Contacts of the helix formed by residues 49 - 54 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C MET* 3.4 24.1 - - - +
44C MET* 3.8 4.7 - - - +
45D GLN 3.5 4.4 + - - -
46D ALA 2.8 21.0 + - - -
47D GLN 3.3 1.8 - - - +
48D GLY* 1.3 81.7 - - - +
50D GLN* 1.3 60.1 + - - +
51D LEU* 3.1 31.5 + - - +
52D THR* 3.3 20.6 + - - +
267D HIS* 3.9 1.7 - - - +
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Residues in contact with GLN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLU* 5.8 0.2 - - + -
23C LYS* 3.8 47.4 + - + +
26C GLN* 2.9 45.9 + - - +
27C GLU* 5.7 1.0 + - - -
44C MET* 4.0 21.2 - - + +
416C TYR* 3.2 35.8 - - + +
49D SER* 1.3 72.7 - - - +
51D LEU* 1.3 57.9 + - + +
52D THR* 2.9 11.1 + - - -
53D ASN* 3.0 15.0 + - - +
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Residues in contact with LEU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C MET* 4.2 22.4 - - + +
22C GLU* 3.3 36.8 - - + -
26C GLN* 4.6 2.5 - - - +
235C ARG* 5.4 0.5 - - - -
49D SER* 3.1 19.1 - - - +
50D GLN* 1.3 77.6 - - + +
52D THR* 1.3 60.3 + - - +
53D ASN 3.0 2.3 + - - -
54D LYS* 3.4 14.4 + - - +
71D VAL* 4.7 7.6 - - + -
74D VAL* 4.2 15.9 - - + -
266D MET* 3.7 29.2 + - + +
267D HIS* 3.7 13.3 - - - +
270D ALA* 3.7 30.5 - - + -
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Residues in contact with THR 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C THR* 3.8 27.3 - - + +
44C MET* 4.2 5.4 - - + -
47C GLN* 3.4 29.8 + - - +
228C HIS* 5.6 0.7 - - - +
233C GLY 5.5 0.2 + - - -
234C PRO* 4.6 3.5 - - - +
235C ARG* 3.0 35.7 + - - +
49D SER 3.3 17.8 + - - +
50D GLN* 4.1 3.8 - - - -
51D LEU* 1.3 79.6 - - - +
53D ASN* 1.3 60.3 + - - +
54D LYS 3.5 0.2 - - - -
267D HIS* 3.5 27.3 + - - +
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Residues in contact with ASN 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C GLN* 3.1 27.9 + - - +
36C GLU* 3.3 24.6 - - - +
37C ASN 3.4 22.1 + - - +
38C TYR* 3.9 7.4 - - + -
39C THR* 3.0 32.5 + - - +
44C MET* 5.2 0.2 - - - -
235C ARG* 3.9 4.1 + - - +
416C TYR* 3.0 25.5 + - - -
50D GLN* 3.0 17.2 + - - +
52D THR* 1.3 82.9 - - - +
54D LYS* 1.3 59.7 + - - +
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Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLU* 3.8 8.1 - - - +
25C ARG* 3.6 30.7 - - - +
26C GLN* 5.1 0.4 - - - +
31C GLU* 4.3 0.7 - - - -
33C ILE* 3.6 7.7 - - - +
36C GLU* 3.1 17.0 + - - +
235C ARG* 3.5 16.0 + - - -
50D GLN 4.5 0.4 + - - -
51D LEU 3.4 14.2 + - - +
53D ASN* 1.3 77.5 - - - +
55D TYR* 1.3 88.7 + - - +
56D ALA* 3.8 3.4 + - + -
65D PHE* 3.7 2.0 - - - +
66D GLY 2.6 30.1 + - - -
67D GLY 3.4 17.0 - - - +
68D CYS* 3.7 11.2 - - - -
71D VAL* 4.0 23.6 - - + -
264D PRO 4.8 2.1 - - - +
266D MET* 4.3 10.5 + - + +
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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