Contacts of the helix formed by residues 516 - 529 (chain 0) in PDB entry 5OA3
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 ASP 516 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5140 GLY 3.8 3.2 + - - -
5150 LEU* 1.3 70.4 - - - +
5170 PRO* 1.3 75.7 - - - +
5180 TYR* 3.1 26.5 + - - +
5190 SER* 3.4 26.7 + - - -
5200 VAL* 3.2 24.3 + - - +
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Residues in contact with PRO 517 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5100 LEU* 4.5 13.7 - - + -
5110 GLU* 3.8 24.5 - - + +
5150 LEU 3.2 11.0 - - - +
5160 ASP* 1.3 90.6 - - - +
5180 TYR* 1.3 55.8 + - + +
5200 VAL* 4.6 0.2 - - + -
5210 ALA* 3.0 28.1 + - - +
5340 VAL* 3.6 24.0 - - + +
5440 LEU* 3.8 28.3 - - + +
5460 VAL* 3.3 22.1 - - + +
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Residues in contact with TYR 518 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5160 ASP* 3.1 22.8 - - - +
5170 PRO* 1.3 77.0 - - + +
5190 SER* 1.3 65.5 + - - +
5210 ALA* 3.2 4.1 + - - +
5220 ALA* 2.9 22.7 + - - +
5340 VAL* 3.8 37.7 + - + +
5440 LEU* 3.7 27.5 - - + +
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Residues in contact with SER 519 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5160 ASP* 3.4 24.6 + - - -
5180 TYR* 1.3 76.5 - - - +
5200 VAL* 1.3 59.4 + - - +
5220 ALA* 3.1 8.1 + - - +
5230 ILE* 2.9 46.7 + - - +
5640 TYR* 4.7 3.3 + - - -
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Residues in contact with VAL 520 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5070 VAL* 6.1 0.9 - - + -
5100 LEU* 4.2 22.7 - - + -
5150 LEU* 4.4 27.4 - - + -
5160 ASP 3.2 16.8 + - - +
5170 PRO 4.0 4.5 - - - +
5190 SER* 1.3 76.9 - - - +
5210 ALA* 1.3 59.0 + - - +
5230 ILE* 3.8 7.6 - - - +
5240 LEU* 2.9 47.8 + - + +
5460 VAL* 4.9 3.1 - - + -
5560 LEU* 5.7 1.1 - - + -
5590 LEU* 4.1 11.7 - - + -
5600 LEU* 6.1 1.6 - - + -
5640 TYR* 4.3 20.6 - - + +
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Residues in contact with ALA 521 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5170 PRO 3.0 20.9 + - - +
5180 TYR* 3.2 5.4 + - - +
5200 VAL* 1.3 77.7 - - - +
5220 ALA* 1.3 55.5 + - - +
5240 LEU* 3.7 1.3 + - - -
5250 GLN* 2.9 22.2 + - - +
5320 THR* 2.9 27.4 + - - +
5330 THR 4.8 1.8 - - - +
5340 VAL* 3.7 19.7 - - + -
5460 VAL* 4.0 18.4 - - + -
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Residues in contact with ALA 522 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5180 TYR 2.9 12.5 + - - +
5190 SER* 3.4 11.9 - - - +
5210 ALA* 1.3 74.7 - - - +
5230 ILE* 1.3 61.8 + - + +
5250 GLN* 2.9 27.1 + - - +
5260 GLN* 2.9 15.1 + - - +
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Residues in contact with ILE 523 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5190 SER* 2.9 34.0 + - - +
5200 VAL* 3.8 7.0 - - - +
5220 ALA* 1.3 75.2 - - + +
5240 LEU* 1.3 56.9 + - - +
5260 GLN* 3.2 7.5 + - - +
5270 ARG* 2.9 26.7 + - - +
5580 TRP* 4.7 12.8 - - + -
5590 LEU* 3.8 23.8 - - + -
5640 TYR* 3.4 28.9 - - + +
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Residues in contact with LEU 524 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5070 VAL* 5.1 1.6 - - + -
5200 VAL* 2.9 34.1 + - + +
5210 ALA 3.9 4.0 - - - +
5230 ILE* 1.3 73.4 - - - +
5250 GLN* 1.3 60.4 + - - +
5270 ARG* 4.3 6.7 - - + -
5280 CYS* 2.9 53.7 + - - +
5320 THR* 4.2 10.3 - - + +
5460 VAL* 4.4 5.8 - - + -
5480 ILE* 3.6 28.9 - - + -
5550 HIS 4.6 9.2 - - - +
5560 LEU* 3.8 28.5 - - + -
5580 TRP* 5.9 0.2 - - + -
5590 LEU* 3.8 22.2 - - + -
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Residues in contact with GLN 525 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5210 ALA 2.9 14.9 + - - +
5220 ALA* 2.9 15.7 + - - +
5240 LEU* 1.3 75.4 - - - +
5260 GLN* 1.3 64.7 + - - +
5290 GLN* 3.1 25.5 + - - +
5300 ALA 3.4 16.4 + - - +
5310 SER* 4.9 0.2 - - - +
5320 THR* 3.5 26.7 + - - +
10612 U 3.8 14.4 + - - +
18492 G 3.1 53.2 + - - +
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Residues in contact with GLN 526 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5220 ALA 2.9 11.6 + - - +
5230 ILE* 3.7 8.7 - - - +
5240 LEU 3.2 0.2 - - - -
5250 GLN* 1.3 83.3 - - - +
5270 ARG* 1.3 61.6 + - - +
5290 GLN* 3.9 19.5 + - - +
17082 C 4.9 2.6 + - - -
18492 G 5.1 13.5 + - - +
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Residues in contact with ARG 527 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5230 ILE 2.9 17.3 + - - +
5240 LEU* 4.1 7.0 - - + +
5260 GLN* 1.3 79.3 - - - +
5280 CYS* 1.3 62.5 - - - +
5290 GLN* 4.6 1.9 - - - +
5550 HIS* 3.3 47.9 + - + +
5580 TRP* 3.2 80.0 - - + +
17082 C 4.8 4.0 + - - -
17092 G 5.6 4.7 - - - +
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Residues in contact with CYS 528 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5240 LEU* 2.9 43.8 + - - +
5270 ARG* 1.3 76.2 - - - +
5290 GLN* 1.3 72.4 + - - +
5300 ALA* 4.6 5.3 - - + +
5320 THR* 6.0 0.2 - - + -
5480 ILE* 4.2 11.4 - - + -
5520 GLN* 3.6 50.8 + - + +
5550 HIS* 4.1 17.8 + - - -
17082 C 5.3 2.8 - - - +
18272 U 5.5 1.9 - - - +
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Residues in contact with GLN 529 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5250 GLN 3.1 19.4 + - - +
5260 GLN* 4.1 18.0 + - - +
5270 ARG 3.3 1.0 - - - +
5280 CYS* 1.3 84.2 - - - +
5300 ALA* 1.3 60.3 + - - +
17072 U 2.9 45.3 + - + +
17082 C 3.3 35.0 - - + +
18272 U 5.0 4.3 - - - +
18282 C 4.4 5.4 + - - +
18492 G 2.5 49.5 + - - +
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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