Contacts of the helix formed by residues 325 - 342 (chain I) in PDB entry 4ZZ7
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 THR 325 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I PHE* 5.7 8.1 - - + -
176I ARG* 4.3 22.6 + - + +
323I VAL* 3.5 6.0 + - - +
324I ILE* 1.3 95.2 - - + +
326I ARG* 1.3 65.4 + - - +
327I GLN* 3.9 9.4 + - - +
328I HIS* 3.1 24.4 + - - +
329I GLN* 3.0 17.5 + - - +
362I PHE* 3.5 18.4 - - + +
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Residues in contact with ARG 326 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I GLY* 5.3 2.4 + - - -
325I THR* 1.3 73.1 - - - +
327I GLN* 1.3 64.3 + - - +
329I GLN* 3.0 24.8 + - - +
330I GLU* 3.0 44.5 + - - +
360I ASN* 3.3 25.7 + - - +
361I GLY 2.8 28.9 + - - -
362I PHE* 3.5 38.9 - - + -
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Residues in contact with GLN 327 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176I ARG* 5.1 9.0 + - - -
325I THR* 3.3 8.3 + - - +
326I ARG* 1.3 78.3 - - - +
328I HIS* 1.3 57.3 + - - +
330I GLU* 3.5 9.2 + - - +
331I LYS* 3.0 34.1 + - - +
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Residues in contact with HIS 328 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I PHE* 4.9 3.6 - + - -
176I ARG* 6.0 2.3 + - - +
278I GLU* 3.6 14.3 + - - -
323I VAL* 3.5 30.3 - - + -
324I ILE* 3.9 9.6 - - + -
325I THR* 3.1 20.0 + - - +
327I GLN* 1.3 77.9 + - - +
329I GLN* 1.3 64.7 + - - +
331I LYS* 3.4 26.6 + - + +
332I VAL* 3.0 26.0 + - + +
383I ILE 3.9 14.1 - - - -
384I PHE* 2.9 44.7 + + + -
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Residues in contact with GLN 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323I VAL* 3.4 12.4 - - + +
325I THR 3.0 14.2 + - - +
326I ARG* 3.0 39.0 + - - +
328I HIS* 1.3 75.6 - - - +
330I GLU* 1.3 60.5 + - + +
332I VAL* 2.9 6.7 + - - +
333I ILE* 2.9 42.1 + - + +
351I ARG 5.5 2.0 + - - -
353I PRO* 5.6 1.6 - - - +
361I GLY 4.1 4.0 + - - -
362I PHE* 3.6 14.0 - - + +
363I PHE 3.3 24.7 + - - +
364I VAL* 3.9 18.1 - - + +
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Residues in contact with GLU 330 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326I ARG* 3.0 40.4 + - + +
327I GLN* 3.8 7.3 - - - +
329I GLN* 1.3 82.7 - - + +
331I LYS* 1.3 57.4 + - - +
333I ILE* 3.7 9.6 - - + +
334I GLY* 2.9 25.3 + - - -
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Residues in contact with LYS 331 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327I GLN* 3.0 26.5 + - + +
328I HIS* 3.7 29.8 + - + +
329I GLN 3.1 0.2 - - - -
330I GLU* 1.3 74.8 - - - +
332I VAL* 1.3 59.5 + - - +
334I GLY* 3.3 2.5 + - - -
335I TYR* 3.0 60.4 + - + +
382I GLU 5.5 1.5 + - - +
383I ILE 5.3 0.9 - - - +
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Residues in contact with VAL 332 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323I VAL* 4.4 4.9 - - + -
328I HIS* 3.0 30.1 + - + +
329I GLN 2.9 8.5 + - - +
331I LYS* 1.3 72.8 - - - +
333I ILE* 1.3 65.9 + - - +
335I TYR* 3.4 8.9 + - - +
336I ILE* 3.2 28.8 + - + +
364I VAL* 3.9 28.9 - - + -
383I ILE* 4.0 24.6 - - + +
385I GLY* 3.9 19.1 - - - +
386I PRO* 4.3 10.8 - - + -
387I VAL* 4.3 1.6 - - + -
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Residues in contact with ILE 333 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329I GLN* 2.9 33.0 + - + +
330I GLU* 3.7 9.2 - - + +
332I VAL* 1.3 74.2 - - - +
334I GLY* 1.3 63.9 + - - +
336I ILE* 3.0 9.5 + - - +
337I ASN* 2.9 37.3 + - - +
351I ARG* 3.4 48.9 - - + +
364I VAL* 4.2 20.9 - - + -
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Residues in contact with GLY 334 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330I GLU 2.9 16.3 + - - -
331I LYS* 3.3 5.4 + - - -
332I VAL 3.3 0.2 - - - -
333I ILE* 1.3 75.8 - - - +
335I TYR* 1.3 56.7 + - - +
337I ASN* 3.1 12.1 + - - +
338I SER* 2.9 29.6 + - - -
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Residues in contact with TYR 335 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331I LYS* 3.0 48.9 + - + +
332I VAL 3.7 7.2 - - - +
334I GLY* 1.3 74.4 - - - +
336I ILE* 1.3 58.7 + - - +
338I SER* 3.5 6.0 + - - -
339I ALA* 3.0 23.4 + - - +
369I ILE* 5.1 0.2 - - - +
377I THR* 4.6 3.4 - - + -
378I SER* 3.5 32.7 - - - -
381I GLU* 2.5 46.5 + - + +
382I GLU 3.8 21.5 + - - -
383I ILE* 3.7 39.9 - - + -
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Residues in contact with ILE 336 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332I VAL* 3.4 22.2 - - + +
333I ILE* 3.0 7.2 + - - +
335I TYR* 1.3 75.3 - - + +
337I ASN* 1.3 64.4 + - - +
339I ALA* 3.4 6.6 + - - +
340I GLU* 3.1 21.5 + - - +
346I ILE* 3.9 20.4 - - + +
349I ASP* 4.7 1.3 - - - +
351I ARG* 3.5 39.0 - - + +
364I VAL* 4.5 5.4 - - + -
367I THR* 3.7 34.1 - - + +
369I ILE* 4.4 9.0 - - + -
383I ILE* 5.9 0.2 - - + -
387I VAL* 4.0 20.2 - - + -
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Residues in contact with ASN 337 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333I ILE* 2.9 33.4 + - - +
334I GLY* 3.1 10.2 + - - +
336I ILE* 1.3 75.2 - - - +
338I SER* 1.3 52.3 + - - +
340I GLU* 3.2 5.5 + - - +
341I GLN* 2.8 36.4 + - - +
351I ARG* 2.7 40.9 + - - +
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Residues in contact with SER 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334I GLY 2.9 16.2 + - - -
335I TYR* 3.7 12.1 - - - -
337I ASN* 1.3 74.2 - - - +
339I ALA* 1.3 63.0 + - - +
341I GLN* 3.7 12.6 + - - +
342I GLN* 3.1 42.5 + - - +
377I THR* 4.4 6.6 - - - -
378I SER* 4.3 10.7 + - - -
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Residues in contact with ALA 339 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335I TYR 3.0 15.1 + - - +
336I ILE 3.6 5.8 - - - +
337I ASN 3.3 0.2 - - - -
338I SER* 1.3 71.6 - - - +
340I GLU* 1.3 62.9 + - - +
342I GLN* 3.4 9.8 + - - +
343I GLY 3.4 0.2 + - - -
344I ALA* 3.0 30.5 + - + +
346I ILE* 4.5 0.7 - - + -
369I ILE* 3.7 34.3 - - + -
376I MET* 4.5 3.5 - - - +
378I SER* 3.4 20.8 + - - +
389I GLN* 4.8 2.0 - - - +
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Residues in contact with GLU 340 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336I ILE 3.1 10.0 + - - +
337I ASN* 3.4 7.8 - - - +
339I ALA* 1.3 79.7 - - - +
341I GLN* 1.3 63.3 + - - +
343I GLY* 3.0 16.1 + - - -
344I ALA 3.8 12.8 + - - +
346I ILE* 3.8 18.8 - - + +
351I ARG* 2.7 41.8 + - - +
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Residues in contact with GLN 341 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337I ASN 2.8 21.2 + - - +
338I SER* 3.7 13.7 + - - +
340I GLU* 1.3 74.1 - - - +
342I GLN* 1.3 63.2 + - + +
343I GLY 3.3 0.9 + - - -
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Residues in contact with GLN 342 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338I SER* 3.1 30.7 + - - +
339I ALA 3.8 2.5 - - - +
340I GLU 3.2 0.6 - - - -
341I GLN* 1.3 83.7 - - + +
343I GLY* 1.3 59.0 + - - +
344I ALA 3.6 2.0 - - - -
375I GLU 4.5 3.8 + - - -
376I MET* 3.4 33.6 - - + +
377I THR* 3.1 41.4 + - - +
378I SER* 4.1 1.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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