Contacts of the helix formed by residues 344 - 355 (chain A) in PDB entry 4NTX
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 CYS 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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321A ASN 3.2 14.6 - - - -
322A CYS* 2.1 50.4 - - + +
340A GLN* 2.9 14.3 + - + +
342A LYS 3.6 0.6 - - - -
343A GLU* 1.3 82.7 - - + +
345A ALA* 1.3 59.8 + - - +
346A ASP 3.6 1.1 - - - -
347A PRO* 3.7 1.6 - - - -
348A ALA* 3.0 32.9 + - - +
1C ASN* 3.6 13.0 - - - -
63C VAL* 3.4 14.8 - - + +
65C PHE* 3.5 12.3 - - - +
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Residues in contact with ALA 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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318A LEU* 4.0 12.6 - - + +
322A CYS* 3.9 9.0 - - - -
324A CYS* 4.8 0.2 - - - -
326A MET* 3.6 17.0 - - + +
336A CYS* 3.8 26.7 - - - -
340A GLN 2.8 19.2 + - - +
341A TYR* 3.9 8.5 - - - -
344A CYS* 1.3 70.0 - - - +
346A ASP* 1.3 65.1 + - - +
348A ALA* 4.0 0.3 - - - +
349A LEU* 3.0 27.2 + - - +
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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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115A LEU* 4.0 2.3 - - - +
191A ARG* 2.8 22.6 + - - +
238A ASP* 3.3 21.6 + - - +
239A GLU* 2.6 36.5 - - - +
326A MET* 3.0 15.1 - - - +
341A TYR* 2.8 32.6 + - - +
342A LYS* 4.6 2.7 - - - +
345A ALA* 1.3 74.1 - - - +
347A PRO* 1.3 59.7 - - + +
350A ASP* 2.9 36.6 + - - +
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Residues in contact with PRO 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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341A TYR 3.7 1.6 - - - +
342A LYS 3.7 21.8 - - - +
343A GLU 3.9 9.9 - - - +
344A CYS 3.6 9.6 - - - +
346A ASP* 1.3 92.6 - - + +
348A ALA* 1.3 51.0 + - - +
350A ASP* 3.2 7.7 + - + +
351A PHE* 2.7 36.2 + - - +
65C PHE* 4.0 17.9 - - + -
87C ARG* 3.3 38.1 - - - +
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Residues in contact with ALA 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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317A TYR* 3.4 13.0 - - + -
318A LEU* 3.7 19.1 - - + -
321A ASN* 4.9 1.1 - - + -
322A CYS* 4.1 4.9 - - - -
344A CYS 3.0 21.0 + - - +
347A PRO* 1.3 75.7 - - - +
349A LEU* 1.3 57.9 + - - +
351A PHE* 3.4 1.0 + - - +
352A LEU* 2.9 30.0 + - - +
65C PHE* 3.4 34.4 - - + -
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Residues in contact with LEU 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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191A ARG* 3.6 33.9 - - + +
314A GLU* 3.7 44.9 - - + +
318A LEU* 4.1 13.4 - - + +
326A MET* 3.6 28.9 - - + -
328A HIS* 4.8 6.1 - - + +
329A MET* 5.5 2.2 - - - -
345A ALA 3.0 17.7 + - - +
346A ASP 4.0 1.8 - - - +
348A ALA* 1.3 72.9 - - - +
350A ASP* 1.3 66.5 - - - +
352A LEU* 4.4 7.0 - - + -
353A VAL* 2.9 37.1 + - + +
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Residues in contact with ASP 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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191A ARG* 2.8 33.8 + - - +
238A ASP* 2.5 26.6 - - - +
346A ASP 2.9 22.8 + - - +
347A PRO* 3.6 5.9 - - + +
349A LEU* 1.3 76.0 - - - +
351A PHE* 1.3 56.1 + - - +
353A VAL* 4.8 1.6 - - - -
354A GLU* 2.9 45.1 + - - +
506A P6G 4.1 3.7 - - - +
509A AMR 3.4 36.9 + - - +
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Residues in contact with PHE 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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317A TYR* 3.3 24.0 - - - -
347A PRO 2.7 21.8 + - - +
348A ALA 3.6 3.4 - - - +
350A ASP* 1.3 72.7 - - - +
352A LEU* 1.3 60.5 + - - +
354A GLU* 5.1 1.1 - - - -
355A LYS* 2.7 70.9 + - + -
356A ASP* 3.0 41.4 + - + -
65C PHE* 3.9 14.1 - + + -
67C SER* 3.4 34.5 - - - -
68C PHE 5.4 2.2 - - - -
69C GLU* 6.4 1.8 - - + -
81C GLY 5.9 0.2 - - - -
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Residues in contact with LEU 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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313A CYS* 4.4 3.4 - - + +
314A GLU* 3.7 43.5 - - + +
317A TYR* 3.7 26.9 - - + -
348A ALA 2.9 18.8 + - - +
349A LEU* 3.8 7.9 - - + +
351A PHE* 1.3 78.0 - - - +
353A VAL* 1.3 65.8 + - - +
356A ASP* 3.6 25.9 + - + +
359A TYR* 3.7 37.2 - - + -
360A CYS* 4.9 7.4 - - + +
503A CL 4.4 7.6 - - + -
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Residues in contact with VAL 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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191A ARG* 5.5 2.9 - - - +
260A ASP* 5.5 1.3 - - - +
261A GLN* 3.5 39.5 - - + +
310A ARG* 4.1 12.2 + - - +
314A GLU* 4.1 19.5 - - - +
349A LEU* 2.9 31.3 + - + +
350A ASP* 3.9 3.4 - - - +
352A LEU* 1.3 81.2 - - - +
354A GLU* 1.3 73.3 + - + +
356A ASP 4.5 4.3 - - - +
503A CL 4.3 10.5 - - + -
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Residues in contact with GLU 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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350A ASP* 2.9 27.1 + - - +
351A PHE* 5.1 0.5 - - - -
353A VAL* 1.3 83.1 - - + +
355A LYS* 1.3 60.5 + - + +
506A P6G 3.9 22.2 - - - +
508A AMR 3.6 14.3 + - - -
509A AMR 2.6 45.8 + - - -
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Residues in contact with LYS 355 (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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351A PHE* 2.7 51.6 + - + +
353A VAL 3.4 0.2 - - - -
354A GLU* 1.3 78.3 - - + +
356A ASP* 1.3 64.7 + - - +
357A ASN* 3.5 17.5 + - - +
69C GLU* 5.7 4.4 + - - -
81C GLY* 3.4 38.7 + - - +
83C ASN* 6.5 0.7 - - - -
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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