Contacts of the helix formed by residues 44 - 51 (chain A) in PDB entry 1FIK
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 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A PRO* 3.7 50.6 - - + +
29A SER* 5.6 1.1 - - - -
42A ILE 4.6 1.1 - - - +
43A THR* 1.3 89.1 - - + +
45A ALA* 1.3 56.9 + - - +
47A VAL* 3.3 2.9 + - + +
48A GLY* 2.8 26.9 + - - -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A THR* 2.9 9.6 - - - +
44A PRO* 1.3 81.7 - - - +
46A GLU* 1.3 62.4 + - + +
48A GLY* 3.2 10.5 + - - -
49A VAL* 3.3 16.8 + - - +
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Residues in contact with GLU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASN 4.1 0.3 - - - +
42A ILE* 3.4 7.9 - - + +
43A THR* 2.7 43.1 + - - +
45A ALA* 1.3 71.5 - - + +
47A VAL* 1.3 66.6 + - - +
49A VAL* 2.9 21.1 + - + +
50A LEU* 3.1 15.5 + - - +
64A THR* 3.4 34.5 + - - +
65A LEU* 5.0 2.0 - - + -
66A GLY* 3.1 23.2 + - - -
67A GLY* 3.1 23.6 + - - -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.7 26.0 - - + -
23A GLY 4.8 0.4 - - - +
24A TYR* 3.6 25.8 - - + -
28A PRO* 3.5 29.2 - - + -
29A SER 5.3 0.2 - - - +
42A ILE* 3.7 13.7 - - + +
43A THR 2.9 17.8 + - - +
44A PRO* 3.6 7.2 - - + +
46A GLU* 1.3 76.8 - - - +
48A GLY* 1.3 62.9 + - - +
50A LEU* 3.2 12.6 + - + +
51A VAL* 3.1 23.7 + - + +
109A LEU* 3.9 12.1 - - + -
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Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PRO* 5.6 2.7 - - - -
44A PRO 2.8 15.0 + - - -
45A ALA 3.5 6.3 - - - -
46A GLU 3.0 0.8 - - - -
47A VAL* 1.3 78.0 - - - +
49A VAL* 1.3 56.1 + - - +
51A VAL* 3.8 8.3 - - - +
52A GLY* 2.9 27.2 + - - -
53A LYS* 4.5 6.2 + - - -
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA 3.5 13.7 - - - +
46A GLU* 2.9 11.4 + - + +
48A GLY* 1.3 74.4 - - - +
50A LEU* 1.3 66.4 + - - +
52A GLY* 3.3 11.5 + - - -
54A ASP 4.8 2.8 - - - +
58A PHE* 3.3 36.6 - - + -
63A LEU* 4.7 13.0 - - + -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ILE* 5.6 3.6 - - + -
46A GLU 3.1 11.9 + - - +
47A VAL* 3.3 18.4 - - + +
49A VAL* 1.3 78.8 - - + +
51A VAL* 1.3 56.4 - - + +
55A ARG* 2.4 36.7 + - - +
58A PHE* 4.8 2.7 - - - -
63A LEU* 4.2 14.1 - - + -
65A LEU* 3.9 31.9 - - + -
77A LEU* 4.1 6.1 - - + +
85A MET* 4.2 25.9 - - + +
87A LEU* 5.5 0.4 - - + -
102A VAL* 4.6 18.2 - - + -
109A LEU* 3.9 28.5 - - + -
111A LEU* 4.7 7.0 - - + -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.8 35.0 - - + +
28A PRO* 6.3 0.4 - - + -
47A VAL* 3.1 22.7 - - + +
48A GLY* 3.8 8.3 - - - +
50A LEU* 1.3 78.8 - - + +
52A GLY* 1.3 68.4 + - - +
77A LEU* 4.5 8.5 - - + -
78A LEU* 4.0 16.6 - - + +
104A LYS* 4.1 8.5 - - - +
109A LEU* 3.8 27.4 - - + -
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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