Contacts of the helix formed by residues 37 - 58 (chain 7) in PDB entry 3J7Y
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 PRO 37 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367 SER* 1.4 88.8 - - - +
387 THR* 1.3 65.5 + - + +
407 LEU* 4.3 9.8 - - + -
417 THR* 3.5 27.8 + - + +
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Residues in contact with THR 38 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367 SER* 4.2 7.6 - - - -
377 PRO* 1.3 81.2 - - + +
397 GLU* 1.3 72.9 + - - +
417 THR* 3.6 10.4 + - - -
427 GLU* 3.7 19.3 - - - +
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Residues in contact with GLU 39 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367 SER* 3.1 34.9 + - - +
387 THR* 1.3 86.0 + - - +
407 LEU* 1.3 68.0 + - - +
427 GLU* 2.9 21.7 + - - +
437 MET* 3.1 28.1 + - + +
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Residues in contact with LEU 40 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367 SER* 2.8 43.2 + - - +
377 PRO* 4.3 8.1 - - + +
387 THR 3.7 0.2 - - - -
397 GLU* 1.3 72.7 - - + +
417 THR* 1.3 58.9 - - + +
437 MET* 3.2 9.8 + - + +
447 ARG* 2.9 61.2 + - + +
2327 HIS* 3.3 46.9 - - + +
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Residues in contact with THR 41 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377 PRO* 3.5 20.1 + - + +
387 THR* 3.6 8.0 + - - -
407 LEU* 1.3 79.3 - - + +
427 GLU* 1.3 72.0 + - - +
447 ARG* 3.4 9.5 + - - +
457 ASN* 3.0 35.8 + - - -
1557 GLU* 4.5 16.8 - - - +
1567 ARG* 4.4 19.3 - - - +
2597 ASP* 4.5 10.7 - - - +
2607 PHE* 6.2 0.4 - - - -
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Residues in contact with GLU 42 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387 THR* 3.7 19.1 - - - +
397 GLU* 2.9 9.0 + - - +
417 THR* 1.3 83.5 + - - +
437 MET* 1.3 66.2 + - - +
457 ASN* 3.2 9.7 + - - +
467 ASP* 2.7 41.2 + - - +
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Residues in contact with MET 43 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397 GLU* 3.1 36.1 + - + +
407 LEU* 3.2 10.1 + - + +
427 GLU* 1.3 88.5 - - - +
447 ARG* 1.3 58.8 + - + +
467 ASP* 3.2 14.4 + - + +
477 LEU* 2.9 37.6 + - + +
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Residues in contact with ARG 44 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407 LEU* 2.9 63.2 + - + +
417 THR* 3.8 8.7 - - - +
437 MET* 1.3 78.0 - - + +
457 ASN* 1.3 57.6 + - - +
477 LEU* 3.2 12.6 + - + +
487 PHE* 2.9 28.8 + - - +
1557 GLU* 5.2 7.7 + - - -
2297 ILE* 2.9 36.2 + - + +
2307 PHE* 3.1 39.2 - - - +
2327 HIS* 4.0 16.8 - - - +
2337 SER* 4.2 9.9 + - - +
2597 ASP 5.9 0.2 - - - +
2617 ILE* 3.6 17.9 - - + +
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Residues in contact with ASN 45 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417 THR* 3.0 24.2 + - - -
427 GLU* 3.2 11.6 + - - +
447 ARG* 1.3 75.5 - - - +
467 ASP* 1.3 60.1 + - - +
487 PHE* 3.2 3.3 + - - +
497 ASN* 2.9 38.2 + - - +
2567 ARG* 2.7 29.5 + - - +
2587 GLY 3.4 3.2 + - - +
2597 ASP* 2.9 47.8 + - - +
2617 ILE* 3.5 9.2 - - - +
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Residues in contact with ASP 46 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427 GLU* 2.7 30.3 + - - +
437 MET* 3.4 18.3 - - + +
457 ASN* 1.3 79.1 - - - +
477 LEU* 1.3 56.5 + - + +
497 ASN* 3.2 12.4 + - - +
507 LYS* 2.9 49.3 + - + +
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Residues in contact with LEU 47 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437 MET* 2.9 22.3 + - + +
447 ARG* 3.2 13.4 + - + +
467 ASP* 1.3 77.4 - - + +
487 PHE* 1.3 56.8 + - - +
507 LYS* 3.2 10.4 + - + +
517 GLU* 2.9 29.2 + - - +
547 ARG* 6.2 2.2 - - - +
2257 VAL* 5.7 3.2 - - + +
2287 GLU* 4.5 15.7 - - + +
2297 ILE* 3.9 44.6 - - + +
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Residues in contact with PHE 48 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447 ARG 2.9 12.5 + - - +
457 ASN 3.4 8.5 - - - +
477 LEU* 1.3 77.1 - - - +
497 ASN* 1.3 59.9 + - - +
517 GLU* 3.2 8.4 + - + +
527 LYS* 2.9 53.4 + - + +
2177 GLU* 4.5 3.4 - - + -
2187 THR 4.1 5.2 - - - -
2197 LEU* 3.4 44.6 - - + -
2297 ILE* 5.1 5.5 - - + +
2547 LEU* 3.8 36.1 - - + -
2567 ARG* 3.6 37.2 - - + -
2617 ILE* 4.0 19.1 - - + -
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Residues in contact with ASN 49 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457 ASN* 2.9 26.9 + - - +
467 ASP* 3.4 14.3 + - - +
487 PHE* 1.3 77.2 - - - +
507 LYS* 1.3 63.8 + - + +
527 LYS* 3.2 12.3 + - - +
537 ALA* 2.9 29.2 + - - +
2567 ARG* 3.9 24.6 + - - +
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Residues in contact with LYS 50 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467 ASP* 2.9 34.1 + - + +
477 LEU* 3.2 14.3 + - + +
497 ASN* 1.3 82.5 - - + +
517 GLU* 1.3 56.5 + - - +
537 ALA* 3.2 9.0 + - + +
547 ARG* 2.9 52.2 + - - +
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Residues in contact with GLU 51 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477 LEU 2.9 13.0 + - - +
487 PHE* 3.2 12.8 + - + +
507 LYS* 1.3 75.9 - - - +
527 LYS* 1.3 57.8 - - - +
547 ARG* 3.2 25.5 + - - +
557 GLN* 2.9 45.5 + - - +
2197 LEU* 3.8 16.4 - - + -
2207 GLU 5.5 0.2 - - - +
2217 VAL* 3.5 37.3 - - + +
2227 GLU* 4.7 8.3 + - - +
2257 VAL* 3.7 25.3 - - + +
2297 ILE* 5.9 1.1 - - + -
2547 LEU* 5.9 0.4 - - + -
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Residues in contact with LYS 52 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487 PHE* 2.9 33.5 + - + +
497 ASN* 3.3 14.6 - - - +
517 GLU* 1.3 76.7 - - - +
537 ALA* 1.3 57.0 + - - +
557 GLN* 3.2 7.1 + - - +
567 LEU* 2.9 40.1 + - + +
2177 GLU* 4.1 26.6 + - - +
2187 THR 4.7 10.1 - - - +
2197 LEU* 3.7 25.1 - - + +
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Residues in contact with ALA 53 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497 ASN 2.9 13.9 + - - +
507 LYS* 3.2 12.3 + - + +
527 LYS* 1.3 77.0 - - - +
547 ARG* 1.3 52.1 + - - +
567 LEU* 3.2 14.3 + - - +
577 SER* 2.7 36.2 + - - -
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Residues in contact with ARG 54 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477 LEU* 6.2 1.6 - - - +
507 LYS* 2.9 38.5 + - - +
517 GLU* 3.3 30.6 + - - +
537 ALA* 1.3 76.3 - - - +
557 GLN* 1.3 65.4 + - - +
577 SER* 3.1 25.1 - - - -
587 LEU* 3.6 5.4 + - - +
2227 GLU* 6.1 0.4 - - - -
2257 VAL* 6.3 1.3 - - - -
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Residues in contact with GLN 55 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517 GLU* 2.9 30.3 + - + +
527 LYS* 3.4 12.1 - - - +
547 ARG* 1.3 78.5 + - - +
567 LEU* 1.3 63.9 + - + +
587 LEU* 3.2 50.4 - - + +
847 ASN* 4.2 7.4 + - - +
2197 LEU* 4.6 17.9 - - + -
2207 GLU 5.2 9.8 + - - +
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Residues in contact with LEU 56 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527 LYS* 2.9 26.4 + - + +
537 ALA* 3.4 15.7 - - - +
557 GLN* 1.3 78.1 - - + +
577 SER* 1.3 63.9 + - - +
587 LEU 3.1 1.6 + - - -
597 THR* 3.4 24.6 + - + +
847 ASN* 5.2 11.9 - - + +
857 ILE* 5.0 21.5 - - + -
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Residues in contact with SER 57 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537 ALA* 2.7 23.8 + - - +
547 ARG* 3.1 15.8 + - - -
567 LEU* 1.3 76.9 - - - +
587 LEU* 1.3 61.1 + - - +
597 THR 3.3 8.1 + - - +
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Residues in contact with LEU 58 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547 ARG 3.6 4.1 + - - +
557 GLN* 3.2 48.0 + - - +
567 LEU 3.1 2.0 + - - -
577 SER* 1.3 78.2 - - - +
597 THR* 1.3 69.1 + - - +
607 PRO* 3.6 6.8 - - - +
837 LYS* 5.5 7.2 - - - +
847 ASN* 3.7 20.6 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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