Contacts of the helix formed by residues 47 - 59 (chain F) in PDB entry 4DVQ
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 ASN 47 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C ARG* 4.8 5.5 + - - -
49C TRP* 4.2 17.6 + - - +
45F PRO 3.8 9.1 + - - -
46F GLY* 1.3 79.3 - - - -
48F ARG* 1.3 57.0 + - - +
49F TRP* 2.7 21.5 + - + +
50F LEU* 3.8 36.1 - - + +
51F ARG* 3.0 22.7 + - - +
81F TYR* 3.6 3.8 + - - -
82F ASN* 6.0 2.2 - - - +
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Residues in contact with ARG 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ASN* 4.0 15.8 + - - +
46F GLY 4.2 0.2 - - - -
47F ASN* 1.3 69.7 - - - +
49F TRP* 1.3 98.2 + - + +
51F ARG* 3.7 4.4 + - - +
52F LEU* 3.0 35.4 + - + +
81F TYR* 3.3 21.2 + - + +
82F ASN* 3.2 37.2 + - - +
83F LEU* 3.9 10.1 - - + -
84F GLY* 3.3 44.3 + - - +
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Residues in contact with TRP 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ASN* 3.9 19.9 + - + -
49C TRP* 3.1 57.2 - + + -
50C LEU* 4.5 21.5 - - + -
53C LEU* 4.1 15.0 - - + -
47F ASN* 2.7 10.4 + - + -
48F ARG* 1.3 121.2 - - + +
50F LEU* 1.3 66.2 + - - +
51F ARG 3.1 1.1 - - - -
52F LEU* 3.2 18.3 + - + +
53F LEU* 2.9 30.3 + - + +
241F PRO* 6.3 2.2 - - + -
244F LEU* 3.8 27.6 - - + -
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Residues in contact with LEU 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C TRP* 4.1 24.6 - - + -
244C LEU* 4.5 19.3 - - + -
247C TRP* 6.3 0.2 - - + -
46F GLY* 6.1 0.4 - - - -
47F ASN* 3.1 34.7 + - + +
49F TRP* 1.3 76.6 - - - +
51F ARG* 1.3 52.8 + - - +
53F LEU* 3.6 7.0 - - + +
54F GLN* 2.6 44.1 + - + +
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Residues in contact with ARG 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44F HIS* 5.8 0.6 - - - -
47F ASN 3.0 16.6 + - - +
48F ARG* 3.7 7.6 + - - +
50F LEU* 1.3 72.2 - - - +
52F LEU* 1.3 68.8 + - + +
54F GLN* 3.1 7.3 + - - +
55F ILE* 2.8 42.1 + - + +
61F TYR* 3.7 31.0 + - + -
64F LEU* 5.3 3.8 - - - +
68F MET* 6.1 2.8 - - - -
81F TYR* 3.1 54.5 + - - +
83F LEU* 3.8 13.9 - - - +
88F MET* 5.1 4.8 - - - -
239F PHE* 3.4 41.8 + - + +
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Residues in contact with LEU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C LEU* 5.1 3.4 - - + -
48F ARG* 3.0 24.9 + - + +
49F TRP* 3.2 22.6 + - + +
51F ARG* 1.3 80.2 - - + +
53F LEU* 1.3 56.5 + - + +
55F ILE* 3.1 6.6 + - - +
56F TRP* 2.6 35.7 + - - +
239F PHE* 2.9 32.8 - - + +
240F MET* 3.7 33.0 - - + +
241F PRO* 5.0 2.2 - - + -
244F LEU* 3.2 35.4 - - + -
248F ILE* 5.4 2.0 - - + -
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Residues in contact with LEU 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C TRP* 3.5 38.1 - - + -
52C LEU* 4.6 2.2 - - + -
53C LEU* 3.9 27.8 - - + -
244C LEU* 3.7 19.1 - - + -
247C TRP* 3.4 23.7 - - + -
248C ILE* 3.7 23.6 - - + -
49F TRP* 2.9 16.6 + - + +
50F LEU* 3.6 7.2 - - + +
52F LEU* 1.3 82.8 - - + +
54F GLN* 1.3 63.0 + - - +
56F TRP* 3.1 10.0 + - + +
57F ARG 3.0 18.2 + - - -
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Residues in contact with GLN 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247C TRP* 4.5 4.0 - - - -
50F LEU* 2.6 27.7 + - + +
51F ARG* 3.7 5.4 - - - +
53F LEU* 1.3 71.0 - - - +
55F ILE* 1.3 58.4 + - + +
57F ARG* 3.2 12.9 + - + +
58F GLU* 2.9 58.1 + - + +
61F TYR* 5.7 4.7 - - - -
63F HIS* 3.4 25.2 + - - -
67F GLU* 5.5 4.0 + - - -
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Residues in contact with ILE 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ARG* 2.8 25.3 + - + +
52F LEU* 3.4 8.5 - - - +
54F GLN* 1.3 69.5 - - + +
56F TRP* 1.3 65.0 + - - +
57F ARG 3.1 1.3 - - - -
59F GLN* 3.0 21.7 + - - -
60F GLY 3.7 26.5 - - - +
61F TYR* 3.9 23.6 - - + -
235F VAL 4.1 1.8 - - - +
236F GLN* 3.9 35.0 - - + +
239F PHE* 3.6 42.6 - - + -
240F MET* 5.2 4.0 - - + -
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Residues in contact with TRP 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C TRP* 4.7 21.4 - + - -
247C TRP* 3.6 41.1 - + + -
248C ILE* 4.9 12.8 - - + -
52F LEU 2.6 17.0 + - - +
53F LEU* 3.1 16.6 + - + +
55F ILE* 1.3 74.5 - - - +
57F ARG* 1.3 66.3 + - + +
59F GLN* 4.0 10.0 + - - +
240F MET* 5.2 5.3 - - + +
248F ILE* 3.5 42.6 + - + +
249F SER* 3.8 13.4 + - - +
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Residues in contact with ARG 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C ARG* 6.2 1.8 - - - +
247C TRP* 3.6 66.2 - - + +
53F LEU 3.0 11.1 + - - +
54F GLN* 3.3 14.7 - - - +
55F ILE 3.1 0.2 - - - -
56F TRP* 1.3 89.7 - - + +
58F GLU* 1.3 67.9 + - + +
59F GLN* 3.6 5.4 + - - +
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Residues in contact with GLU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F GLN* 2.9 48.9 + - + +
57F ARG* 1.3 83.8 - - + +
59F GLN* 1.3 70.9 + - - +
60F GLY* 3.3 19.4 + - - +
61F TYR* 4.9 1.6 - - - -
62F GLU 5.5 0.5 + - - -
63F HIS* 4.4 9.5 + - - -
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Residues in contact with GLN 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ILE 3.0 12.1 + - - -
56F TRP 4.4 6.7 - - - +
57F ARG 3.4 7.4 - - - +
58F GLU* 1.3 79.7 - - - +
60F GLY* 1.3 56.7 + - - +
232F LYS* 4.0 30.0 - - + +
236F GLN* 3.8 40.4 - - - +
255F GLU* 5.5 2.8 + - - -
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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