Contacts of the helix formed by residues 38 - 48 (chain 1) in PDB entry 6Q8O
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 TYR 38 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291 LEU* 3.4 29.2 - - + -
321 TYR* 3.6 23.8 - + - -
331 LEU* 4.2 12.8 - - + -
361 GLY 3.9 0.2 + - - -
371 GLY* 1.3 69.2 - - - +
391 GLU* 1.3 62.9 + - - +
401 THR 3.2 2.4 + - - -
411 ALA* 3.6 10.8 + - + +
421 LYS* 3.5 17.8 + - - +
1121 HIS* 2.4 45.5 + - + +
1151 ILE* 4.0 19.5 - - + +
1161 GLU* 3.1 34.2 + - + -
1191 ILE* 5.2 5.4 - - + -
1521 ALA* 4.9 3.9 - - + +
1571 TYR* 5.1 31.0 - + + -
1581 LEU* 6.2 0.7 - - + -
1631 PHE* 5.9 6.5 - + - -
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Residues in contact with GLU 39 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361 GLY* 4.0 21.5 + - - +
371 GLY 3.0 8.8 + - - +
381 TYR* 1.3 77.2 - - - +
401 THR* 1.3 65.8 + - - +
421 LYS* 3.2 14.5 + - + +
431 ARG* 3.0 27.1 + - - +
2321 GLU* 5.3 5.3 - - + +
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Residues in contact with THR 40 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 GLU* 1.3 76.5 - - - +
411 ALA* 1.3 60.6 + - - +
431 ARG* 3.0 11.2 - - - +
441 VAL* 2.9 29.0 + - + +
1161 GLU* 3.1 18.1 + - - -
1201 LEU* 4.1 11.9 - - + -
2281 VAL* 3.4 27.7 - - - +
2311 MET* 3.5 19.7 - - + +
2321 GLU* 3.1 41.2 + - - +
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Residues in contact with ALA 41 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381 TYR* 3.6 13.0 + - + +
391 GLU 3.3 0.4 - - - -
401 THR* 1.3 79.6 - - - +
421 LYS* 1.3 62.7 + - - +
451 LEU* 2.9 46.2 + - + +
1161 GLU* 3.6 19.3 + - + +
1191 ILE* 4.7 12.6 - - + -
1201 LEU* 4.0 14.8 - - + +
1631 PHE* 4.6 10.3 - - + -
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Residues in contact with LYS 42 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381 TYR 3.5 10.4 + - - +
391 GLU* 3.2 17.6 + - + +
411 ALA* 1.3 80.9 - - - +
431 ARG* 1.3 63.1 + - - +
451 LEU* 5.2 0.2 - - - -
461 LYS* 3.8 31.9 - - - +
471 GLU* 5.4 0.2 - - - +
1631 PHE* 5.0 23.9 - - + -
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Residues in contact with ARG 43 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391 GLU* 3.0 13.2 + - - +
401 THR* 3.0 30.5 - - - +
421 LYS* 1.3 79.9 - - - +
441 VAL* 1.3 70.6 + - + +
471 GLU* 2.9 54.3 + - - +
481 LYS* 3.8 24.0 - - - +
2311 MET 2.6 19.4 + - - -
2321 GLU* 2.5 33.9 + - - +
2341 GLY 5.3 1.6 - - - +
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Residues in contact with VAL 44 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401 THR 2.9 21.5 + - - +
431 ARG* 1.3 83.4 - - + +
451 LEU* 1.3 61.0 + - + +
481 LYS* 2.7 68.3 + - + +
531 VAL* 4.6 13.9 - - + -
1201 LEU* 3.7 21.3 - - + -
1231 TYR* 4.5 14.1 - - + -
2311 MET* 3.8 28.5 - - + -
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Residues in contact with LEU 45 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411 ALA* 2.9 22.4 + - - +
421 LYS 4.7 0.2 - - - +
441 VAL* 1.3 78.1 - - + +
461 LYS* 1.3 64.2 + - + +
1191 ILE* 4.0 23.8 - - + +
1201 LEU* 5.5 2.7 - - + -
1231 TYR* 3.4 64.6 + - + -
1621 LEU* 4.9 8.3 - - + +
1631 PHE* 3.5 37.5 - - + -
1651 THR* 4.7 17.7 + - + +
1671 PHE* 5.0 10.8 - - + -
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Residues in contact with LYS 46 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421 LYS* 3.8 26.5 - - - +
431 ARG 3.6 1.6 + - - +
441 VAL 3.2 0.2 - - - -
451 LEU* 1.3 82.1 - - + +
471 GLU* 1.3 66.3 + - + +
481 LYS 4.9 0.4 - - - -
1631 PHE* 3.1 46.0 + - - +
1651 THR* 5.3 12.6 - - - +
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Residues in contact with GLU 47 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431 ARG* 2.9 48.7 + - - +
441 VAL* 5.2 0.2 - - - -
461 LYS* 1.3 83.1 - - + +
481 LYS* 1.3 70.2 + - + +
491 THR* 3.8 5.5 + - - +
521 GLU* 3.9 8.2 - - - +
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Residues in contact with LYS 48 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431 ARG* 3.8 24.5 - - - +
441 VAL* 2.7 46.9 + - + +
451 LEU 4.2 0.5 - - - +
471 GLU* 1.3 83.9 - - + +
491 THR* 1.3 62.9 + - - +
521 GLU* 3.4 28.3 + - + +
531 VAL 4.8 3.4 - - - +
561 GLU* 3.9 17.3 + - - +
1231 TYR* 2.9 17.5 + - - -
2311 MET* 3.5 32.3 - - + -
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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