Contacts of the helix formed by residues 41 - 48 (chain C) in PDB entry 6E7P
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 LEU 41 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C GLU* 5.3 4.0 - - - -
39C GLU 3.4 2.4 - - - +
40C ASP* 1.3 83.1 - - + +
42C ARG* 1.3 62.4 + - - +
43C ARG 3.5 2.0 - - - -
44C ARG* 4.0 30.7 - - + +
45C LEU* 3.2 48.5 + - + +
326C LEU* 6.2 0.2 - - + -
329C GLU* 4.7 22.0 - - + +
330C PHE 5.5 0.2 - - - +
333C PHE* 3.8 36.1 - - + +
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Residues in contact with ARG 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 GLU* 3.2 29.8 - - + +
39C GLU* 3.5 11.9 - - - +
40C ASP 3.2 2.8 - - - -
41C LEU* 1.3 79.1 - - - +
43C ARG* 1.3 68.6 + - + +
45C LEU* 4.1 0.6 - - - -
46C LYS* 3.2 34.4 + - + +
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Residues in contact with ARG 43 (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 ASP 4.6 3.4 + - - +
41C LEU* 4.5 0.2 - - - +
42C ARG* 1.3 81.4 - - + +
44C ARG* 1.3 67.5 + - + +
46C LYS* 3.4 3.1 + - - +
47C TYR* 3.1 47.4 + - + +
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Residues in contact with ARG 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 ASP 5.4 3.5 + - - +
41C LEU* 4.0 29.2 + - + +
43C ARG* 1.3 79.6 - - + +
45C LEU* 1.3 66.7 + - + +
46C LYS 3.4 0.7 + - - -
47C TYR* 3.5 21.7 + - + +
48C PHE* 3.6 11.4 + - - +
322C ARG* 4.7 18.8 + - - +
325C LEU* 5.7 2.2 - - - +
326C LEU* 3.4 41.4 - - + +
329C GLU* 5.6 5.3 + - - +
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Residues in contact with LEU 45 (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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41C LEU* 3.2 49.2 + - + +
42C ARG 4.7 0.4 - - - +
44C ARG* 1.3 79.2 - - + +
46C LYS* 1.3 62.1 + - + +
48C PHE* 4.2 10.1 - - + +
49C PHE* 4.1 23.0 + - - -
326C LEU* 4.5 31.0 - - + +
329C GLU* 6.5 0.9 - - + -
330C PHE* 4.7 24.2 - - + -
333C PHE* 4.9 2.9 - - + -
350C PHE* 6.6 0.2 - - + -
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Residues in contact with LYS 46 (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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42C ARG* 3.2 24.1 + - + +
43C ARG* 4.2 2.2 - - - +
44C ARG 3.2 0.4 - - - -
45C LEU* 1.3 82.1 - - + +
47C TYR* 1.3 63.6 + - + +
48C PHE 3.2 1.8 - - - -
49C PHE* 2.9 41.5 - - + +
50C MET* 3.3 9.0 - - - +
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Residues in contact with TYR 47 (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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43C ARG* 3.1 37.6 + - + +
44C ARG* 3.5 14.8 + - + +
46C LYS* 1.3 77.9 - - - +
48C PHE* 1.3 61.9 + - - +
50C MET* 3.2 29.2 + - + +
55C LYS* 5.2 3.8 - - - -
58C ALA* 4.9 12.3 - - + -
59C LYS* 3.1 50.5 + - + +
322C ARG* 6.1 2.9 - - - +
801C HZ7 4.5 28.9 - - + +
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Residues in contact with PHE 48 (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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44C ARG 3.6 10.8 + - - +
45C LEU* 4.4 11.4 - - + +
46C LYS 3.2 0.6 - - - -
47C TYR* 1.3 79.3 - - - +
49C PHE* 1.3 81.7 + + - +
50C MET 3.5 3.8 + - - +
319C SER* 4.6 14.1 - - - -
322C ARG* 5.2 17.3 - - + +
323C GLY* 4.5 23.6 - - - -
326C LEU* 6.3 6.1 - - + -
350C PHE* 3.2 36.3 - + + -
351C VAL* 5.5 0.4 - - - -
352C ASN* 3.6 23.2 + - - +
801C HZ7 5.7 10.5 - - - -
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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