Contacts of the helix formed by residues 50 - 60 (chain D) in PDB entry 3AQQ
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 THR 50 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C GLU* 3.2 16.4 - - - +
48D THR 3.2 5.6 + - - +
49D ARG* 1.3 73.7 - - - +
51D PHE* 1.3 59.4 + - - +
52D SER* 3.7 7.6 + - - -
53D ALA* 3.1 25.6 + - + +
54D THR* 2.8 30.0 + - - -
115D PRO* 5.4 12.1 - - + -
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Residues in contact with PHE 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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97C GLY* 5.9 0.7 - - - -
98C GLU* 3.0 13.8 + - - +
99C TYR* 3.4 38.8 - + + -
128C ILE* 3.7 26.1 - - + +
129C THR 3.3 26.9 - - - -
130C HIS* 4.6 6.1 - + - -
131C LEU* 3.8 25.4 - - + -
49D ARG 3.5 1.3 + - - -
50D THR* 1.3 70.6 - - - +
52D SER* 1.3 73.7 + - - +
54D THR* 3.2 13.6 + - - -
55D VAL* 3.0 33.4 + - + +
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Residues in contact with SER 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D THR* 3.2 6.5 + - - -
51D PHE* 1.3 86.6 - - - +
53D ALA* 1.3 67.7 + - - +
55D VAL* 3.0 17.1 + - - +
56D ARG* 3.2 20.9 + - - +
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Residues in contact with ALA 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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49D ARG* 3.8 17.3 - - + -
50D THR* 3.1 23.3 + - + +
52D SER* 1.3 79.2 - - - +
54D THR* 1.3 63.8 + - - +
56D ARG* 3.1 15.0 - - - +
57D ALA* 3.0 24.0 + - - +
112D CYS* 4.4 11.0 - - - -
113D SER 5.6 3.4 - - - +
115D PRO* 5.8 6.5 - - + -
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Residues in contact with THR 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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96C GLU* 3.6 36.6 - - + +
97C GLY* 3.8 5.9 - - - -
127C VAL* 4.3 17.0 - - + -
128C ILE 6.0 0.2 - - - -
49D ARG* 3.5 30.2 + - - +
50D THR 2.8 21.2 + - - -
51D PHE* 3.4 9.7 - - - -
52D SER 3.1 0.2 - - - -
53D ALA* 1.3 76.8 - - - +
55D VAL* 1.3 67.1 + - - +
57D ALA* 3.5 3.5 - - + +
58D SER* 3.0 20.5 + - - -
125D GLU* 6.1 0.2 - - - +
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Residues in contact with VAL 55 (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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127C VAL* 4.5 4.0 - - + -
128C ILE 4.3 10.3 - - - +
129C THR* 4.5 23.1 - - + +
51D PHE* 3.0 42.0 - - + +
52D SER* 3.0 8.3 + - - +
54D THR* 1.3 73.9 - - - +
56D ARG* 1.3 59.3 + - - +
58D SER* 2.6 25.4 + - - +
59D GLN* 2.8 38.4 + - + +
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Residues in contact with ARG 56 (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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52D SER* 3.2 15.9 - - - +
53D ALA* 3.1 26.2 - - - +
55D VAL* 1.3 74.8 - - - +
57D ALA* 1.3 62.8 + - - +
59D GLN* 2.8 13.1 + - - +
60D GLY* 2.8 23.2 + - - -
113D SER* 6.1 2.8 - - - -
118D ASN* 5.2 9.5 - - - +
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Residues in contact with ALA 57 (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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49D ARG* 5.1 1.1 - - - -
53D ALA 3.0 18.2 + - - +
54D THR* 3.5 7.6 - - + +
56D ARG* 1.3 78.3 - - - +
58D SER* 1.3 62.8 + - - +
60D GLY* 3.3 7.8 + - - -
110D LYS* 3.2 21.1 - - - +
111D MET 3.5 24.4 + - - +
112D CYS* 4.0 12.8 - - - +
124D VAL* 3.8 20.0 - - + -
125D GLU* 5.8 0.2 - - - +
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Residues in contact with SER 58 (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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108C THR* 5.3 2.5 + - - -
127C VAL* 3.8 22.5 - - - +
54D THR* 3.0 9.1 + - - -
55D VAL* 2.6 24.2 + - - +
57D ALA* 1.3 79.9 - - - +
59D GLN* 1.3 62.9 + - - +
60D GLY 3.7 1.4 - - - +
110D LYS* 3.2 27.9 - - - -
125D GLU* 3.3 19.7 + - - -
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Residues in contact with GLN 59 (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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59B GLN* 4.8 7.8 + - - +
129C THR* 5.8 3.6 - - - +
55D VAL* 2.8 38.9 + - + +
56D ARG* 2.8 12.8 + - - +
58D SER* 1.3 77.3 - - - +
60D GLY* 1.3 65.7 + - - +
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Residues in contact with GLY 60 (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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59B GLN* 4.6 8.5 + - - +
56D ARG 2.8 13.5 + - - -
57D ALA 3.3 7.6 + - - -
58D SER 3.7 6.9 - - - +
59D GLN* 1.3 84.4 - - - +
61D PRO* 1.3 76.3 - - - +
62D VAL* 5.0 1.6 - - - +
110D LYS* 4.2 5.9 - - - +
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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