Contacts of the helix formed by residues 39 - 44 (chain C) in PDB entry 3D5K
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 GLY 39 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ASP 3.5 4.4 + - - -
38C ILE* 1.3 76.7 - - - +
40C TRP* 1.3 55.5 + - - -
41C ARG 3.2 2.5 - - - -
42C GLU* 3.1 5.6 + - - +
43C PHE* 2.8 32.9 + - - +
443C TYR* 3.5 0.7 - - - -
451C ASN 3.2 14.1 - - - -
452C GLN 3.3 14.8 - - - -
453C GLN* 3.8 7.4 - - - -
454C THR* 3.6 10.5 + - - +
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Residues in contact with TRP 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLY* 1.3 69.8 - - - -
41C ARG* 1.3 93.8 + - - +
43C PHE* 3.8 2.5 - - - -
44C PHE* 3.0 56.3 + - + +
50C GLN* 3.3 29.4 - - - -
53C ILE* 3.7 29.4 - - + +
54C GLY* 4.2 8.1 - - - -
57C LEU* 3.5 30.3 - - + +
154C GLN* 4.1 3.0 - - - +
158C VAL* 4.4 9.4 - - + +
443C TYR* 3.4 12.3 + - - +
449C GLY* 3.4 21.7 + - - -
451C ASN 3.1 25.6 + - - -
452C GLN* 3.4 31.1 - - + +
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Residues in contact with ARG 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLY 3.2 0.4 - - - -
40C TRP* 1.3 100.2 - - + +
42C GLU* 1.3 55.3 + - - +
44C PHE 3.3 2.4 - - - +
50C GLN* 3.1 71.8 + - - +
51C GLN* 4.6 2.8 - - - +
54C GLY* 5.7 2.8 - - - -
452C GLN* 2.5 51.2 + - + +
453C GLN* 3.1 22.8 - - - +
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Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 3.9 23.6 - - + +
39C GLY* 3.1 10.5 + - - +
41C ARG* 1.3 79.1 - - - +
43C PHE* 1.3 57.0 + - - +
44C PHE 3.5 0.4 + - - -
45C ARG* 4.1 7.3 - - - +
258C THR* 2.7 35.2 + - + +
452C GLN 4.4 0.4 + - - -
453C GLN* 5.2 6.2 + - - +
454C THR* 2.5 35.1 + - - +
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Residues in contact with PHE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ILE* 4.4 5.6 - - + -
39C GLY 2.8 19.2 + - - +
40C TRP* 4.1 2.7 - - - -
42C GLU* 1.3 73.8 - - - +
44C PHE* 1.3 97.3 + + - +
257C LEU* 3.4 34.2 - - + -
258C THR* 3.0 56.7 + - - -
260C VAL* 4.7 8.3 - - + -
439C GLU* 4.0 17.3 - - + -
440C VAL* 4.2 5.8 - - - -
443C TYR* 3.6 57.2 - + + -
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Residues in contact with PHE 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C TRP* 3.0 29.7 + - + +
41C ARG 3.3 6.9 - - - +
42C GLU 4.3 0.4 - - - -
43C PHE* 1.3 103.3 - + - +
45C ARG* 1.3 54.3 + - - +
46C ASP 3.5 1.8 - - - +
49C LEU* 3.6 27.4 - - + -
50C GLN* 2.6 37.3 + - + -
53C ILE* 3.5 15.7 - - + -
158C VAL* 3.5 30.5 - - + -
162C ALA* 3.5 31.0 - - + -
256C LEU 4.0 2.5 - - - -
257C LEU* 3.5 18.8 - - + -
440C VAL* 4.2 9.0 - - + -
443C TYR* 4.5 3.1 - + - -
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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