Contacts of the helix formed by residues 257 - 265 (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 GLY 257 (chain 9).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419 ALA* 4.2 0.8 + - - +
439 VAL* 3.9 12.3 - - - -
2559 ARG 2.9 7.0 + - - -
2569 GLY* 1.3 69.9 - - - -
2589 ALA* 1.3 54.2 + - - -
2599 ALA 2.4 16.8 + - - -
2609 LEU* 2.6 38.2 + - - +
2619 SER* 2.6 13.8 + - - -
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Residues in contact with ALA 258 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429 ASP* 1.5 46.0 - - - +
439 VAL* 2.8 20.9 - - - +
2279 GLN* 2.8 27.8 - - + +
2569 GLY 2.9 1.0 + - - -
2579 GLY* 1.3 69.4 - - - -
2599 ALA* 1.3 65.8 + - - +
2619 SER* 2.7 12.2 + - - -
2629 ILE* 2.6 24.6 + - - +
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Residues in contact with ALA 259 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2219 VAL* 5.8 0.7 - - + -
2229 ASP 5.1 0.2 - - - +
2239 ALA* 3.5 25.4 - - + -
2269 GLY* 3.2 28.5 - - - +
2279 GLN 3.0 4.2 - - - +
2299 ALA* 5.4 2.3 - - + +
2479 LEU* 3.8 12.8 - - + -
2569 GLY 2.4 18.0 + - - +
2579 GLY 2.4 6.5 + - - -
2589 ALA* 1.3 76.6 - - - +
2609 LEU* 1.3 65.1 + - - +
2629 ILE* 3.1 8.0 + - - +
2639 ARG* 3.2 17.9 + - - +
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Residues in contact with LEU 260 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869 MET* 3.7 41.4 - - + +
879 GLY 5.6 0.2 + - - -
2479 LEU* 3.1 23.2 - - + +
2569 GLY* 4.1 4.3 - - - -
2579 GLY* 2.6 53.0 + - - +
2599 ALA* 1.3 74.6 - - - +
2619 SER* 1.3 79.8 + - - +
2639 ARG* 3.0 20.6 - - - +
2649 HIS* 3.2 7.8 + - - +
2709 ILE* 5.4 2.4 - - + +
2739 LEU* 5.6 11.9 - - + -
2909 ILE* 6.2 1.3 - - + -
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Residues in contact with SER 261 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439 VAL* 4.3 8.7 - - - +
449 ALA* 4.8 7.4 - - - -
859 ALA 5.1 4.4 - - - +
869 MET* 5.6 3.1 - - - -
2579 GLY* 2.6 37.5 + - - -
2589 ALA* 2.7 13.6 + - - -
2599 ALA 2.9 0.4 + - - -
2609 LEU* 1.3 83.3 - - - +
2629 ILE* 1.3 72.5 + - - +
2649 HIS* 3.0 17.9 + - - +
2659 ILE* 3.3 10.5 + - - +
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Residues in contact with ILE 262 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449 ALA* 3.8 16.8 - - + -
2279 GLN* 2.1 64.2 - - + +
2309 ALA* 1.7 62.8 - - + +
2589 ALA 2.6 13.1 + - - +
2599 ALA 3.5 2.5 - - - +
2619 SER* 1.3 73.8 - - - +
2639 ARG* 1.3 69.7 + - - +
2659 ILE* 2.9 22.2 + - + +
2669 THR* 3.6 3.0 - - + +
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Residues in contact with ARG 263 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2209 VAL* 5.3 0.2 - - - +
2219 VAL* 2.3 35.3 - - + +
2299 ALA* 5.9 4.3 - - + -
2309 ALA* 5.2 2.9 - - - +
2339 ALA* 5.7 3.7 - - + +
2459 VAL* 3.2 29.9 - - - +
2469 VAL 3.2 7.6 + - - -
2479 LEU* 1.0 172.0 - - - +
2599 ALA 3.3 8.5 - - - +
2609 LEU* 3.0 12.5 - - - +
2629 ILE* 1.3 84.7 - - - +
2649 HIS* 1.3 59.9 + - - +
2659 ILE 2.9 0.2 + - - -
2669 THR* 2.3 30.3 + - - -
2689 LYS* 3.0 27.2 - - + +
2709 ILE* 4.1 18.6 - - + -
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Residues in contact with HIS 264 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
849 ALA 2.6 18.3 + - - -
859 ALA 3.2 10.3 - - - +
869 MET* 2.3 36.9 + - - -
879 GLY* 3.0 10.4 - - - +
889 GLU* 2.7 31.7 + - + +
2609 LEU 3.2 6.0 + - - +
2619 SER 3.0 11.9 + - - +
2639 ARG* 1.3 76.5 - - - +
2659 ILE* 1.3 72.2 - - + +
2669 THR 2.2 20.6 + - - -
2679 GLY* 2.5 18.6 + - - -
2689 LYS* 3.0 12.5 + - - +
2709 ILE* 4.7 5.2 - - + +
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Residues in contact with ILE 265 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479 VAL* 4.1 37.7 - - + -
509 GLU* 5.3 5.4 - - - +
859 ALA* 4.6 5.2 - - - +
2619 SER* 3.8 14.1 - - - +
2629 ILE* 2.9 12.6 + - - +
2639 ARG 2.9 2.0 + - - -
2649 HIS* 1.3 90.5 - - + +
2669 THR* 1.3 70.0 + - - +
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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