Contacts of the helix formed by residues 241 - 249 (chain 5) 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 241 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2385 THR* 5.8 0.2 - - - -
2395 ILE 4.0 1.0 + - - -
2405 ALA* 1.3 77.6 - - - +
2425 ARG* 1.3 63.7 + - - +
2435 GLU* 3.6 12.4 + - - +
2445 GLU* 3.3 23.5 + - - +
2455 ILE* 3.3 24.6 + - - +
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Residues in contact with ARG 242 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2415 SER* 1.3 72.2 - - - +
2435 GLU* 1.3 65.2 + - + +
2455 ILE* 3.9 17.5 + - + +
2465 GLU* 3.5 18.4 + - - +
3375 GLU* 4.6 16.8 + - - +
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Residues in contact with GLU 243 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2415 SER* 3.2 10.5 - - - +
2425 ARG* 1.3 78.1 - - + +
2445 GLU* 1.3 64.7 + - - +
2455 ILE 3.2 0.2 - - - -
2465 GLU* 3.1 19.7 + - - +
2475 ALA* 3.2 10.7 + - - +
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Residues in contact with GLU 244 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275 LYS* 4.1 14.9 + - - -
1295 ILE* 4.3 9.4 - - - +
2405 ALA* 3.7 10.5 - - + -
2415 SER* 3.3 24.9 + - - +
2435 GLU* 1.3 79.1 - - - +
2455 ILE* 1.3 54.8 + - - +
2475 ALA* 2.8 42.6 + - - +
2485 THR* 3.3 5.2 + - - +
3735 LEU* 3.6 30.2 - - + +
3755 TRP* 5.0 1.6 - - + -
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Residues in contact with ILE 245 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2405 ALA* 4.8 2.2 - - + +
2415 SER 3.3 16.7 + - - +
2425 ARG* 3.9 19.3 - - + +
2435 GLU 3.2 0.4 - - - -
2445 GLU* 1.3 72.4 - - - +
2465 GLU* 1.3 68.1 + - - +
2485 THR* 2.8 33.1 + - - +
3355 VAL* 5.5 3.4 - - + -
3365 LEU 6.0 1.3 - - - +
3395 PRO* 4.3 12.3 - - + -
3585 GLN* 4.0 15.3 - - - +
3605 ASN* 3.8 41.3 - - + +
3705 VAL* 3.6 29.8 - - + +
3735 LEU* 4.3 4.7 - - + -
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Residues in contact with GLU 246 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2425 ARG 3.5 11.2 + - - +
2435 GLU* 3.1 16.7 + - - +
2455 ILE* 1.3 78.5 - - - +
2475 ALA* 1.3 61.9 + - - +
2485 THR 3.4 0.5 + - - -
2495 LYS* 3.4 46.5 + - + +
2505 ASN* 5.0 1.7 + - - -
3705 VAL* 4.3 11.9 - - - +
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Residues in contact with ALA 247 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275 LYS* 5.4 3.8 + - - +
2435 GLU 3.2 7.8 + - - +
2445 GLU* 2.8 32.0 + - - +
2465 GLU* 1.3 77.2 - - - +
2485 THR* 1.3 62.0 + - - +
2495 LYS 3.0 1.4 + - - -
2505 ASN* 3.2 26.8 + - - +
2515 HIS* 5.0 0.5 + - - -
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Residues in contact with THR 248 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275 LYS* 4.4 22.0 - - + +
2445 GLU* 3.7 9.6 - - - +
2455 ILE* 2.8 24.7 + - - +
2475 ALA* 1.3 76.4 - - - +
2495 LYS* 1.3 64.5 + - - +
2505 ASN 3.0 1.3 + - - -
2515 HIS* 3.4 20.7 + - - -
3705 VAL* 3.7 1.6 - - - -
3715 LYS* 3.3 56.5 + - - +
3725 ASN 5.0 0.7 - - - +
3735 LEU* 4.3 20.2 - - + -
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Residues in contact with LYS 249 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2465 GLU* 3.4 40.3 + - + +
2475 ALA 3.0 1.2 + - - -
2485 THR* 1.3 79.5 + - - +
2505 ASN* 1.3 66.6 + - - +
2515 HIS 3.4 1.2 + - - +
3695 GLY* 3.7 34.2 - - - +
3705 VAL* 3.8 24.5 - - + +
3715 LYS* 3.7 12.4 + - - +
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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