Contacts of the helix formed by residues 40 - 46 (chain C) in PDB entry 1FL7
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 40 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C TYR* 4.1 9.9 - - + -
38C PRO 3.5 7.2 - - - +
39C THR* 1.3 90.2 - - + +
41C LEU* 1.3 66.6 + - - +
42C ARG 4.6 0.2 - - - +
43C SER* 3.0 16.1 + - - +
44C LYS* 2.9 18.2 + - - -
54C THR* 4.6 3.1 - - + +
11D ALA 5.7 4.7 - - - +
99D LEU* 4.5 4.5 - - + +
100D GLY 2.9 35.9 - - - +
101D PRO 4.5 4.9 - - - +
103D TYR* 4.4 28.0 - - + +
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Residues in contact with LEU 41 (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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39C THR 3.8 1.8 + - - -
40C PRO* 1.3 70.7 - - - +
42C ARG* 1.3 64.6 + - - +
44C LYS* 2.9 32.7 + - + +
45C LYS* 3.1 29.3 + - + +
50C GLN* 5.9 2.0 - - - +
11D ALA 5.8 1.2 + - - -
13D GLU* 3.8 41.8 + - + +
15D GLU* 3.8 33.0 - - + +
74D TYR* 5.4 12.4 + - + +
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Residues in contact with ARG 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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42B PRO* 3.6 42.1 + - + -
44B ARG* 6.2 1.6 - - + -
40C PRO* 3.3 1.0 - - - +
41C LEU* 1.3 77.8 - - - +
43C SER* 1.3 57.2 + - - +
45C LYS* 3.3 37.1 + - - +
46C THR* 3.1 25.1 + - - +
13D GLU* 3.3 13.5 + - - +
15D GLU* 4.7 7.7 + - - -
99D LEU* 3.8 9.9 - - + -
103D TYR* 3.4 33.0 - - + +
105D SER* 2.8 33.9 + - - -
106D PHE* 5.4 1.2 - - - -
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Residues in contact with SER 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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39C THR* 4.2 8.7 - - - -
40C PRO* 3.0 15.2 + - - +
42C ARG* 1.3 74.8 - - - +
44C LYS* 1.3 63.0 + - - +
45C LYS 3.0 6.5 + - - -
46C THR* 3.3 13.8 + - - +
47C MET* 3.0 26.5 + - - +
93D ASP* 5.9 1.3 - - - -
99D LEU* 2.9 41.2 + - - +
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Residues in contact with LYS 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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39C THR* 3.7 23.0 + - + +
40C PRO 2.9 11.2 + - - +
41C LEU* 2.9 23.6 + - + +
43C SER* 1.3 76.3 - - - +
45C LYS* 1.3 58.3 + - - +
47C MET* 3.4 17.7 - - - +
50C GLN* 2.9 59.5 + - + +
51C LYS 4.7 2.7 - - - +
52C ASN* 3.2 37.7 + - - +
74D TYR* 4.1 19.2 + - - -
77D PRO* 5.8 4.4 - - - +
1H NAG 4.2 12.9 + - - +
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Residues in contact with LYS 45 (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 LEU* 3.1 30.4 + - + +
42C ARG* 3.3 32.6 - - - +
43C SER 3.0 0.4 - - - -
44C LYS* 1.3 77.9 - - - +
46C THR* 1.3 52.4 + - - +
47C MET 2.6 25.3 + - - +
50C GLN* 4.4 6.2 + - - +
15D GLU* 3.9 26.1 + - - -
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Residues in contact with THR 46 (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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44B ARG* 3.2 45.4 - - - +
42C ARG* 3.1 19.4 + - - +
43C SER* 3.3 10.0 + - - -
45C LYS* 1.3 74.0 - - - +
47C MET* 1.3 58.3 + - - +
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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