Contacts of the helix formed by residues 97 - 103 (chain A) 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 ARG 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A ALA* 3.5 16.0 + - - +
94A PHE 3.0 6.6 + - - +
96A ASP* 1.3 83.7 - - + +
98A LEU* 1.3 65.9 + - - +
99A GLU 3.2 2.9 - - - -
100A GLU* 2.7 64.3 + - + +
101A PHE* 3.7 6.0 - - + -
188A VAL* 3.7 35.1 - - + +
189A ASP* 2.9 32.3 + - - +
192A LEU* 4.3 11.9 - - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PHE 3.0 7.0 + - - +
95A GLY* 3.3 16.3 + - - +
96A ASP 3.5 1.0 - - - -
97A ARG* 1.3 78.1 - - - +
99A GLU* 1.3 57.8 + - - +
101A PHE* 2.9 22.6 + - + +
102A ARG* 3.0 58.8 + - + +
108A VAL* 3.7 39.0 - - + +
136A ARG* 3.8 39.4 - - + +
137A ILE* 4.1 11.9 - - + -
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ARG 3.1 1.8 + - - -
98A LEU* 1.3 76.2 - - - +
100A GLU* 1.3 57.5 + - + +
102A ARG* 3.6 24.1 - - - +
103A SER* 3.0 35.9 + - - -
136A ARG* 3.0 40.1 + - - +
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A ARG* 2.7 64.6 + - + +
99A GLU* 1.3 77.7 - - - +
101A PHE* 1.3 63.7 + - + +
103A SER* 3.5 12.8 + - - -
104A ILE* 3.5 18.2 - - - +
192A LEU* 3.7 22.9 - - + +
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Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 4.1 6.7 - - + -
94A PHE* 3.7 30.3 - + - -
97A ARG* 3.7 18.2 - - + -
98A LEU* 2.9 11.2 + - + +
100A GLU* 1.3 79.0 - - + +
102A ARG* 1.3 61.1 + - - +
103A SER 3.1 1.3 - - - -
104A ILE* 2.9 24.6 + - + +
106A THR* 2.9 48.4 + - + +
108A VAL* 4.0 20.6 - - + -
188A VAL* 3.9 25.1 - - + -
191A THR* 4.1 17.0 - - + -
192A LEU* 4.2 32.1 - - + -
195A VAL* 4.5 3.6 - - + -
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Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A LEU* 3.0 36.2 + - + +
99A GLU* 3.6 24.5 - - - +
101A PHE* 1.3 76.6 - - - +
103A SER* 1.3 58.2 + - - +
105A ASN* 3.1 17.5 + - - +
106A THR 3.4 14.4 - - - +
107A GLU* 3.1 34.7 + - - +
108A VAL 5.9 0.6 + - - -
136A ARG* 3.0 49.9 + - - +
138A PRO* 5.2 5.3 - - - +
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A GLU* 3.0 23.4 + - - -
100A GLU* 3.5 12.1 + - - -
102A ARG* 1.3 76.6 - - - +
104A ILE* 1.3 65.0 + - - +
105A ASN 3.4 1.4 + - - -
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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