Contacts of the helix formed by residues 50 - 57 (chain B) in PDB entry 5C6E
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 ASN 50 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B VAL* 5.3 0.4 - - - -
47B ASP* 4.9 1.4 + - - -
48B LEU 3.4 0.4 - - - -
49B SER* 1.3 92.1 + - - +
51B PRO* 1.3 75.4 - - + +
52B GLY* 2.9 27.9 + - - -
53B ALA* 2.9 18.2 + - - +
54B VAL* 3.2 25.0 + - - +
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Residues in contact with PRO 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PRO* 4.9 2.2 - - + -
120A ALA* 4.6 13.9 - - + -
347A DOD 4.1 18.6 - - - +
33B VAL* 3.9 37.2 - - + -
50B ASN* 1.3 89.4 - - + +
52B GLY* 1.3 61.3 + - - +
54B VAL 4.0 0.4 - - - -
55B MET* 3.1 31.5 + - - +
355B DOD 4.0 3.7 + - - +
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Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ASN* 2.9 9.2 + - - -
51B PRO* 1.3 76.8 - - - +
53B ALA* 1.3 64.9 + - - +
55B MET* 4.2 2.3 - - - +
56B GLY* 3.3 19.9 + - - -
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ASP* 3.8 30.1 - - - +
50B ASN* 2.9 25.8 + - - +
52B GLY* 1.3 75.4 - - - +
54B VAL* 1.3 63.6 + - - +
56B GLY 3.8 0.7 - - - -
57B ASN* 3.0 14.0 + - - +
316B DOD 2.7 29.5 + - - +
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLY* 3.7 33.2 - - - +
32B LEU* 4.1 20.6 - - + -
33B VAL* 4.2 13.0 - - + -
39B GLN* 5.5 2.5 - - - +
48B LEU* 3.7 40.6 - - + +
50B ASN 3.2 19.2 + - - +
51B PRO 4.0 3.8 - - - +
53B ALA* 1.3 77.2 - - - +
55B MET* 1.3 63.8 + - - +
57B ASN* 3.2 15.9 + - - +
60B VAL* 3.7 13.0 - - + +
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Residues in contact with MET 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A PRO* 3.8 27.4 - - + -
26B GLU* 3.9 41.1 - - + +
29B GLY* 3.6 28.0 - - - +
30B ARG* 4.1 2.7 - - + +
33B VAL* 4.5 2.2 - - - -
51B PRO 3.1 19.9 + - - +
52B GLY* 4.4 2.2 - - - +
54B VAL* 1.3 81.3 - - - +
56B GLY* 1.3 58.1 + - - +
57B ASN 3.4 0.4 + - - -
60B VAL* 5.4 0.4 - - - -
61B LYS* 3.8 10.6 - - - +
345B DOD 4.6 3.8 - - - +
347B DOD 3.2 25.0 + - - +
355B DOD 3.8 16.6 - - - +
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Residues in contact with GLY 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLY 3.3 15.4 + - - -
53B ALA 3.8 1.8 - - - -
54B VAL 3.2 0.6 - - - -
55B MET* 1.3 76.5 - - - +
57B ASN* 1.3 65.9 + - - +
58B PRO* 3.3 8.0 - - - +
61B LYS* 3.9 15.0 + - - -
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Residues in contact with ASN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B PHE* 2.9 26.9 + - - +
47B ASP 3.8 9.9 + - - +
48B LEU* 3.8 8.1 - - - +
53B ALA 3.0 17.7 + - - +
54B VAL* 3.2 12.3 + - - +
56B GLY* 1.3 76.2 - - - +
58B PRO* 1.3 72.6 - - - +
59B LYS* 2.7 35.6 + - - +
60B VAL* 3.3 25.2 + - + +
61B LYS* 3.3 14.6 + - - +
316B DOD 3.5 14.8 + - - +
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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