Contacts of the helix formed by residues 339 - 353 (chain A) in PDB entry 3ZG2
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 MET 339 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A LEU* 5.7 1.1 - - + -
322A GLU* 3.3 16.4 - - + +
323A ILE* 4.5 6.1 - - + -
326A PHE* 4.0 21.8 - - + -
330A LEU* 5.2 0.9 - - - -
334A ASN 3.7 0.8 + - - +
335A VAL* 3.4 45.4 + - - +
336A MET 4.9 0.6 + - - -
338A GLU* 1.3 81.3 - - - +
340A PRO* 1.3 64.7 - - - +
341A PHE 3.2 2.2 - - - -
342A ALA* 3.2 23.8 + - + -
343A GLU 3.2 8.5 + - - -
433A LYS* 2.9 51.9 - - + +
436A LEU* 5.6 1.1 - - + -
437A ALA* 3.4 22.0 - - + +
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Residues in contact with PRO 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU* 3.2 9.4 - - - +
336A MET 5.8 1.0 - - - +
337A ASP 4.5 5.2 - - - +
338A GLU* 3.1 13.0 - - - +
339A MET* 1.3 91.0 - - - +
341A PHE* 1.3 62.2 + - + +
343A GLU* 3.3 20.7 - - + +
344A ARG* 3.3 14.0 + - - +
433A LYS* 5.1 1.1 - - - +
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A TRP* 3.3 61.2 - + - -
318A LYS* 4.0 30.1 - - + +
319A LEU* 3.7 23.1 - - + -
322A GLU* 3.1 17.1 + - + +
340A PRO* 1.3 77.4 - - + +
342A ALA* 1.3 64.4 + - - +
344A ARG* 3.0 37.5 + - - +
345A CYS* 3.2 29.9 + - - -
402A PRO* 4.0 13.7 - - + -
403A GLU* 4.5 5.2 - - + -
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Residues in contact with ALA 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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319A LEU* 4.2 15.3 - - + -
322A GLU* 3.2 14.9 + - - +
339A MET* 3.2 31.0 + - + +
341A PHE* 1.3 77.7 - - - +
343A GLU* 1.3 64.4 + - - +
345A CYS* 3.3 12.0 + - - +
346A VAL* 3.2 27.9 + - - +
433A LYS* 4.6 7.6 - - + -
436A LEU* 4.8 6.8 - - + +
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Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A MET 5.3 0.5 - - - +
339A MET 3.2 6.1 + - - +
340A PRO* 3.3 14.6 - - + +
342A ALA* 1.3 77.9 - - - +
344A ARG* 1.3 63.7 + - + +
346A VAL* 3.3 5.8 + - - +
347A ARG* 3.0 40.1 + - + +
429A LEU* 4.0 25.4 - - + +
433A LYS* 3.0 40.2 + - - +
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Residues in contact with ARG 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A PRO 3.7 12.3 - - - +
341A PHE* 3.0 23.8 + - + +
343A GLU* 1.3 79.8 - - + +
345A CYS* 1.3 56.2 - - - +
347A ARG* 3.4 6.1 + - - +
348A GLU* 2.8 32.1 + - - +
402A PRO* 2.8 47.7 + - + +
403A GLU* 3.4 18.5 + - - +
404A ARG 3.3 8.5 + - - -
405A ASP* 2.9 37.5 + - - -
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Residues in contact with CYS 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A SER* 4.7 1.3 - - - -
307A LEU* 4.3 18.6 - - + -
319A LEU* 5.6 1.8 - - - -
341A PHE* 3.5 44.2 - - - -
342A ALA* 3.5 11.0 - - - +
344A ARG* 1.3 75.3 - - - +
346A VAL* 1.3 60.9 + - + +
348A GLU 3.4 0.2 + - - -
349A SER* 2.9 34.0 + - - -
400A TRP* 3.4 34.6 - - + -
402A PRO* 3.9 6.1 - - - -
436A LEU* 5.3 2.7 - - + -
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Residues in contact with VAL 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A THR* 3.5 23.8 - - + -
303A SER* 4.0 8.5 - - - +
342A ALA 3.2 15.1 + - - +
343A GLU* 3.3 7.8 + - - +
345A CYS* 1.3 77.0 - - - +
347A ARG* 1.3 56.7 + - - +
349A SER* 3.4 3.3 + - - -
350A ILE* 3.0 35.0 + - + +
429A LEU* 3.6 26.7 - - + -
432A VAL* 3.5 31.4 - - + -
433A LYS* 4.6 8.5 - - + -
436A LEU* 3.8 15.0 - - + -
1480A HEM 6.2 0.2 - - + -
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Residues in contact with ARG 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLU* 3.0 36.7 + - - +
344A ARG* 3.9 6.1 - - - +
346A VAL* 1.3 73.0 - - - +
348A GLU* 1.3 54.6 + - - +
350A ILE* 3.1 8.0 + - - +
351A ARG* 2.6 35.4 + - - +
406A GLU* 5.4 3.6 + - - -
412A PHE* 3.3 53.0 - - + +
415A PHE* 5.0 4.9 - - + -
425A GLN* 4.8 12.0 - - - +
429A LEU* 4.8 14.6 - - + -
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Residues in contact with GLU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ARG 2.8 22.5 + - - +
345A CYS 3.8 3.6 - - - +
347A ARG* 1.3 69.6 - - - +
349A SER* 1.3 58.1 + - - +
351A ARG* 2.6 52.8 + - - +
352A ARG* 2.7 34.0 + - - +
400A TRP* 3.5 15.5 - - + +
401A ASP 2.9 44.6 + - - +
402A PRO* 3.9 10.5 - - + -
404A ARG* 2.9 12.7 + - + +
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Residues in contact with SER 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A THR* 4.3 4.0 - - - -
302A TRP* 4.1 19.4 - - - +
303A SER* 3.2 32.7 + - - -
306A HIS* 3.7 4.1 - - - -
345A CYS 2.9 17.4 + - - -
346A VAL 3.5 9.6 - - - -
348A GLU* 1.3 76.1 - - - +
350A ILE* 1.3 63.6 + - - +
352A ARG* 4.0 0.7 - - - +
353A ASP* 3.0 27.7 + - - +
400A TRP* 3.2 18.7 + - - +
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Residues in contact with ILE 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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299A THR* 3.7 34.1 - - + +
346A VAL* 3.0 24.3 + - + +
347A ARG* 3.6 8.5 - - - +
349A SER* 1.3 73.9 - - - +
351A ARG* 1.3 65.1 + - - +
353A ASP 4.4 4.5 - - - -
354A PRO* 3.1 24.3 - - - +
355A PRO* 4.0 19.3 - - + -
388A HIS* 3.6 1.8 - - - -
412A PHE* 4.3 5.2 - - + -
414A GLY* 4.1 27.4 - - - +
415A PHE* 3.6 32.8 - - + -
429A LEU* 4.9 0.2 - - + -
1480A HEM 4.0 5.6 - - + -
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Residues in contact with ARG 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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347A ARG 2.6 18.2 + - - +
348A GLU* 2.6 48.4 + - - +
350A ILE* 1.3 75.2 - - - +
352A ARG* 1.3 82.0 + - - +
353A ASP 3.5 0.2 + - - -
354A PRO* 3.5 0.9 - - - +
388A HIS* 2.7 62.1 + - + +
389A HIS* 5.0 0.6 - - - -
394A PHE* 3.6 36.8 - - + -
397A PRO* 2.6 26.0 + - - +
399A LEU 3.2 15.8 + - - -
404A ARG* 3.0 19.2 - - - +
412A PHE* 3.9 18.1 - - + -
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Residues in contact with ARG 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TRP* 4.1 9.5 - - - -
306A HIS* 3.4 32.6 - - - -
348A GLU 2.7 19.9 + - - +
349A SER* 4.0 2.0 - - - +
351A ARG* 1.3 91.3 - - - +
353A ASP* 1.3 99.2 + - - +
354A PRO* 3.5 1.7 - - - +
385A LEU* 5.0 0.3 - - - +
389A HIS* 3.3 23.9 + - - -
397A PRO 4.1 13.7 - - - +
398A ARG* 2.9 60.5 + - - +
400A TRP* 4.0 18.1 - - + +
452A VAL* 5.2 9.1 + - - +
453A PRO 5.3 4.0 + - - -
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Residues in contact with ASP 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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302A TRP* 3.5 48.0 + - + +
306A HIS* 4.1 2.1 + - - -
349A SER 3.0 13.5 + - - +
350A ILE* 3.5 4.0 - - - -
352A ARG* 1.3 112.5 + - - +
354A PRO* 1.3 71.1 - - - +
355A PRO* 3.3 7.1 - - - +
385A LEU* 5.6 2.0 - - - +
398A ARG* 2.9 24.4 + - - -
455A PRO* 4.0 13.5 - - + +
457A TYR* 5.1 0.5 + - - -
462A VAL* 5.1 1.1 - - + +
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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
------------------------------------------------------------
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