Contacts of the helix formed by residues 40 - 48 (chain C) in PDB entry 3P9K
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 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C ALA 3.1 0.2 + - - -
37C ILE* 2.8 17.8 + - - -
38C GLU 3.2 0.8 - - - -
39C LEU* 1.3 80.4 - - - +
41C LEU* 1.3 64.4 + - - +
42C LEU 3.4 2.2 - - - -
43C GLU* 3.3 25.2 + - - +
44C ILE* 3.1 29.3 + - - +
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Residues in contact with LEU 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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36C ALA* 2.8 25.2 + - + +
39C LEU* 3.3 19.5 - - + -
40C GLY* 1.3 78.2 - - - +
42C LEU* 1.3 63.0 + - + +
44C ILE* 3.2 6.9 + - - +
45C LEU* 3.1 25.9 + - - +
58C VAL* 3.7 25.5 - - + +
62C LEU* 4.1 26.7 - - + -
74C VAL* 4.3 13.7 - - + -
77C ILE* 4.0 28.5 - - + -
78C LEU* 4.2 25.1 - - + -
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Residues in contact with LEU 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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33C LEU* 4.0 8.7 - - + -
36C ALA* 3.9 11.4 + - + +
37C ILE* 3.9 27.1 - - + +
40C GLY* 3.4 0.6 - - - -
41C LEU* 1.3 78.5 - - + +
43C GLU* 1.3 58.7 + - + +
45C LEU* 3.1 7.4 + - + +
46C VAL* 2.8 32.7 + - - +
78C LEU* 5.2 0.7 - - + -
81C LEU* 4.6 10.3 - - + -
86C VAL* 4.5 7.6 - - + -
87C VAL* 3.7 30.1 - - + -
109C CYS* 4.1 13.9 - - - -
112C LEU* 4.0 32.1 - - + +
113C THR* 3.8 13.5 - - + -
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Residues in contact with GLU 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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37C ILE 5.3 3.1 - - - +
40C GLY* 3.6 22.7 - - - +
41C LEU 3.3 0.6 - - - -
42C LEU* 1.3 75.9 - - + +
44C ILE* 1.3 59.5 + - + +
46C VAL* 3.9 3.2 - - - +
47C ALA* 3.0 31.2 + - - +
112C LEU 5.6 0.2 - - - +
113C THR* 3.8 20.6 - - + -
114C PRO* 3.3 27.9 - - + +
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Residues in contact with ILE 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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39C LEU 4.9 0.2 - - - +
40C GLY 3.1 18.2 + - - +
41C LEU* 3.4 7.6 - - - +
42C LEU 3.2 0.2 - - - -
43C GLU* 1.3 76.6 - - + +
45C LEU* 1.3 61.6 + - - +
47C ALA* 3.3 7.0 + - - +
48C ALA* 3.1 21.0 + - - +
53C LEU* 3.9 21.2 - - + +
58C VAL* 3.7 24.2 - - + +
61C LYS* 3.5 44.7 + - + +
62C LEU* 3.7 24.9 - - + -
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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 3.1 12.9 + - - +
42C LEU* 3.1 11.9 + - + +
44C ILE* 1.3 78.0 - - - +
46C VAL* 1.3 61.2 + - - +
48C ALA* 3.2 18.2 + - + +
49C GLY 4.0 4.5 + - - +
51C LYS 4.9 1.2 - - - +
53C LEU* 4.6 7.9 - - + -
58C VAL* 4.4 20.9 - - + -
78C LEU* 4.1 16.8 - - + -
87C VAL* 3.6 33.0 - - + -
103C TYR* 3.3 34.8 - - + +
104C GLY* 3.9 8.7 - - - +
105C ALA* 3.9 23.5 + - + +
109C CYS* 5.6 0.2 - - - -
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Residues in contact with VAL 46 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42C LEU 2.8 18.8 + - - +
43C GLU* 3.9 6.3 - - - +
45C LEU* 1.3 76.7 - - - +
47C ALA* 1.3 63.4 + - - +
49C GLY* 3.2 16.7 + - - +
105C ALA* 4.0 10.8 - - + -
109C CYS* 3.8 26.7 - - + +
110C LYS* 4.8 4.3 - - + +
113C THR* 3.7 26.9 - - + +
114C PRO 6.1 0.4 - - - +
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Residues in contact with ALA 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 GLU 3.0 19.1 + - - +
44C ILE* 3.8 6.5 - - - +
46C VAL* 1.3 75.0 - - + +
48C ALA* 1.3 56.6 + - - +
49C GLY* 2.8 11.6 + - - -
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Residues in contact with ALA 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 ILE 3.1 12.2 + - - +
45C LEU* 3.4 14.4 - - - +
46C VAL 3.1 0.6 - - - -
47C ALA* 1.3 75.7 - - - +
49C GLY* 1.3 61.4 + - - +
50C GLY 3.2 4.0 + - - -
51C LYS* 3.3 35.5 + - + +
53C LEU* 3.8 27.8 - - + -
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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