Contacts of the helix formed by residues 49 - 62 (chain M) 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 PRO 49 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M GLN 3.1 10.5 - - - +
48M ALA* 1.4 73.7 - - - +
50M LYS* 1.3 64.2 + - - +
51M PRO 3.7 0.4 - - - -
52M ARG* 3.9 14.8 - - + -
53M LEU* 3.3 23.7 + - + +
93M GLU* 5.8 7.6 - - + -
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Residues in contact with LYS 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46M GLN 3.1 7.1 + - - -
47M GLY* 3.5 16.4 - - - -
48M ALA* 3.1 8.5 - - + +
49M PRO* 1.3 77.5 - - - +
51M PRO* 1.3 63.1 - - - +
53M LEU* 3.8 6.4 + - - +
54M ASN* 4.1 9.9 + - - +
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Residues in contact with PRO 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLU* 5.1 13.2 - - + -
45M LYS* 3.7 24.2 - - + -
46M GLN 4.3 5.9 - - - +
47M GLY* 4.4 1.9 - - - +
50M LYS* 1.3 77.3 - - - +
52M ARG* 1.3 56.1 + - - +
54M ASN* 5.7 0.7 - - + -
55M GLN* 2.7 44.4 + - + +
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Residues in contact with ARG 52 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M ILE* 4.2 20.6 - - + +
45M LYS* 4.4 13.5 - - - +
46M GLN 4.6 0.6 + - - -
49M PRO* 3.4 20.8 + - + +
50M LYS 3.3 1.4 - - - -
51M PRO* 1.3 79.1 - - - +
53M LEU* 1.3 57.7 + - - +
55M GLN* 4.9 0.2 - - - -
56M LEU* 2.5 40.1 + - + +
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Residues in contact with LEU 53 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M PRO* 3.3 17.7 + - + +
50M LYS* 3.8 3.6 + - - +
51M PRO 3.3 0.2 - - - -
52M ARG* 1.3 78.8 - - - +
54M ASN* 1.3 52.0 + - - +
57M TYR* 2.7 40.7 + - - +
93M GLU* 5.5 11.4 - - + -
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Residues in contact with ASN 54 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M LYS 4.1 8.5 + - - +
51M PRO* 3.9 1.9 + - + +
53M LEU* 1.3 76.7 - - - +
55M GLN* 1.3 63.0 + - - +
57M TYR* 4.0 2.9 - - - +
58M GLU* 2.9 33.6 + - - +
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Residues in contact with GLN 55 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLU 6.0 1.3 - - - +
28M ILE* 5.7 10.5 - - + +
29M MET* 6.1 4.7 - - + +
32M GLN* 5.1 1.6 - - - +
42M ILE* 6.4 1.8 - - - -
51M PRO* 2.7 27.5 + - + +
52M ARG* 4.9 0.2 - - - -
54M ASN* 1.3 78.5 - - - +
56M LEU* 1.3 58.0 + - - +
58M GLU* 4.4 2.1 - - - +
59M ARG* 2.9 31.9 + - - +
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Residues in contact with LEU 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42M ILE* 3.9 27.5 - - + +
52M ARG* 2.5 27.0 + - + +
55M GLN* 1.3 75.5 - - - +
57M TYR* 1.3 59.5 + - - +
59M ARG* 3.9 5.1 - - - +
60M ALA* 2.9 32.4 + - - +
97M ASN* 6.5 0.4 - - + -
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Residues in contact with TYR 57 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53M LEU 2.7 23.3 + - - +
54M ASN* 4.0 3.6 - - - +
56M LEU* 1.3 77.4 - - - +
58M GLU* 1.3 56.9 + - - +
60M ALA* 3.9 3.4 - - - +
61M LEU* 2.9 31.3 + - - +
97M ASN* 6.1 8.7 - - + +
100M GLU* 5.7 10.7 - - + +
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Residues in contact with GLU 58 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54M ASN 2.9 18.3 + - - +
55M GLN* 4.4 2.5 - - - +
57M TYR* 1.3 74.4 - - - +
59M ARG* 1.3 60.6 + - - +
61M LEU* 3.8 6.3 - - - +
62M LYS* 2.9 32.2 + - - +
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Residues in contact with ARG 59 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M GLN* 3.6 38.7 - - + +
38M TRP* 4.3 17.7 - - + +
55M GLN 2.9 23.2 + - - +
56M LEU* 3.9 6.1 - - - +
58M GLU* 1.3 77.7 - - - +
60M ALA* 1.3 61.1 + - - +
62M LYS* 3.5 4.6 + - - +
63M LEU* 3.4 23.4 + - - +
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Residues in contact with ALA 60 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38M TRP* 6.1 0.7 - - - -
56M LEU 2.9 19.4 + - - +
57M TYR* 4.1 2.7 - - - +
59M ARG* 1.3 76.6 - - - +
61M LEU* 1.3 61.0 + - - +
63M LEU* 3.5 20.3 + - - +
64M LEU 5.2 1.7 - - - +
71M TRP* 5.6 8.3 - - + -
97M ASN 6.0 0.4 - - - +
100M GLU 6.4 0.2 - - - -
101M ARG* 4.8 24.2 - - + -
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Residues in contact with LEU 61 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M TYR 2.9 21.2 + - - +
58M GLU* 3.9 6.1 - - - +
60M ALA* 1.3 78.3 - - - +
62M LYS* 1.3 58.5 + - - +
63M LEU 3.3 6.1 + - - +
100M GLU* 5.5 11.7 - - + +
919U LEU 4.6 14.7 - - - +
920U GLY* 5.1 5.9 - - - +
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Residues in contact with LYS 62 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M GLN* 6.2 0.7 - - + -
33M PHE* 4.7 19.1 - - + +
58M GLU 2.9 18.9 + - - +
59M ARG* 3.5 5.1 + - - +
60M ALA 3.3 0.2 - - - -
61M LEU* 1.3 76.3 - - - +
63M LEU* 1.3 57.7 + - - +
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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