Contacts of the helix formed by residues 50 - 65 (chain 7) in PDB entry 2J28
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 LEU 50 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517 GLY* 1.3 67.8 + - - +
527 PHE* 3.1 5.8 + - - +
537 PRO* 3.4 12.4 - - - +
547 ILE* 3.1 51.0 + - + +
3079 ILE* 6.0 0.4 - - + -
3119 VAL* 5.6 4.0 - - + -
3129 ASP* 5.4 10.5 - - - +
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Residues in contact with GLY 51 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507 LEU* 1.3 78.9 - - - +
527 PHE* 1.3 55.7 + - - +
557 ASN* 2.5 10.7 + - - +
3049 ILE* 5.1 12.3 - - - +
3079 ILE* 2.5 45.6 - - - +
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Residues in contact with PHE 52 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507 LEU 3.1 3.9 + - - +
517 GLY* 1.3 75.9 - - - +
537 PRO* 1.4 71.1 - - + +
557 ASN* 3.7 0.9 - - - +
567 PHE* 2.6 73.5 + + + +
3579 MET 4.5 18.2 - - - -
3589 GLY* 4.8 8.7 - - - -
3599 GLN* 5.5 5.6 - - + -
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Residues in contact with PRO 53 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507 LEU* 3.4 17.9 - - - +
527 PHE* 1.4 103.7 - - + +
547 ILE* 1.3 57.6 + - + +
567 PHE* 2.8 8.6 + - + +
577 LEU* 2.5 39.8 + - + +
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Residues in contact with ILE 54 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507 LEU* 3.1 44.9 + - + +
537 PRO* 1.3 80.9 - - + +
557 ASN* 1.3 54.6 + - - +
577 LEU* 4.2 7.4 - - - +
587 THR* 2.4 38.5 + - - +
3079 ILE* 3.2 11.7 - - + -
3119 VAL* 2.7 61.7 - - + -
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Residues in contact with ASN 55 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517 GLY 2.8 8.8 + - - +
527 PHE 3.2 2.1 + - - +
537 PRO 3.1 0.4 - - - -
547 ILE* 1.3 78.6 - - - +
567 PHE* 1.3 58.7 + - - +
587 THR* 3.6 7.1 - - - +
597 LEU* 3.0 28.2 + - - +
3039 LEU 4.4 4.7 - - - +
3049 ILE* 3.6 15.5 + - + +
3069 ASP* 5.6 0.2 - - - +
3079 ILE* 0.2 136.1 + - + +
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Residues in contact with PHE 56 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527 PHE* 2.6 51.1 + + + +
537 PRO* 2.8 6.4 + - + +
557 ASN* 1.3 73.6 - - - +
577 LEU* 1.3 61.2 + - - +
597 LEU* 3.5 25.1 - - + +
607 TYR* 2.8 48.2 + + + +
3539 LYS 6.2 1.8 - - - -
3619 PRO* 5.3 7.2 - - + -
3659 LYS* 5.2 20.6 - - + -
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Residues in contact with LEU 57 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537 PRO* 2.5 21.9 + - + +
547 ILE* 4.2 6.7 - - - +
567 PHE* 1.3 72.2 - - - +
587 THR* 1.3 58.9 + - - +
607 TYR* 3.7 9.8 - - + +
617 VAL* 2.8 24.9 + - + +
4239 MET* 1.8 68.6 - - + +
4269 MET* 5.7 3.6 - - + -
4279 MET* 2.5 58.3 - - + +
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Residues in contact with THR 58 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547 ILE* 2.4 30.0 + - - +
557 ASN* 3.6 9.1 + - - +
577 LEU* 1.3 78.9 - - - +
597 LEU* 1.3 61.3 + - - +
617 VAL* 4.0 1.7 - - - +
627 THR* 3.1 27.2 + - - -
3109 LYS* 5.4 2.0 + - + +
3379 GLN* 2.2 60.5 + - - +
4239 MET* 3.3 10.7 - - - +
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Residues in contact with LEU 59 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557 ASN 3.0 18.9 + - - +
567 PHE* 3.5 28.0 - - + +
587 THR* 1.3 76.4 - - - +
607 TYR* 1.3 67.1 + - - +
617 VAL 3.2 1.0 + - - -
627 THR* 3.3 11.3 + - - -
637 VAL* 3.3 24.6 + - + +
3379 GLN* 5.7 0.2 - - - +
3519 MET* 2.8 54.1 - - + -
3539 LYS* 5.4 11.0 - - + +
3659 LYS* 3.5 25.4 - - + +
3669 SER* 4.8 0.4 - - - -
3699 ASP 6.1 0.2 - - - +
3739 LEU* 6.0 0.9 - - + -
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Residues in contact with TYR 60 (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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567 PHE* 2.8 43.5 + + + +
577 LEU* 3.9 9.4 - - + +
597 LEU* 1.3 75.6 - - - +
617 VAL* 1.3 69.0 + - + +
637 VAL* 3.8 8.1 + - + +
647 GLN* 3.4 51.1 + - + +
3659 LYS* 5.6 15.9 - - + -
4239 MET* 5.9 3.8 - - - -
4269 MET* 4.5 28.5 - - + +
49U PRO* 4.7 24.6 - - + +
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Residues in contact with VAL 61 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577 LEU* 2.8 12.9 + - + +
587 THR 4.0 2.7 - - - +
607 TYR* 1.3 79.6 - - + +
627 THR* 1.3 62.6 + - - +
637 VAL 3.2 0.7 + - - -
647 GLN* 3.2 4.7 + - - +
657 HIS* 3.1 20.8 + - - -
3349 PHE* 3.3 29.4 - - + -
4199 GLN* 2.6 29.1 - - - +
4209 PHE* 4.4 0.2 - - - -
4239 MET* 2.2 81.2 - - + -
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Residues in contact with THR 62 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587 THR* 3.1 15.9 + - - +
597 LEU* 3.3 6.9 + - - -
617 VAL* 1.3 78.0 - - - +
637 VAL* 1.3 60.0 + - - +
657 HIS 3.2 6.2 - - - +
3349 PHE* 5.2 3.1 - - - -
3379 GLN* 4.4 10.0 + - - -
3739 LEU* 3.4 31.1 - - + +
3769 MET* 1.7 77.8 - - + +
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Residues in contact with VAL 63 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597 LEU* 3.3 24.2 - - + +
607 TYR* 4.1 9.0 - - + +
617 VAL 3.3 0.8 - - - -
627 THR* 1.3 73.8 - - - +
647 GLN* 1.3 66.3 + - - +
657 HIS 4.3 0.3 - - - -
667 LYS* 4.0 14.4 - - - +
3649 VAL* 4.0 11.2 - - + +
3659 LYS* 3.0 27.8 - - - +
3699 ASP* 1.5 88.0 - - + +
3739 LEU* 4.8 4.9 - - + +
4199 GLN* 3.2 4.3 + - - +
48U VAL* 4.5 1.3 - - + +
49U PRO 4.4 13.0 - - - +
50U ALA* 5.5 0.7 - - - -
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Residues in contact with GLN 64 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607 TYR* 3.4 45.9 + - + +
617 VAL* 3.2 2.0 + - - +
637 VAL* 1.3 74.0 - - - +
657 HIS 1.3 22.9 - - - +
4189 LYS* 3.6 7.9 + - - -
4199 GLN* 0.6 226.1 + - + +
4229 ASP* 3.8 18.1 - - - +
4239 MET* 4.1 6.7 - - - +
48U VAL* 4.0 20.5 - - + +
49U PRO* 4.6 3.0 - - - +
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Residues in contact with HIS 65 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617 VAL* 3.1 12.6 + - + +
627 THR 3.2 3.7 - - - +
637 VAL 3.3 0.6 - - - -
647 GLN* 1.3 43.2 - - - +
667 LYS* 1.3 53.8 + - - +
677 LYS 3.1 0.7 + - - -
3769 MET* 3.0 31.0 - - - +
4169 LEU* 1.6 23.8 + - - +
4189 LYS 1.6 17.7 - - - -
4199 GLN* 0.4 366.7 + - + +
4209 PHE* 1.0 68.0 + + + -
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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
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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