Contacts of the helix formed by residues 98 - 103 (chain D) in PDB entry 3TKR
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 LEU 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D PHE 3.0 7.0 + - - +
95D GLY* 3.3 15.5 + - - +
96D ASP 3.5 1.0 + - - -
97D ARG* 1.3 77.0 - - - +
99D GLU* 1.3 58.3 + - - +
101D PHE* 3.0 10.6 + - + +
102D ARG* 2.8 70.4 + - + +
107D GLU* 4.8 1.3 - - - +
108D VAL* 3.9 27.1 - - + +
136D ARG* 3.8 39.7 - - + +
137D ILE* 3.8 22.2 - - + -
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Residues in contact with GLU 99 (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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97D ARG 3.1 1.4 + - - -
98D LEU* 1.3 78.0 - - - +
100D GLU* 1.3 57.3 + - + +
102D ARG* 4.0 19.9 - - - +
103D SER* 2.7 36.9 + - - -
136D ARG* 2.8 36.1 + - - +
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Residues in contact with GLU 100 (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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97D ARG* 2.9 66.2 + - - +
99D GLU* 1.3 77.9 - - + +
101D PHE* 1.3 56.2 + - - +
103D SER* 3.9 6.7 + - - -
104D ILE* 3.5 17.0 - - - +
192D LEU* 3.2 31.9 - - + +
196D GLN* 5.6 0.3 + - - -
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Residues in contact with PHE 101 (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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75D VAL* 4.0 19.1 - - + -
94D PHE* 3.6 36.6 - + - -
97D ARG 3.8 16.4 - - - -
98D LEU* 3.0 10.6 + - + +
100D GLU* 1.3 77.4 - - - +
102D ARG* 1.3 59.9 + - - +
103D SER 3.2 1.8 - - - -
104D ILE* 2.9 23.9 + - + +
106D THR* 3.0 47.5 + - + +
108D VAL* 3.8 19.3 - - + -
188D VAL* 3.9 15.7 - - + -
191D THR* 4.1 10.3 - - + -
192D LEU* 3.5 36.1 - - + -
195D VAL* 4.5 5.8 - - + -
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Residues in contact with ARG 102 (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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98D LEU* 2.8 46.1 + - + +
99D GLU* 4.0 20.4 + - - +
101D PHE* 1.3 73.3 - - - +
103D SER* 1.3 59.2 + - - +
104D ILE 3.1 1.1 + - - -
105D ASN* 3.3 12.0 + - - -
106D THR 3.4 10.8 - - - +
107D GLU* 3.1 40.0 + - - +
136D ARG* 3.5 36.8 + - - +
138D PRO* 5.6 4.2 - - - +
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Residues in contact with SER 103 (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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99D GLU* 2.7 26.5 + - - -
100D GLU* 3.9 9.4 + - - -
101D PHE 3.2 0.2 - - - -
102D ARG* 1.3 74.5 - - - +
104D ILE* 1.3 66.9 + - - +
105D ASN 3.5 1.3 + - - -
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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