Contacts of the helix formed by residues 49 - 54 (chain B) in PDB entry 1EQB
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A MET* 3.4 24.4 - - - +
44A MET* 3.8 5.0 - - - +
45B GLN 3.5 4.7 + - - -
46B ALA 2.8 19.8 + - - -
47B GLN 3.3 1.3 - - - +
48B GLY* 1.3 82.3 - - - +
50B GLN* 1.3 59.2 + - - +
51B LEU* 3.1 32.4 + - - +
52B THR* 3.3 20.1 + - - +
267B HIS* 4.0 2.6 - - - +
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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
----------------------------------------------------------
22A GLU* 5.7 0.4 - - + -
23A LYS* 3.7 29.2 + - + +
26A GLN* 2.8 52.0 + - - +
27A GLU* 5.7 1.6 + - - +
44A MET* 4.0 21.3 - - + -
416A TYR* 3.5 23.1 - - + -
4B ARG* 2.7 36.1 + - - +
49B SER* 1.3 71.1 - - - +
51B LEU* 1.3 61.2 + - + +
52B THR* 2.9 7.9 + - - -
53B ASN* 3.1 14.5 + - - +
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Residues in contact with LEU 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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19A MET* 4.2 23.6 - - + +
22A GLU* 3.2 36.3 - - + -
26A GLN* 4.6 2.5 - - - +
235A ARG* 5.4 0.3 - - - -
49B SER* 3.1 20.0 - - - +
50B GLN* 1.3 77.9 - - + +
52B THR* 1.3 59.6 + - - +
53B ASN 3.0 3.1 + - - -
54B LYS* 3.4 13.6 + - - +
71B VAL* 4.8 7.9 - - + -
74B VAL* 4.3 14.8 - - + -
266B MET* 3.7 29.4 + - + +
267B HIS* 3.7 13.3 + - - +
270B ALA* 3.6 31.2 - - + -
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Residues in contact with THR 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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39A THR* 3.8 28.0 - - + +
44A MET* 4.2 5.2 - - + -
47A GLN* 3.4 30.2 + - - +
228A HIS* 5.6 0.9 - - - +
234A PRO* 4.6 3.8 - - - +
235A ARG* 3.0 35.6 + - - +
49B SER 3.3 17.3 + - - +
50B GLN* 4.1 3.4 - - - -
51B LEU* 1.3 78.8 - - - +
53B ASN* 1.3 60.9 + - - +
54B LYS 3.5 0.2 - - - -
267B HIS* 3.5 27.1 + - - +
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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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26A GLN* 3.1 28.4 + - - +
36A GLU* 3.3 24.9 - - - +
37A ASN 3.5 21.2 + - - +
38A TYR* 3.5 7.9 - - + -
39A THR* 3.0 32.6 + - - +
235A ARG* 3.8 4.6 + - - +
416A TYR* 3.2 25.4 + - - -
50B GLN* 3.1 17.1 + - - +
51B LEU 3.0 0.8 - - - -
52B THR* 1.3 81.9 - - - +
54B LYS* 1.3 56.9 + - - +
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Residues in contact with LYS 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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22A GLU* 3.8 7.9 - - - +
25A ARG* 3.6 31.9 - - - +
26A GLN* 4.7 0.6 - - - +
31A GLU* 4.3 0.9 - - - -
33A ILE* 3.6 8.3 - - - +
36A GLU* 3.1 16.9 + - - +
235A ARG* 3.4 16.1 + - - -
50B GLN 4.5 0.4 + - - -
51B LEU* 3.4 14.3 + - - +
53B ASN* 1.3 78.9 - - - +
55B TYR* 1.3 87.7 + - - +
56B ALA* 3.8 3.3 + - + -
65B PHE* 3.7 1.6 - - - +
66B GLY 2.6 29.5 + - - -
67B GLY 3.3 17.0 - - - +
68B CYS* 3.7 11.6 - - - -
71B VAL* 4.0 23.3 - - + -
264B PRO 4.8 1.7 - - - +
266B MET* 4.4 10.6 + - + +
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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