Contacts of the helix formed by residues 46 - 56 (chain C) in PDB entry 3KDH
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 PRO 46 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C ALA* 1.3 91.8 - - + +
47C ALA* 1.3 66.4 + - - +
48C SER* 3.6 18.2 - - - +
49C VAL* 3.0 29.0 + - + +
50C VAL* 3.2 11.1 + - - +
132C GLU* 3.4 12.6 - - + +
141C VAL* 3.9 21.5 - - + -
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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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46C PRO* 1.3 72.3 - - - +
48C SER* 1.3 58.4 + - - +
50C VAL 4.4 1.1 - - - +
51C TRP* 2.9 35.0 + - - +
108C ARG* 3.6 35.0 - - - +
130C VAL* 4.0 11.7 - - + -
132C GLU* 2.8 30.8 + - + +
143C THR* 3.2 13.5 + - - +
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Residues in contact with SER 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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46C PRO* 3.6 15.7 - - - +
47C ALA* 1.3 79.1 - - - +
49C VAL* 1.3 62.7 + - - +
51C TRP* 5.2 0.9 - - - -
52C PRO* 3.2 23.1 - - - +
108C ARG* 4.1 15.0 - - - +
132C GLU* 4.3 1.4 + - - -
186C MET* 3.7 8.7 - - - +
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Residues in contact with VAL 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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45C ALA* 4.7 1.1 - - + -
46C PRO* 3.0 29.0 + - + +
48C SER* 1.3 90.3 - - - +
50C VAL* 1.3 64.6 + - - +
51C TRP 3.5 0.2 - - - -
52C PRO* 3.4 9.6 - - - +
53C LEU* 3.8 14.3 - - + +
180C ALA 5.4 0.4 - - - +
181C ALA* 3.4 31.4 - - - +
184C ALA 5.8 2.2 - - - +
186C MET* 4.2 35.8 - - + +
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Residues in contact with VAL 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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43C ILE* 4.1 12.8 - - + -
45C ALA* 4.3 2.9 - - + -
46C PRO 3.2 15.5 + - - +
47C ALA 3.3 2.7 + - - +
49C VAL* 1.3 75.5 - - - +
51C TRP* 1.3 65.3 + - - +
53C LEU* 3.2 20.3 + - - +
54C ILE* 3.7 8.4 + - + +
130C VAL* 4.1 12.8 - - + -
143C THR* 3.9 17.7 - - + +
145C VAL* 3.8 27.1 - - + -
177C LEU* 4.0 19.3 - - + -
181C ALA* 3.6 23.8 - - + -
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Residues in contact with TRP 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 21.1 + - - +
48C SER* 5.2 0.9 - - - -
50C VAL* 1.3 74.6 - - - +
52C PRO* 1.3 65.4 - - + +
54C ILE* 3.0 15.8 + - + -
55C ARG* 2.9 46.4 + - + +
103C VAL* 3.9 3.4 - - + -
104C ASP 3.8 9.6 - - - -
105C ASP* 3.3 38.4 + - - +
108C ARG* 3.3 53.2 - - + +
109C VAL 3.4 31.6 - - - -
110C LEU* 4.0 15.3 - - + -
128C THR 4.9 1.1 - - - -
130C VAL* 3.9 15.7 - - + +
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Residues in contact with PRO 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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48C SER* 3.2 28.0 - - - +
49C VAL 3.4 11.7 - - - +
51C TRP* 1.3 99.2 - - + +
53C LEU* 1.3 59.4 + - + +
55C ARG* 4.2 7.4 - - + -
56C ARG* 3.1 26.9 + - - +
186C MET* 4.3 12.6 - - + -
187C HIS* 6.2 5.4 - - + +
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Residues in contact with LEU 53 (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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49C VAL* 3.8 18.4 - - + +
50C VAL 3.2 6.8 + - - +
51C TRP 3.1 1.0 - - - -
52C PRO* 1.3 79.2 - - + +
54C ILE* 1.3 63.0 + - - +
56C ARG* 4.0 12.5 + - - +
59C ASN 4.7 4.9 - - - +
62C ARG* 3.6 55.7 - - + +
63C TYR* 3.6 17.1 - - + -
177C LEU* 3.6 24.2 - - + -
180C ALA* 3.8 11.7 - - + +
181C ALA* 3.8 31.9 - - + +
186C MET* 6.4 0.2 - - - -
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Residues in contact with ILE 54 (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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50C VAL* 3.7 10.5 + - + +
51C TRP* 3.0 13.2 + - + +
53C LEU* 1.3 76.7 - - - +
55C ARG* 1.3 67.0 + - - +
56C ARG 3.3 4.9 + - - +
57C PHE* 4.5 3.6 + - - -
63C TYR* 3.9 33.4 + - + +
83C ARG* 5.6 1.7 + - - -
110C LEU* 3.4 38.2 - - + +
128C THR* 3.9 22.9 - - + +
130C VAL* 3.6 30.3 - - + -
145C VAL* 4.6 0.7 - - + -
177C LEU* 3.7 28.0 - - + -
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Residues in contact with ARG 55 (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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51C TRP* 2.9 37.1 + - + +
52C PRO* 4.1 7.4 - - + +
53C LEU 3.4 0.2 - - - -
54C ILE* 1.3 77.9 - - - +
56C ARG* 1.3 57.2 + - - +
57C PHE* 2.9 10.6 + - - +
77C GLY 2.9 23.8 + - - -
78C ASP* 2.9 31.1 + - - +
79C VAL 4.9 0.6 - - - +
100C LEU* 4.2 6.3 - - - +
103C VAL* 3.3 28.2 - - - +
105C ASP* 3.0 34.5 + - - +
110C LEU* 4.0 10.0 - - - +
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Residues in contact with ARG 56 (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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52C PRO 3.1 18.6 + - - +
53C LEU* 4.1 9.2 - - - +
54C ILE 3.2 3.4 - - - +
55C ARG* 1.3 71.8 - - - +
57C PHE* 1.3 63.1 - - - +
58C ASP* 3.0 36.8 + - - +
59C ASN* 3.2 24.1 + - + -
60C PRO* 5.1 0.7 - - - +
76C ASP 5.5 4.4 + - - -
77C GLY* 6.3 1.0 - - - -
83C ARG* 4.9 1.2 + - - -
187C HIS* 3.9 31.8 + - + -
189C ASP* 3.4 29.0 + - - +
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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