Contacts of the helix formed by residues 49 - 53 (chain B) in PDB entry 2XLR
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 GLY 49 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA 3.0 7.3 + - - -
16B GLY* 3.8 8.1 - - - -
17B PRO* 3.6 2.7 - - - +
20B MET* 4.2 12.5 - - - +
48B TRP* 1.3 80.1 - - - +
50B GLY* 1.3 59.5 + - - +
51B GLN 3.3 0.9 + - - -
52B TRP* 2.9 34.7 + - - +
53B ASN 4.0 2.2 - - - -
109B TRP* 3.6 15.9 - - - -
112B ILE* 4.5 2.7 - - - -
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Residues in contact with GLY 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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16B GLY* 3.5 5.5 - - - -
45B GLN* 3.6 14.2 + - - +
47B ASP 5.2 0.6 + - - -
48B TRP 3.6 2.0 - - - -
49B GLY* 1.3 73.2 - - - +
51B GLN* 1.3 64.9 + - - +
52B TRP 3.1 0.7 + - - -
53B ASN* 3.2 14.9 + - - +
68B HIS* 4.1 4.7 - - - -
69B SER* 4.3 2.4 - - - -
500B FAD 3.2 39.8 + - - -
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Residues in contact with GLN 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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49B GLY 3.3 0.4 + - - -
50B GLY* 1.3 71.8 - - - -
52B TRP* 1.3 61.3 + - - +
53B ASN 3.3 1.4 + - - +
68B HIS* 3.9 2.3 + - - -
69B SER* 2.7 27.2 + - - +
70B SER* 2.7 30.5 + - - -
71B MET* 3.4 28.4 + - + +
170B PHE* 3.1 33.5 + - - +
171B SER* 3.3 15.8 + - - -
500B FAD 2.9 71.7 + - + +
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Residues in contact with TRP 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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17B PRO* 4.0 10.5 - - + -
49B GLY 2.9 14.8 + - - +
51B GLN* 1.3 72.8 - - - +
53B ASN* 1.3 58.5 + - - +
54B TYR 3.1 0.8 + - - -
71B MET* 3.6 31.3 - - + +
75B LEU* 4.5 5.6 - - + -
77B SER* 5.4 0.7 - - - -
105B ARG* 3.0 57.8 + - + -
108B LEU* 3.7 37.0 - - + -
109B TRP* 3.3 32.2 - - + -
112B ILE* 4.3 8.1 - - + -
327B PHE* 3.9 19.1 - + - -
500B FAD 3.3 72.9 + + - -
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Residues in contact with ASN 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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45B GLN* 3.0 27.0 + - - +
46B ALA 5.1 0.6 - - - +
47B ASP* 3.6 30.4 + - - +
48B TRP 3.7 17.9 - - - +
49B GLY 3.8 1.8 + - - -
50B GLY 3.2 13.5 + - - +
51B GLN 3.2 1.9 - - - -
52B TRP* 1.3 75.4 - - - +
54B TYR* 1.3 68.2 + - - +
55B THR* 4.8 1.2 - - - -
69B SER* 3.6 17.3 - - - -
105B ARG* 5.3 0.2 - - - +
109B TRP* 3.8 20.9 - - + +
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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