Contacts of the helix formed by residues 415 - 428 (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 GLN 415 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11 MET* 2.4 41.6 - - - +
4142 SER* 1.3 79.8 - - - +
4162 VAL* 1.3 61.2 + - - +
4172 ASP* 4.6 14.0 + - - +
4182 PHE* 3.1 34.0 + - + -
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Residues in contact with VAL 416 (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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11 MET* 3.6 7.0 - - - -
4152 GLN* 1.3 72.8 + - - +
4172 ASP* 1.3 56.1 + - - +
4192 GLU* 3.0 9.7 + - - +
4202 LEU* 2.9 34.4 + - + +
4372 ALA* 5.8 2.9 - - + +
4402 LEU* 4.0 25.8 - - + -
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Residues in contact with ASP 417 (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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4152 GLN* 3.2 17.1 + - + +
4162 VAL* 1.3 76.3 - - - +
4182 PHE* 1.3 62.2 + - + +
4202 LEU* 3.2 9.8 + - - +
4212 LEU* 2.8 38.1 + - - +
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Residues in contact with PHE 418 (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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11 MET* 2.8 39.5 - - + +
21 VAL* 4.7 3.6 - - + +
4142 SER* 4.8 4.3 - - - -
4152 GLN* 3.1 38.0 + - + -
4172 ASP* 1.3 79.0 - - + +
4192 GLU* 1.3 60.6 + - - +
4212 LEU* 4.6 15.5 - - + -
4222 LEU* 3.0 38.4 + - + +
4592 LYS 4.4 18.4 - - - -
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Residues in contact with GLU 419 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11 MET* 2.9 28.6 - - - -
4132 LEU* 3.4 18.6 - - + -
4162 VAL* 3.0 7.7 + - - +
4182 PHE* 1.3 73.8 - - - +
4202 LEU* 1.3 55.9 + - - +
4222 LEU* 3.3 2.5 + - - +
4232 ALA* 2.7 38.8 + - + +
4352 ASN* 3.8 5.5 + - - +
4362 SER 3.8 0.7 - - - -
4372 ALA* 3.3 32.1 - - - +
4402 LEU* 3.3 18.6 - - + +
4412 MET 3.1 23.6 + - - +
4422 VAL* 3.5 23.6 - - + +
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Residues in contact with LEU 420 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4162 VAL* 2.9 22.9 + - + +
4172 ASP* 3.7 8.5 - - - +
4192 GLU* 1.3 77.5 + - - +
4212 LEU* 1.3 56.2 + - - +
4232 ALA* 4.3 7.0 - - + -
4242 HIS* 2.8 42.3 + - + +
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Residues in contact with LEU 421 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4172 ASP* 2.8 28.6 + - - +
4182 PHE* 4.5 15.0 - - + +
4202 LEU* 1.3 70.7 - - - +
4222 LEU* 1.3 74.5 + - + +
4232 ALA 3.3 0.3 + - - -
4242 HIS* 3.9 4.2 - - - +
4252 ALA* 3.0 33.2 + - + +
4552 TRP* 5.8 5.2 - - + -
4592 LYS* 4.1 46.7 - - + +
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Residues in contact with LEU 422 (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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11 MET* 4.1 1.6 - - + -
21 VAL* 2.5 52.0 - - + +
4102 ASN* 4.0 15.5 - - - +
4132 LEU* 4.9 1.3 - - + -
4182 PHE* 3.0 30.2 + - + +
4192 GLU* 3.3 3.2 + - - +
4212 LEU* 1.3 90.7 - - + +
4232 ALA* 1.3 57.0 + - - +
4262 ARG* 3.1 32.6 + - - +
4422 VAL* 6.1 1.6 - - + -
4522 LYS* 3.4 23.7 - - + +
4552 TRP* 4.8 2.2 - - + -
4562 LYS* 3.6 22.4 - - + +
4592 LYS 6.3 1.6 - - - -
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Residues in contact with ALA 423 (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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4192 GLU* 2.7 25.2 + - + +
4202 LEU* 3.7 9.0 - - + +
4222 LEU* 1.3 68.8 - - - +
4242 HIS* 1.3 60.1 + - - +
4262 ARG* 2.9 36.0 + - - +
4272 GLU* 3.0 17.3 + - - +
4322 VAL* 4.2 1.6 - - - +
4352 ASN* 3.6 27.4 - - - +
4422 VAL* 4.5 6.9 - - + +
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Residues in contact with HIS 424 (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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4202 LEU* 2.8 29.2 + - + +
4212 LEU* 3.9 4.7 - - - +
4232 ALA* 1.3 69.6 - - - +
4252 ALA* 1.3 58.0 + - - +
4272 GLU* 3.2 20.7 + - + +
4282 LEU* 3.0 41.2 + - + +
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Residues in contact with ALA 425 (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* 3.0 29.7 + - + +
4242 HIS* 1.3 77.5 - - + +
4262 ARG* 1.3 57.3 + - - +
4282 LEU* 4.5 5.8 - - - +
4292 GLY* 4.4 7.7 + - - -
4512 VAL* 5.4 4.5 - - - +
4522 LYS* 2.9 27.4 + - - +
4552 TRP* 4.5 20.9 + - + +
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Residues in contact with ARG 426 (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* 6.0 0.9 - - - +
4222 LEU* 3.1 18.8 + - - +
4232 ALA* 2.9 20.0 + - - +
4252 ALA* 1.3 74.6 - - - +
4272 GLU* 1.3 59.5 + - - +
4282 LEU 3.4 0.7 - - - -
4292 GLY* 3.2 5.2 + - - -
4302 VAL 3.0 21.0 + - - -
4312 LEU* 3.2 16.9 + - - +
4322 VAL* 3.5 40.6 - - + +
4342 GLU 3.9 0.2 + - - -
4352 ASN* 3.7 11.9 - - - +
4422 VAL* 3.3 42.3 - - - +
4432 VAL 2.9 33.3 + - - +
4442 THR* 3.3 24.8 - - + +
4482 HIS* 5.4 1.1 + - - -
4512 VAL* 6.5 0.4 - - - -
4522 LYS* 3.6 20.6 - - + +
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Residues in contact with GLU 427 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4232 ALA* 3.0 13.2 + - - +
4242 HIS* 3.5 23.6 + - + +
4262 ARG* 1.3 73.1 - - - +
4282 LEU* 1.3 57.7 + - - +
4302 VAL* 2.9 24.1 + - - +
4322 VAL* 3.3 16.9 - - + +
4352 ASN* 5.4 5.4 + - - -
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Residues in contact with LEU 428 (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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4242 HIS* 3.0 30.2 + - + +
4252 ALA* 5.0 4.0 - - - -
4272 GLU* 1.3 75.5 - - - +
4292 GLY* 1.3 58.8 + - - +
4302 VAL* 3.3 6.4 + - - +
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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