Contacts of the helix formed by residues 413 - 428 (chain 9) 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 VAL 413 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677 LYS* 1.2 166.1 - - + +
3799 ILE* 3.4 16.4 - - + -
3999 LYS* 3.4 31.0 - - + -
4039 ALA* 4.4 18.8 - - + -
4089 MET 4.8 1.1 - - - +
4109 VAL* 2.9 15.5 + - - +
4119 GLN 2.5 4.4 + - - -
4129 ASP* 1.3 62.0 - - - +
4149 ASN* 1.3 72.3 + - - +
4159 ARG 2.7 0.9 - - - -
4169 LEU* 2.4 39.7 + - + +
4179 LEU* 2.9 6.0 + - + -
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Residues in contact with ASN 414 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3999 LYS* 2.2 28.1 + - - +
4109 VAL* 3.1 22.0 - - - +
4119 GLN 3.0 5.8 + - - +
4139 VAL* 1.3 76.7 - - - +
4159 ARG* 1.3 52.7 + - + +
4169 LEU 2.5 16.3 + - - -
4179 LEU* 3.1 22.7 + - - +
4189 LYS* 4.1 10.0 + - - +
485B C 3.8 12.6 + - - +
486B C 2.0 37.4 + - - -
487B C 5.5 1.6 + - - -
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Residues in contact with ARG 415 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667 LYS* 2.5 46.8 + - + +
4119 GLN* 2.7 37.9 + - + +
4129 ASP* 2.7 9.4 - - - +
4149 ASN* 1.3 72.6 - - + +
4169 LEU* 1.3 54.6 + - - +
4199 GLN* 4.7 3.1 - - - -
483B A 3.2 2.2 + - - -
484B C 1.6 57.0 + - - -
485B C 4.4 7.4 + - - +
45U GLN* 3.5 30.5 - - - +
46U LYS 3.6 17.8 + - - +
47U PRO* 4.2 5.3 - - - +
48U VAL* 5.2 8.9 - - + +
51U LEU* 6.5 0.4 - - - -
53U GLN* 5.6 0.2 - - - -
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Residues in contact with LEU 416 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657 HIS* 1.6 55.9 + - - +
667 LYS 3.0 4.0 - - - +
677 LYS* 1.2 93.3 - - + +
3799 ILE* 5.1 1.6 - - + -
4129 ASP 3.0 2.5 - - - +
4139 VAL* 2.4 31.3 + - + +
4149 ASN 2.5 9.1 + - - -
4159 ARG* 1.3 68.1 - - - +
4179 LEU* 1.3 80.2 + - + +
4189 LYS* 2.8 4.9 - - - +
4199 GLN* 2.5 3.4 + - - -
4209 PHE* 2.5 17.2 - - + -
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Residues in contact with LEU 417 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3949 ILE* 3.9 18.4 - - + +
3999 LYS* 2.5 45.1 - - + +
4139 VAL* 3.0 17.7 - - + +
4149 ASN* 3.2 16.6 - - - +
4169 LEU* 1.3 96.7 - - + +
4189 LYS* 1.3 58.7 + - + +
4209 PHE* 3.1 24.7 - - + +
4219 ASP* 3.3 17.4 + - - +
490B C 4.4 0.9 - - - +
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Residues in contact with LYS 418 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647 GLN* 4.0 2.5 - - - +
657 HIS* 1.6 13.2 + - - -
4149 ASN 4.1 10.3 + - - +
4169 LEU 2.6 6.1 + - - +
4179 LEU* 1.3 75.5 - - + +
4199 GLN* 1.3 49.7 - - + +
4209 PHE 2.4 7.3 + - - -
4219 ASP 3.9 0.2 - - - +
4229 ASP* 2.6 39.1 + - - +
490B C 1.4 94.8 + - + +
491B G 4.4 5.4 + - - -
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Residues in contact with GLN 419 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617 VAL* 2.6 26.3 - - - +
637 VAL 3.2 3.9 + - - +
647 GLN* 0.6 172.6 + - + +
657 HIS* 0.4 418.6 + - + +
667 LYS* 3.0 22.4 - - - +
4159 ARG 4.1 3.8 + - - -
4169 LEU* 2.5 2.6 + - - +
4189 LYS* 1.3 36.3 - - + +
4209 PHE* 1.3 12.0 + - - -
4239 MET* 3.6 3.1 - - - +
48U VAL* 3.7 14.5 - - - +
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Residues in contact with PHE 420 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617 VAL* 4.4 0.9 - - - -
657 HIS* 1.0 98.7 + + + -
677 LYS 4.9 2.2 - - - -
3349 PHE* 1.9 70.9 - + + -
3769 MET* 4.4 12.3 - - + -
3809 ILE* 5.8 2.9 - - + -
3919 PRO* 6.1 3.1 - - + -
4169 LEU* 2.5 44.9 - - + -
4179 LEU* 3.1 14.6 - - + +
4199 GLN 1.3 12.6 - - - -
4219 ASP* 1.3 65.4 + - - +
4229 ASP 3.1 4.3 + - - -
4239 MET* 3.7 5.3 - - - +
4249 GLN* 3.6 21.1 + - - +
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Residues in contact with ASP 421 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3919 PRO* 3.5 31.9 - - - +
3929 GLU* 4.7 11.4 - - - +
3949 ILE* 5.3 1.6 - - - +
4179 LEU* 3.3 15.1 + - - +
4189 LYS 2.9 1.6 + - - -
4209 PHE* 1.3 82.5 - - - +
4229 ASP* 1.3 54.4 + - - +
4249 GLN* 4.6 9.4 - - - +
4259 ARG* 3.0 25.4 + - - +
490B C 2.3 49.2 + - + +
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Residues in contact with ASP 422 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647 GLN* 3.8 17.4 + - - +
4189 LYS* 2.6 28.5 + - - +
4219 ASP* 1.3 67.7 - - - +
4239 MET* 1.3 71.3 + - - +
4249 GLN 3.2 1.3 - - - -
4259 ARG* 2.7 27.6 + - + +
4269 MET* 2.8 6.9 + - - +
490B C 1.2 102.3 + - - +
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Residues in contact with MET 423 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577 LEU* 1.8 92.1 - - + +
587 THR* 3.3 9.9 - - - +
607 TYR* 5.9 4.7 - - - -
617 VAL* 2.2 64.4 - - + -
647 GLN* 4.1 6.6 - - - +
3349 PHE* 5.7 1.6 - - + -
4189 LYS 3.8 2.6 + - - -
4199 GLN 3.6 5.2 - - - +
4209 PHE* 3.7 8.0 + - - +
4229 ASP* 1.3 82.2 - - - +
4249 GLN* 1.3 52.3 + - + +
4269 MET* 3.0 4.5 + - - +
4279 MET* 2.4 44.4 + - + +
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Residues in contact with GLN 424 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3929 GLU* 5.3 4.3 - - - +
4209 PHE 3.6 13.1 + - - +
4219 ASP* 4.6 8.1 - - - +
4239 MET* 1.3 79.0 - - - +
4259 ARG* 1.3 54.4 - - - +
4279 MET* 2.4 42.7 + - + +
4289 LYS* 2.3 68.4 + - + +
1283B G 4.9 5.7 + - - -
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Residues in contact with ARG 425 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4219 ASP 3.0 20.3 + - - -
4229 ASP* 2.7 27.1 + - + +
4249 GLN* 1.3 73.2 - - - +
4269 MET* 1.3 59.1 + - + +
4289 LYS* 2.7 35.0 - - + +
4299 LYS* 3.6 5.2 + - - +
490B C 3.1 37.0 + - - +
1318B U 4.7 9.3 + - - +
1319B C 3.5 42.3 + - - +
1320B C 5.5 2.6 + - - -
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Residues in contact with MET 426 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577 LEU* 5.7 3.4 - - + -
607 TYR* 4.5 29.4 - - + +
4229 ASP 2.8 6.6 + - - +
4239 MET* 3.5 6.1 - - - +
4249 GLN 2.7 4.1 + - - -
4259 ARG* 1.3 73.6 - - + +
4279 MET* 1.3 55.4 + - - +
4299 LYS* 2.4 73.6 + - + +
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Residues in contact with MET 427 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577 LEU* 2.5 43.9 - - + +
4239 MET* 2.4 48.0 + - + +
4249 GLN* 2.4 44.6 + - + +
4269 MET* 1.3 67.3 - - - +
4289 LYS* 1.3 57.3 + - + +
4299 LYS* 2.5 22.2 + - - +
4309 MET* 4.7 7.6 - - - +
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Residues in contact with LYS 428 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4249 GLN* 2.3 59.6 + - + +
4259 ARG* 2.7 51.4 - - + +
4279 MET* 1.3 70.8 - - + +
4299 LYS* 1.3 49.7 + - - -
4309 MET* 2.6 29.1 + - - +
1283B G 4.5 12.9 + - - -
1318B U 4.5 4.6 + - - +
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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) + - + + + + + -
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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