Contacts of the helix formed by residues 49 - 56 (chain M) in PDB entry 5A15
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 SER 49 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ARG* 3.9 9.0 - - - +
43M LEU 4.6 3.6 + - - -
46M ILE* 2.6 31.6 + - - +
47M PRO 3.1 1.0 - - - -
48M HIS* 1.3 82.0 - - - +
50M LEU* 1.3 64.9 + - - +
51M LEU* 4.1 3.5 + - - +
52M TRP* 3.2 14.1 + - - +
53M LYS* 3.0 23.0 + - - +
89M LEU* 5.6 2.5 - - - +
113M PHE 3.8 9.6 - - - -
114M GLN* 3.8 13.9 - - - -
115M LEU* 4.1 7.6 - - - -
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Residues in contact with LEU 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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49M SER* 1.3 74.8 - - - +
51M LEU* 1.3 62.5 + - - +
53M LYS* 3.2 9.6 + - + +
54M MET* 3.1 45.6 + - + +
112M TYR* 3.2 59.2 - - + +
113M PHE* 3.2 29.1 + - + +
114M GLN* 3.6 15.4 + - - +
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Residues in contact with LEU 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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29M LEU* 5.6 0.7 - - + -
43M LEU* 3.6 26.7 - - + +
49M SER* 3.5 3.9 + - - +
50M LEU* 1.3 79.7 - - + +
52M TRP* 1.3 56.4 + - - +
54M MET* 4.3 7.6 - - - -
55M PHE* 3.0 58.3 + - + +
75M ILE* 4.2 20.2 - - + -
82M PHE* 4.1 19.5 - - + -
85M ILE* 5.2 1.1 - - + -
89M LEU* 3.6 32.8 - - + -
113M PHE* 4.0 29.3 + - + -
115M LEU* 6.5 0.2 - - + -
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Residues in contact with TRP 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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43M LEU 3.6 8.0 + - - +
44M ILE* 3.3 31.8 + - + +
46M ILE 3.3 7.0 - - - +
47M PRO* 3.6 25.0 - - + +
48M HIS* 3.2 44.9 - + - -
49M SER* 3.2 24.3 + - - +
50M LEU 3.1 0.2 - - - -
51M LEU* 1.3 76.7 - - - +
53M LYS* 1.3 85.3 + - + +
56M SER* 2.6 51.9 + - - -
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Residues in contact with LYS 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 SER 3.0 13.2 + - - +
50M LEU* 3.2 13.9 + - + +
52M TRP* 1.3 91.7 - - + +
54M MET* 1.3 63.4 + - + +
56M SER* 4.1 10.8 - - - +
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Residues in contact with MET 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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23M PHE* 4.1 9.5 - - - -
50M LEU* 3.1 39.7 + - + +
51M LEU* 3.8 4.9 - - - +
52M TRP 3.2 0.2 - - - -
53M LYS* 1.3 81.4 - - + +
55M PHE* 1.3 80.7 + - + +
56M SER 3.7 4.3 + - - +
66M ALA* 6.1 3.1 - - + -
73M PHE* 6.5 0.4 - - + -
74M PHE 4.8 5.2 - - - +
75M ILE* 3.5 34.8 - - + -
112M TYR* 6.0 1.1 - - - -
113M PHE* 6.5 0.2 - - - -
39N ARG* 6.1 2.2 - - - +
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Residues in contact with PHE 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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23M PHE* 3.4 40.4 - + - -
27M VAL* 3.8 16.2 - - + -
29M LEU* 3.6 23.8 - - + -
40M HIS* 2.7 38.3 + + + +
43M LEU* 3.6 28.0 - - + -
44M ILE* 3.9 10.8 - - + -
51M LEU* 3.0 46.3 + - + +
54M MET* 1.3 96.1 - - + +
56M SER* 1.3 61.4 + - - +
57M PRO 3.6 0.7 - - - -
73M PHE* 4.3 13.2 - + + -
75M ILE* 4.5 4.0 - - + -
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Residues in contact with SER 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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23M PHE* 5.0 0.8 - - - -
44M ILE* 3.8 9.1 - - - +
52M TRP* 2.6 49.7 + - - -
53M LYS* 4.1 11.0 - - - +
54M MET 3.4 4.1 - - - +
55M PHE* 1.3 78.1 - - - +
57M PRO* 1.4 73.8 - - - +
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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