Contacts of the helix formed by residues 448 - 456 (chain 2) in PDB entry 5IY6
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 HIS 448 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4262 ARG* 6.3 0.4 - - - -
4292 GLY* 3.0 39.0 + - - -
4302 VAL* 5.5 1.4 - - + +
4312 LEU* 3.3 35.6 - - + +
4442 THR* 4.4 7.1 + - + +
4452 PRO 4.1 2.5 - - - -
4462 ALA 3.2 0.4 - - - -
4472 GLY* 1.3 87.4 - - - +
4492 SER* 1.3 66.1 + - - +
4502 ASP 3.2 2.2 - - - +
4512 VAL* 3.4 30.5 - - + +
4522 LYS* 3.2 21.5 + - - +
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Residues in contact with SER 449 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4082 LEU* 3.5 34.5 - - - -
4442 THR* 4.2 8.5 - - - -
4452 PRO 3.7 3.2 + - - -
4462 ALA* 2.9 23.7 + - - +
4482 HIS* 1.3 74.1 - - - +
4502 ASP* 1.3 64.0 + - - +
4522 LYS* 3.2 7.4 + - - +
4532 ARG* 2.8 40.5 + - - +
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Residues in contact with ASP 450 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4462 ALA 4.7 1.2 + - - +
4472 GLY 5.2 5.0 + - - +
4482 HIS* 3.2 1.0 - - - +
4492 SER* 1.3 84.0 + - - +
4512 VAL* 1.3 60.9 + - + +
4532 ARG* 3.1 13.7 + - - +
4542 PHE* 2.9 31.0 + - - +
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Residues in contact with VAL 451 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4252 ALA 5.4 3.6 - - - +
4262 ARG* 6.5 0.2 - - - -
4292 GLY* 6.0 0.9 - - - -
4472 GLY 5.5 1.6 - - - +
4482 HIS* 3.4 47.7 - - + +
4502 ASP* 1.3 75.5 - - + +
4522 LYS* 1.3 63.5 + - + +
4542 PHE* 3.5 6.4 + - - +
4552 TRP* 3.0 48.5 + - + +
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Residues in contact with LYS 452 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4102 ASN* 5.7 1.1 - - - +
4222 LEU* 3.4 46.4 - - + +
4252 ALA* 2.9 40.1 + - - +
4262 ARG* 3.6 21.9 - - + +
4442 THR* 5.0 7.4 - - + +
4482 HIS 3.2 13.0 + - - +
4492 SER* 3.2 11.0 + - - +
4512 VAL* 1.3 77.2 - - + +
4532 ARG* 1.3 58.2 + - + +
4552 TRP* 3.4 13.2 + - - -
4562 LYS* 2.9 48.9 + - - +
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Residues in contact with ARG 453 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51 LEU* 4.6 22.8 - - + +
4082 LEU* 5.4 1.3 - - + +
4492 SER* 2.8 29.0 + - - +
4502 ASP* 3.5 16.5 + - - +
4522 LYS* 1.3 70.1 - - + +
4542 PHE* 1.3 61.5 - - - +
4562 LYS* 3.8 20.0 + - - +
4572 ARG* 3.5 19.2 + - - +
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Residues in contact with PHE 454 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4502 ASP 2.9 15.7 + - - +
4512 VAL* 3.8 7.4 - - - +
4532 ARG* 1.3 74.4 - - - +
4552 TRP* 1.3 70.4 + + + +
4572 ARG* 2.9 28.4 + - + +
4582 GLN* 3.2 51.9 + - + -
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Residues in contact with TRP 455 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4212 LEU* 5.8 4.9 - - + -
4222 LEU* 4.8 5.6 - - + -
4252 ALA* 4.5 16.9 + - + +
4512 VAL* 3.0 39.5 + - + +
4522 LYS* 4.0 24.7 - - - +
4542 PHE* 1.3 83.2 - + - +
4562 LYS* 1.3 63.0 + - - +
4572 ARG 3.0 1.9 + - - -
4582 GLN* 3.1 38.3 + - + +
4592 LYS* 4.1 7.2 - - + +
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Residues in contact with LYS 456 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21 VAL* 2.5 59.6 + - + +
41 VAL 4.8 0.8 + - - -
51 LEU* 4.3 20.0 - - - +
4102 ASN* 2.5 36.8 + - - +
4222 LEU* 3.6 12.7 - - + +
4522 LYS* 2.9 42.7 + - + +
4532 ARG* 3.8 19.2 - - - +
4552 TRP* 1.3 70.3 - - - +
4572 ARG* 1.3 58.1 + - - +
4582 GLN 5.0 0.2 - - - -
4592 LYS 5.1 6.9 - - - +
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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