Contacts of the helix formed by residues 103 - 111 (chain T) in PDB entry 3P71
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 103 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48T ASP* 2.4 35.7 + - - +
50T TYR* 4.0 9.6 - - + -
51T ILE* 3.8 26.9 - - + +
54T PHE* 3.9 13.5 - - + -
101T MET 3.5 15.5 - - - +
102T ASP* 1.3 75.3 + - - +
104T THR* 1.3 64.6 + - - +
105T PHE 3.2 3.1 - - - -
106T TRP* 3.1 23.5 + - - +
107T ARG* 2.9 27.5 + - - +
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Residues in contact with THR 104 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81T ILE* 4.5 22.6 - - + +
102T ASP* 2.6 35.4 + - - -
103T THR* 1.3 77.0 - - - +
105T PHE* 1.3 56.5 + - - +
107T ARG* 3.2 23.9 + - + +
108T LEU* 2.8 62.7 + - + +
118T TYR* 3.5 13.4 + - + +
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Residues in contact with PHE 105 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102T ASP 5.3 0.2 + - - -
103T THR 3.1 1.2 + - - -
104T THR* 1.3 78.6 - - - +
106T TRP* 1.3 90.8 + + + +
108T LEU* 3.3 5.5 + - - +
109T LYS* 3.1 24.0 + - + +
114T LEU* 3.8 23.6 - - + +
118T TYR* 3.8 26.7 - - + -
120T GLU* 5.5 0.8 + - - +
143T PRO* 4.6 5.2 - - + -
144T ILE* 3.9 30.5 - - + -
147T LEU* 4.2 20.6 - - + -
164T ARG* 3.8 14.6 - - + -
165T TYR* 3.5 55.2 - + + -
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Residues in contact with TRP 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50T TYR* 3.5 34.5 + + + -
54T PHE* 3.8 23.6 - + - -
102T ASP 3.8 17.5 - - - -
103T THR* 3.1 20.8 + - - +
105T PHE* 1.3 88.2 - + + +
107T ARG* 1.3 57.5 + - - +
109T LYS* 3.4 8.1 + - - +
110T ASP* 3.2 30.5 + - - +
134T ILE* 4.1 9.4 - - + -
139T PRO 4.1 6.1 - - - -
140T LEU* 2.8 38.8 + - + +
143T PRO* 3.8 27.9 - - + +
144T ILE* 3.8 23.0 - - + +
165T TYR* 3.4 31.6 - + - -
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Residues in contact with ARG 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46T TRP* 5.5 9.7 - - - +
47T HIS* 3.8 23.3 - - + +
48T ASP* 3.5 12.5 + - - -
49T PRO* 5.0 2.7 - - + -
50T TYR* 4.0 21.3 - - + -
74T VAL* 5.6 7.6 - - - +
78T SER* 5.0 9.3 + - - -
102T ASP* 4.1 5.5 + - - -
103T THR* 2.9 27.1 + - - +
104T THR* 3.2 39.2 + - + +
106T TRP* 1.3 74.6 - - - +
108T LEU* 1.3 65.2 + - + +
110T ASP* 3.4 5.7 + - - +
111T GLU* 3.2 41.1 + - - +
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Residues in contact with LEU 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81T ILE* 4.6 5.6 - - + -
82T LYS* 6.1 2.7 - - + -
85T LEU* 3.8 24.2 - - + -
94T ILE* 4.2 15.9 - - + -
104T THR* 2.8 46.0 + - + +
105T PHE 3.7 3.1 - - - +
107T ARG* 1.3 73.5 - - - +
109T LYS* 1.3 57.6 + - - +
111T GLU* 3.5 7.9 + - - +
112T ASP 3.2 5.5 + - - -
113T LEU* 2.8 48.0 + - + +
114T LEU* 3.6 19.7 + - + -
115T SER 5.1 1.1 - - - +
118T TYR* 4.1 22.7 - - + -
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Residues in contact with LYS 109 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105T PHE* 3.1 18.4 + - + +
106T TRP* 3.6 11.0 - - - +
107T ARG 3.3 0.2 - - - -
108T LEU* 1.3 78.5 - - - +
110T ASP* 1.3 65.8 + - - +
112T ASP* 3.6 10.2 + - - +
114T LEU* 4.0 24.2 - - + +
143T PRO* 3.3 43.7 - - + +
146T GLU* 2.9 25.6 + - - +
147T LEU* 3.7 20.2 - - + +
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Residues in contact with ASP 110 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T PRO* 4.8 3.8 - - - +
50T TYR* 2.5 41.8 + - - -
106T TRP 3.2 7.0 + - - +
107T ARG* 3.8 8.9 - - - +
108T LEU 3.3 0.2 - - - -
109T LYS* 1.3 79.9 - - - +
111T GLU* 1.3 59.1 + - + +
112T ASP* 3.1 9.2 + - - +
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Residues in contact with GLU 111 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82T LYS* 3.7 22.9 - - - +
107T ARG* 3.2 30.5 + - - +
108T LEU* 4.1 9.8 - - - +
109T LYS 3.4 0.2 - - - -
110T ASP* 1.3 77.4 - - + +
112T ASP* 1.3 69.1 + - - +
113T LEU* 3.4 35.7 + - + +
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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