -
404A ALA* 3.8 13.2 - - + -
405A ALA* 3.5 31.4 - - + +
408A LEU* 3.7 26.9 - - + -
409A LEU* 3.3 31.9 - - + -
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 3.9 16.8 - - + -
345A PHE* 3.0 48.9 + - + +
346A TYR* 3.6 8.1 - - - +
348A LEU* 1.3 74.5 - - - +
350A ARG* 1.3 59.8 + - - +
353A GLY* 2.6 33.1 + - - +
354A GLY 3.4 0.5 + - - -
357A VAL* 3.9 30.9 - - + +
360A VAL* 4.0 9.9 - - + -
380A ILE* 4.6 2.5 - - + -
401A LEU* 3.9 21.8 - - + -
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Residues in contact with ARG 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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33A LYS* 3.8 21.5 - - + -
145A ASP 5.6 0.2 + - - -
146A GLN 4.0 3.0 + - - -
147A ILE* 3.7 46.7 - - + +
148A ASP 4.6 0.8 + - - -
151A HIS 2.8 32.5 + - - -
152A TYR* 3.5 27.1 - - - +
153A PRO* 3.6 31.4 - - + +
294A ARG* 4.7 6.3 - - - +
346A TYR* 3.1 20.3 + - + +
347A ASP* 3.2 13.0 + - - +
349A VAL* 1.3 77.2 - - - +
351A THR* 1.3 58.4 - - - +
354A GLY* 3.0 36.8 + - - +
355A ASP* 4.8 1.8 + - - -
357A VAL* 4.7 9.6 + - - +
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Residues in contact with THR 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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31A THR* 4.6 9.5 + - - +
32A ARG* 5.3 12.3 + - + +
33A LYS* 3.5 31.6 + - + +
347A ASP 2.9 17.3 + - - -
348A LEU* 3.6 13.4 - - + -
350A ARG* 1.3 79.7 - - - +
352A ILE* 1.3 70.1 + - + +
354A GLY* 4.4 1.7 + - - -
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Residues in contact with ILE 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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348A LEU* 2.9 33.9 + - + +
351A THR* 1.3 86.1 - - + +
353A GLY* 1.3 63.1 + - - +
354A GLY 3.4 0.8 + - - -
397A ILE* 3.8 40.9 - - + +
400A ALA* 4.1 19.1 - - + +
401A LEU* 4.1 13.9 - - + +
404A ALA* 4.3 19.7 - - + -
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Residues in contact with GLY 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A VAL* 2.6 19.9 + - - +
352A ILE* 1.3 76.8 - - - +
354A GLY* 1.3 66.1 + - - +
355A ASP 3.4 0.2 + - - -
356A LEU* 2.9 27.5 + - - +
357A VAL* 3.9 15.9 - - - -
397A ILE* 4.0 15.7 - - - -
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Residues in contact with GLY 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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33A LYS* 4.6 13.2 - - - -
349A VAL 3.4 3.0 + - - +
350A ARG* 3.0 37.1 + - - +
351A THR 4.3 1.5 - - - -
352A ILE 3.4 2.8 + - - -
353A GLY* 1.3 79.9 - - - +
355A ASP* 1.3 63.4 + - - +
356A LEU 3.1 2.3 + - - -
357A VAL* 3.6 13.2 + - - +
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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