Contacts of the helix formed by residues 48 - 61 (chain Y) in PDB entry 6FF7
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 ILE 48 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44Y ASN 4.8 6.0 - - - +
45Y LEU* 3.1 16.2 + - - +
47Y VAL* 1.3 79.5 - - - +
49Y LYS* 1.3 63.4 + - - +
50Y PRO 3.6 0.2 - - - -
51Y TRP* 3.5 8.7 + - - +
52Y ILE* 3.3 22.1 + - - +
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Residues in contact with LYS 49 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45Y LEU 3.5 10.7 + - - +
46Y GLU* 4.1 8.9 + - - +
47Y VAL 3.5 0.8 - - - -
48Y ILE* 1.3 78.8 - - - +
50Y PRO* 1.4 59.2 - - - +
52Y ILE* 3.3 7.6 + - - +
53Y THR* 2.9 26.8 + - - -
68Y ILE* 6.1 1.0 - - - +
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Residues in contact with PRO 50 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46Y GLU 4.8 5.0 - - - +
47Y VAL 4.8 2.8 - - - +
48Y ILE 3.6 0.4 - - - -
49Y LYS* 1.4 76.5 - - - +
51Y TRP* 1.3 57.2 + - - +
53Y THR* 3.5 9.0 - - - -
54Y LYS* 2.9 28.6 + - - +
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Residues in contact with TRP 51 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47Y VAL 4.9 7.0 + - - +
48Y ILE* 3.5 12.4 + - - +
49Y LYS 3.3 0.4 - - - -
50Y PRO* 1.3 78.3 - - - +
52Y ILE* 1.3 56.9 + - - +
54Y LYS* 3.2 7.6 + - - +
55Y ARG* 2.9 27.9 + - - +
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Residues in contact with ILE 52 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48Y ILE 3.3 10.1 + - - +
49Y LYS* 3.3 10.3 + - - +
51Y TRP* 1.3 74.5 - - - +
53Y THR* 1.3 60.6 + - - +
55Y ARG* 3.3 7.2 + - - +
56Y VAL* 2.9 31.2 + - - +
68Y ILE* 6.5 1.3 - - - -
71Y ILE* 5.5 11.2 - - + -
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Residues in contact with THR 53 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Y LYS 2.9 15.2 + - - -
50Y PRO* 3.5 13.2 - - - -
52Y ILE* 1.3 76.9 - - - +
54Y LYS* 1.3 56.2 + - - +
56Y VAL* 3.5 3.9 + - - +
57Y THR* 2.9 29.6 + - - -
68Y ILE* 5.7 12.0 - - - +
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Residues in contact with LYS 54 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50Y PRO 2.9 17.4 + - - +
51Y TRP* 3.2 7.8 + - - +
53Y THR* 1.3 75.2 - - - +
55Y ARG* 1.3 57.4 + - - +
57Y THR* 3.3 8.5 + - - -
58Y GLU* 3.0 26.9 + - - +
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Residues in contact with ARG 55 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51Y TRP 2.9 17.1 + - - +
52Y ILE* 3.8 8.1 - - - +
53Y THR 3.3 0.2 - - - -
54Y LYS* 1.3 77.5 - - - +
56Y VAL* 1.3 57.7 + - - +
58Y GLU* 3.1 9.0 + - - +
59Y ILE* 2.9 28.2 + - - +
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Residues in contact with VAL 56 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Y ILE 2.9 17.9 + - - +
53Y THR* 4.3 4.0 - - - +
55Y ARG* 1.3 73.7 - - - +
57Y THR* 1.3 63.7 + - - +
59Y ILE* 3.9 6.5 - - - +
60Y LEU* 3.5 20.4 + - - +
62Y PHE 3.6 9.5 - - - +
67Y VAL* 5.7 9.2 - - + -
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Residues in contact with THR 57 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53Y THR 2.9 17.9 + - - -
54Y LYS* 3.4 9.9 - - - -
56Y VAL* 1.3 78.3 - - - +
58Y GLU* 1.3 61.4 + - - +
61Y GLY* 3.3 28.1 + - - +
62Y PHE 3.7 14.4 - - - -
63Y GLU* 5.5 6.1 - - - +
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Residues in contact with GLU 58 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54Y LYS 3.0 14.4 + - - +
55Y ARG* 3.1 11.4 + - - +
57Y THR* 1.3 79.8 - - - +
59Y ILE* 1.3 63.9 + - - +
61Y GLY* 4.1 3.3 + - - -
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Residues in contact with ILE 59 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55Y ARG 2.9 14.8 + - - +
56Y VAL* 3.7 6.5 + - - +
57Y THR 3.4 0.4 - - - -
58Y GLU* 1.3 79.7 - - - +
60Y LEU* 1.3 61.5 + - + +
61Y GLY 3.3 0.8 + - - -
97Y ASN* 5.0 16.8 - - + -
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Residues in contact with LEU 60 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Y VAL 3.5 12.0 + - - +
59Y ILE* 1.3 77.8 - - + +
61Y GLY* 1.3 55.5 + - - +
62Y PHE* 3.1 14.1 + - - +
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Residues in contact with GLY 61 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57Y THR* 3.3 23.1 + - - +
58Y GLU 4.1 3.1 + - - -
59Y ILE 3.3 4.0 + - - -
60Y LEU* 1.3 74.7 - - - +
62Y PHE* 1.3 56.9 + - - +
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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