Contacts of the helix formed by residues 41 - 53 (chain C) in PDB entry 4K2S
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 ARG 41 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 2.9 28.3 + - + +
39C ASN 3.1 4.6 - - - +
40C GLY* 1.3 93.2 + - - +
42C GLU* 1.3 66.1 + - - +
43C MET 3.3 2.5 - - - -
44C ALA* 3.1 27.0 + - + +
45C VAL* 3.8 6.8 + - - +
83C VAL* 5.4 2.2 - - + -
179C PRO* 6.1 1.4 - - - +
391C SER* 4.8 11.7 + - - -
392C LEU 6.0 0.4 - - - +
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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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17C ARG* 3.1 23.0 + - - -
18C ASN* 3.8 29.2 + - + +
20C VAL* 4.0 21.4 - - + +
37C THR* 4.5 7.6 - - + -
38C LEU* 3.1 22.8 + - - +
39C ASN* 3.4 1.7 - - - +
40C GLY* 3.0 34.2 + - - -
41C ARG* 1.3 78.9 + - - +
43C MET* 1.3 63.9 + - - +
45C VAL* 3.3 6.9 + - - +
46C ALA* 3.2 19.9 + - - +
387C TYR* 4.4 19.9 + - + -
390C ALA 4.4 4.7 + - - +
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Residues in contact with MET 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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12C VAL* 4.5 19.1 - - + -
20C VAL* 5.4 0.2 - - - -
41C ARG 3.3 1.0 - - - -
42C GLU* 1.3 77.2 - - - +
44C ALA* 1.3 60.2 + - - +
46C ALA* 3.7 22.0 - - + +
47C ALA* 3.0 30.1 + - - +
50C ASP* 5.9 0.7 - - - +
387C TYR* 4.0 43.9 + - + +
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Residues in contact with ALA 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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41C ARG* 3.1 19.9 + - + +
43C MET* 1.3 79.4 - - - +
45C VAL* 1.3 56.8 + - - +
47C ALA* 3.6 5.1 + - - +
48C TYR* 3.0 27.5 + - - +
83C VAL* 3.6 25.2 - - + +
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Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 5.7 0.2 - - + -
36C ALA* 3.5 31.6 - - + +
38C LEU* 3.7 41.7 - - + -
41C ARG 3.8 2.7 + - - +
42C GLU 3.3 6.8 + - - +
43C MET 3.3 0.2 - - - -
44C ALA* 1.3 72.9 - - - +
46C ALA* 1.3 59.7 + - - +
48C TYR* 3.1 2.5 + - - +
49C LEU* 2.9 33.6 + - + +
83C VAL* 3.9 20.9 - - + +
86C THR* 3.9 15.3 - - + -
87C ALA* 4.0 14.8 - - + +
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Residues in contact with ALA 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C THR* 4.8 4.5 - - - +
12C VAL* 4.6 6.3 - - + -
20C VAL* 4.4 19.9 - - + +
42C GLU 3.2 10.4 + - - +
43C MET* 3.7 33.4 - - + +
44C ALA 3.4 0.2 - - - -
45C VAL* 1.3 78.8 - - - +
47C ALA* 1.3 55.7 + - - +
49C LEU* 3.8 4.1 - - - +
50C ASP* 2.8 43.7 + - - +
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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 MET* 3.0 18.9 + - - +
44C ALA* 3.9 5.4 - - - +
46C ALA* 1.3 73.4 - - - +
48C TYR* 1.3 62.2 + - - +
50C ASP* 4.4 5.6 - - - -
51C GLU* 2.9 38.0 + - + +
52C HIS* 4.0 2.8 - - + -
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Residues in contact with TYR 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 ALA 3.0 18.3 + - - +
45C VAL* 3.1 6.5 + - - +
47C ALA* 1.3 75.9 - - - +
49C LEU* 1.3 62.1 + - - +
52C HIS* 3.2 34.8 + + + +
53C VAL* 3.2 26.8 + - + -
72C LEU 5.1 0.5 + - - -
76C ALA* 3.5 27.4 - - - +
78C TRP 4.9 0.3 + - - -
83C VAL* 3.7 21.8 - - + -
84C THR* 3.6 34.2 + - - +
87C ALA* 3.4 23.8 - - + -
88C ILE* 5.6 3.4 - - + +
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Residues in contact with LEU 49 (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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10C THR* 3.8 24.0 - - + -
20C VAL* 5.2 0.7 - - + -
22C LEU* 4.4 12.8 - - + -
36C ALA* 3.7 30.1 - - + -
45C VAL* 2.9 23.5 + - + +
46C ALA* 3.8 3.1 - - - +
48C TYR* 1.3 75.6 - - - +
50C ASP* 1.3 64.8 + - - +
53C VAL* 3.1 24.5 + - + -
54C VAL* 2.8 34.5 + - + +
87C ALA* 3.6 34.3 - - + +
90C ALA* 4.3 6.7 - - + -
91C VAL* 4.2 7.2 - - + -
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Residues in contact with ASP 50 (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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9C TYR* 5.3 0.5 - - - -
10C THR* 2.7 38.8 + - - +
43C MET* 5.9 0.7 - - - +
46C ALA* 2.8 33.6 + - - +
47C ALA* 4.1 4.3 - - - +
49C LEU* 1.3 74.9 - - - +
51C GLU* 1.3 61.3 + - + +
54C VAL* 4.0 11.7 - - - +
55C PRO* 3.6 15.2 - - - +
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Residues in contact with GLU 51 (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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47C ALA* 2.9 20.4 + - + +
50C ASP* 1.3 77.3 - - + +
52C HIS* 1.3 88.7 + - + +
55C PRO* 3.7 14.4 - - - +
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Residues in contact with HIS 52 (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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47C ALA* 4.0 9.0 - - + -
48C TYR* 3.2 25.9 + + + +
51C GLU* 1.3 110.4 + - + +
53C VAL* 1.3 67.0 + - + +
55C PRO* 4.1 4.6 - - - +
56C ALA* 4.5 9.2 + - - +
72C LEU* 5.8 0.5 - - - +
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Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C TYR* 3.2 37.9 + - + +
49C LEU* 3.1 20.5 + - + +
52C HIS* 1.3 81.2 - - - +
54C VAL* 1.3 68.4 + - - +
55C PRO 3.4 1.3 - - - -
56C ALA* 3.0 16.2 + - - +
57C LEU* 3.3 16.7 + - + +
72C LEU* 3.9 31.6 - - + -
87C ALA* 4.7 3.4 - - + +
88C ILE* 6.3 1.1 - - + -
91C VAL* 3.9 26.5 - - + -
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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