Contacts of the helix formed by residues 105 - 114 (chain D) in PDB entry 5DPR
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 PRO 105 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D ASP 3.6 13.2 - - - +
68D HIS* 4.2 18.6 - - + +
69D VAL 4.0 5.4 - - - +
70D ASN* 4.6 0.7 - - - -
103D SER 3.6 4.2 - - - +
104D THR* 1.3 94.5 - - + +
106D ILE* 1.3 61.6 + - - +
107D ALA* 4.3 3.8 - - + +
108D ASP* 2.9 40.4 + - - +
109D ILE* 3.3 7.1 + - - +
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Residues in contact with ILE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ILE* 3.9 15.5 - - + -
44D VAL* 3.7 30.5 - - + -
65D VAL* 3.9 18.4 - - + -
66D PRO 3.4 25.8 - - - +
67D ASP 3.4 3.7 + - - +
69D VAL 3.0 19.5 + - - +
71D MET* 4.2 17.3 - - - -
74D LEU* 4.6 2.9 - - + -
104D THR 3.6 1.9 + - - -
105D PRO* 1.3 71.5 - - - +
107D ALA* 1.3 59.5 + - - +
109D ILE* 3.2 9.4 + - + +
110D TYR* 2.8 27.5 + - - +
120D LEU* 3.9 16.8 - - + -
122D MET* 4.0 10.3 - - + -
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Residues in contact with ALA 107 (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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42D ILE* 4.0 13.2 - - + +
67D ASP* 3.2 39.0 + - + +
105D PRO* 3.1 3.1 - - + -
106D ILE* 1.3 82.0 - - - +
108D ASP* 1.3 66.2 + - - +
110D TYR* 3.5 14.2 + - - +
111D GLU* 3.7 13.0 + - - +
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Residues in contact with ASP 108 (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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104D THR* 3.6 13.4 - - + +
105D PRO* 2.9 35.5 + - - +
107D ALA* 1.3 79.8 - - - +
109D ILE* 1.3 66.4 + - - +
110D TYR 3.4 0.2 + - - -
111D GLU* 3.8 10.5 + - - +
112D GLN* 3.9 15.9 + - - +
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Residues in contact with ILE 109 (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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71D MET* 4.5 15.5 - - + -
94D VAL* 4.1 19.7 - - + -
102D VAL* 4.4 9.2 - - + -
104D THR* 3.5 29.2 - - + +
105D PRO 3.6 12.6 - - - +
106D ILE* 3.2 16.5 + - + +
108D ASP* 1.3 77.3 - - - +
110D TYR* 1.3 58.7 + - - +
112D GLN* 3.3 4.1 + - - +
113D GLU* 2.9 50.8 + - + +
120D LEU* 4.5 8.7 - - + +
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Residues in contact with TYR 110 (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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31D VAL* 4.2 4.0 - - - +
35D ARG* 3.2 45.7 - - - -
42D ILE* 3.4 32.5 - - + -
43D PRO* 4.0 14.6 - - + +
106D ILE 2.8 16.2 + - - +
107D ALA 3.5 8.5 - - - +
108D ASP 3.2 0.4 - - - -
109D ILE* 1.3 75.8 - - - +
111D GLU* 1.3 75.4 + - + +
114D LYS* 3.0 62.2 + - + +
118D GLY* 2.6 32.1 + - - -
120D LEU* 4.1 16.6 - - + +
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Residues in contact with GLU 111 (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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35D ARG* 3.8 13.5 + - - -
107D ALA 3.7 11.5 + - - +
108D ASP* 3.8 6.9 + - - +
109D ILE 3.5 0.6 - - - -
110D TYR* 1.3 94.6 - - - +
112D GLN* 1.3 62.6 + - + +
114D LYS* 3.2 34.6 + - - +
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Residues in contact with GLN 112 (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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108D ASP 3.9 12.0 + - - +
109D ILE* 3.3 7.7 + - - +
110D TYR 3.2 0.6 - - - -
111D GLU* 1.3 82.8 - - + +
113D GLU* 1.3 73.8 + - + +
114D LYS 3.6 2.1 + - - +
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Residues in contact with GLU 113 (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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94D VAL* 3.9 22.0 - - + -
95D ASN* 2.9 56.0 + - - +
97D HIS* 5.1 11.3 - - - -
109D ILE* 2.9 32.3 + - + +
112D GLN* 1.3 85.7 - - + +
114D LYS* 1.3 67.4 + - - +
120D LEU* 3.9 6.4 - - + +
121D TYR 5.4 0.7 + - - -
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Residues in contact with LYS 114 (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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35D ARG* 5.2 1.0 - - - +
95D ASN* 5.3 0.2 + - - -
110D TYR* 3.0 63.8 + - + +
111D GLU* 3.2 41.2 + - - +
112D GLN 3.6 2.2 - - - +
113D GLU* 1.3 82.3 - - - +
115D ASP* 1.3 70.0 + - - +
118D GLY* 4.3 5.8 - - - +
119D PHE 3.6 12.1 - - - +
120D LEU* 4.0 7.8 - - - +
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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