Contacts of the helix formed by residues 233 - 247 (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 SER 233 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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447 ARG* 4.2 7.3 + - - -
1657 ASN* 4.6 17.0 - - - -
1667 LEU 5.7 0.4 - - - -
2307 PHE* 2.8 31.2 + - - +
2317 GLN 4.5 0.7 - - - -
2327 HIS* 1.3 77.2 - - - +
2347 LYS* 1.3 63.7 + - - +
2357 TYR 3.5 0.4 - - - -
2367 LYS* 3.4 37.2 - - - +
2377 VAL* 3.2 13.5 + - - +
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Residues in contact with LYS 234 (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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1657 ASN* 4.5 16.6 + - - +
2317 GLN 5.3 2.2 - - - +
2327 HIS 4.1 15.5 - - - +
2337 SER* 1.3 70.9 - - - +
2357 TYR* 1.3 83.1 + - + +
2377 VAL* 3.2 9.3 + - - +
2387 ASP* 2.9 38.4 + - - +
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Residues in contact with TYR 235 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1657 ASN* 3.5 37.8 + - - +
1667 LEU 4.6 0.7 - - - +
1677 VAL* 3.6 46.6 - - + +
1847 VAL* 3.6 27.5 - - + +
2337 SER* 4.6 0.2 - - - +
2347 LYS* 1.3 94.4 + - + +
2367 LYS* 1.3 57.2 + - - +
2387 ASP* 3.2 12.9 + - - +
2397 PHE* 2.9 28.4 + - - +
2947 ILE* 6.4 0.4 - - + -
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Residues in contact with LYS 236 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1557 GLU* 5.3 2.6 + - - -
1667 LEU* 3.3 49.3 - - - +
1677 VAL 4.5 3.8 - - - +
1817 TYR* 4.8 1.1 - - - -
2307 PHE* 4.1 28.3 - - + -
2337 SER* 3.4 29.5 + - - +
2347 LYS 3.2 0.4 - - - -
2357 TYR* 1.3 77.9 - - - +
2377 VAL* 1.3 55.2 - - - +
2397 PHE* 3.2 10.7 + - + +
2407 ILE* 2.9 36.5 + - + +
2607 PHE* 4.5 3.8 - - - -
2617 ILE 4.2 10.3 + - - -
2627 ASP* 3.7 30.9 + - - +
2637 VAL* 5.4 3.8 - - + +
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Residues in contact with VAL 237 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2277 LEU* 3.5 27.3 - - + +
2307 PHE* 3.1 36.1 - - + +
2317 GLN* 3.7 12.6 - - - +
2337 SER 3.2 5.1 + - - +
2347 LYS* 3.2 13.3 + - - +
2367 LYS* 1.3 79.3 - - - +
2387 ASP* 1.3 60.1 + - - +
2407 ILE* 3.2 10.9 + - - +
2417 GLU* 2.9 40.9 + - - +
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Residues in contact with ASP 238 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2347 LYS* 2.9 28.8 + - - +
2357 TYR* 3.3 14.7 - - - +
2377 VAL* 1.3 77.7 - - - +
2397 PHE* 1.3 58.7 + - - +
2417 GLU* 3.2 16.0 + - - +
2427 GLU* 2.9 29.0 + - - +
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Residues in contact with PHE 239 (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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1677 VAL 4.9 6.7 - - - +
1687 ARG* 5.2 23.1 - - + -
1697 ALA 5.6 7.9 - - - -
2357 TYR 2.9 13.9 + - - +
2367 LYS* 3.2 12.8 + - + +
2387 ASP* 1.3 77.2 - - - +
2407 ILE* 1.3 56.0 + - - +
2427 GLU* 3.2 13.2 + - + +
2437 LYS* 2.9 62.4 + - + +
2637 VAL* 3.7 45.8 - - + -
2647 SER* 4.6 1.3 - - - -
2657 GLU* 4.8 9.0 - - + -
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Residues in contact with ILE 240 (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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2237 ALA* 4.2 10.5 - - + +
2267 ALA* 3.7 36.3 - - + +
2277 LEU* 4.3 9.6 - - + +
2307 PHE* 3.8 32.3 - - + -
2367 LYS* 2.9 25.0 + - + +
2377 VAL* 3.4 10.8 - - - +
2397 PHE* 1.3 76.2 - - - +
2417 GLU* 1.3 57.9 + - - +
2437 LYS* 3.2 10.2 + - - +
2447 ALA* 2.9 27.7 + - - +
2527 VAL* 3.8 16.7 - - + +
2637 VAL* 3.8 23.3 - - + -
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Residues in contact with GLU 241 (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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2237 ALA* 6.3 0.4 - - - -
2277 LEU* 4.0 22.3 - - + +
2377 VAL* 2.9 30.1 + - - +
2387 ASP* 3.4 18.1 - - - +
2407 ILE* 1.3 75.6 - - - +
2427 GLU* 1.3 57.1 + - - +
2447 ALA* 3.2 8.6 + - - +
2457 SER* 2.9 29.6 + - - -
2507 ARG* 5.3 1.1 + - - +
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Residues in contact with GLU 242 (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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2387 ASP 2.9 13.4 + - - +
2397 PHE* 3.3 17.5 - - + +
2417 GLU* 1.3 78.8 - - - +
2437 LYS* 1.3 60.1 + - + +
2457 SER* 2.5 29.2 + - - -
2467 GLN* 2.9 17.2 + - + +
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Residues in contact with LYS 243 (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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1717 GLU* 5.5 0.2 + - - -
2397 PHE* 2.9 56.3 + - + +
2407 ILE* 3.2 10.7 + - - +
2427 GLU* 1.3 80.7 - - - +
2447 ALA* 1.3 62.1 + - - +
2467 GLN* 3.2 40.7 + - - +
2477 ASN* 3.3 10.0 + - - +
2507 ARG 4.7 3.1 - - - +
2527 VAL* 5.2 12.1 - - + -
2637 VAL* 5.0 5.6 - - + -
2647 SER 5.7 0.7 - - - -
2657 GLU* 2.9 48.1 + - + +
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Residues in contact with ALA 244 (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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2237 ALA* 4.1 16.2 - - + -
2407 ILE 2.9 13.2 + - - +
2417 GLU* 3.3 11.7 - - - +
2437 LYS* 1.3 76.3 - - - +
2457 SER* 1.3 59.7 + - - +
2477 ASN* 2.8 26.5 + - - +
2497 GLU 4.3 3.5 - - - +
2507 ARG* 3.8 49.1 + - - +
2527 VAL* 4.8 1.1 - - + +
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Residues in contact with SER 245 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2417 GLU 2.9 13.6 + - - -
2427 GLU* 2.5 33.8 + - - -
2447 ALA* 1.3 78.7 - - - +
2467 GLN* 1.3 62.2 + - - +
2477 ASN 3.3 5.2 + - - +
2507 ARG* 4.9 3.5 - - - +
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Residues in contact with GLN 246 (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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2427 GLU* 2.9 8.9 + - + +
2437 LYS* 3.2 45.9 + - - +
2457 SER* 1.3 85.0 + - - +
2477 ASN* 1.3 66.9 + - + +
2487 PRO* 4.8 0.5 - - - +
2657 GLU* 4.2 10.3 + - - +
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Residues in contact with ASN 247 (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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2437 LYS 3.3 10.0 + - - +
2447 ALA 2.8 16.0 + - - +
2457 SER 3.3 5.7 - - - +
2467 GLN* 1.3 89.0 - - - +
2487 PRO* 1.4 76.8 - - + +
2497 GLU 3.3 14.4 - - - +
2507 ARG 5.0 0.4 - - - +
2517 ILE* 3.5 22.7 - - + +
2537 LYS* 5.0 12.1 - - - +
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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
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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