Contacts of the helix formed by residues 49 - 54 (chain B) in PDB entry 5F85
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 ASP 49 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A ASP* 5.5 1.2 - - - +
293A VAL* 4.2 28.3 - - - +
48B GLY* 1.3 74.6 - - - -
50B GLN* 1.3 75.0 + - - +
51B CYS 3.2 3.6 + - - -
52B GLU* 3.3 38.2 + - + +
53B SER 4.7 0.3 + - - -
64B ASP* 3.7 2.7 - - - -
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Residues in contact with GLN 50 (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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121A MET* 4.8 1.7 - - - -
122A PHE* 3.0 35.8 - - + -
125A ARG* 5.0 0.7 + - - -
150A ARG* 3.7 29.1 + - - +
151A ASP* 5.0 7.4 - - - +
48B GLY* 5.3 2.6 - - - -
49B ASP* 1.3 90.6 + - - +
51B CYS* 1.3 61.0 + - - +
52B GLU 3.3 0.9 + - - -
53B SER* 3.7 10.4 + - - -
55B PRO* 3.6 15.4 - - - +
64B ASP* 3.0 4.7 + - - +
67B ASN 5.0 5.0 - - - +
68B SER* 4.0 22.4 - - - +
69B TYR* 3.9 24.5 - - + -
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Residues in contact with CYS 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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259A GLN* 3.4 16.1 - - - +
260A GLY* 3.4 13.5 + - - -
49B ASP 3.2 0.2 - - - -
50B GLN* 1.3 75.4 - - - +
52B GLU* 1.3 58.4 + - - +
53B SER 3.2 0.4 - - - -
54B ASN* 3.0 17.9 + - - +
55B PRO* 3.5 1.7 - - - +
62B CYS* 2.1 53.2 - - + -
63B LYS 3.3 24.2 - - - -
64B ASP* 2.9 29.7 + - - +
69B TYR* 4.1 2.9 - - - -
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Residues in contact with GLU 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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231A SER* 4.6 0.5 + - - -
232A ARG 3.4 20.8 - - - +
233A THR* 3.6 26.1 - - + +
258A ASN* 3.4 47.2 + - - +
260A GLY* 4.6 8.5 - - - +
266A ASP* 5.7 0.7 - - - +
293A VAL* 3.9 21.2 - - + +
501A UDP 4.9 3.1 + - - +
49B ASP* 3.4 29.5 - - + +
50B GLN 3.2 0.8 - - - -
51B CYS* 1.3 77.7 - - - +
53B SER* 1.3 57.5 + - - +
54B ASN* 3.3 3.8 + - - +
64B ASP* 5.9 0.7 - - - +
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Residues in contact with SER 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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125A ARG* 3.7 15.7 + - - -
151A ASP* 2.4 30.4 + - - -
191A PRO* 3.4 20.5 - - - +
233A THR* 5.8 1.7 - - - +
293A VAL* 4.7 3.8 - - - +
501A UDP 5.5 2.9 + - - -
502A GOL 2.8 33.6 + - - -
49B ASP 4.7 0.6 + - - -
50B GLN 3.7 6.3 + - - -
51B CYS 3.2 1.0 - - - -
52B GLU* 1.3 75.1 - - - +
54B ASN* 1.3 72.3 + - - +
55B PRO* 3.5 2.6 - - - +
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Residues in contact with ASN 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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190A GLY 4.7 1.0 - - - +
191A PRO* 3.9 5.4 - - + +
192A ALA* 2.8 47.7 + - - +
193A THR* 4.6 9.9 - - - +
257A LYS 5.0 2.4 + - - -
258A ASN* 3.3 17.3 - - - +
259A GLN* 2.8 46.3 + - - +
501A UDP 5.7 4.1 + - - -
51B CYS 3.0 5.2 + - - -
52B GLU 3.5 1.0 - - - +
53B SER* 1.3 81.4 - - - +
55B PRO* 1.3 66.6 - - - +
56B CYS 3.2 4.0 + - - -
57B LEU* 5.0 0.9 - - - +
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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