Contacts of the helix formed by residues 118 - 125 (chain A) in PDB entry 1T9A
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 ILE 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A PRO 4.2 0.4 - - - -
115A GLY 3.4 28.0 - - - +
117A ALA* 1.3 77.0 - - - +
119A LEU* 1.3 64.1 + - - +
120A PRO* 3.3 4.5 - - - -
121A VAL* 3.1 35.7 + - + -
122A TYR* 3.2 27.5 + - + -
160A LEU* 3.7 24.7 - - + -
161A VAL 3.7 13.5 - - - +
162A THR* 3.6 17.6 + - - +
189A GLY* 3.8 20.4 - - - +
249A LEU* 4.3 11.0 - - + +
254A THR* 5.4 0.7 - - + -
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Residues in contact with LEU 119 (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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114A PRO* 5.8 1.3 - - + -
115A GLY 3.2 12.9 + - - +
116A GLY* 3.0 29.9 + - - +
118A ILE* 1.3 76.7 - - - +
120A PRO* 1.3 69.7 - - + +
122A TYR* 3.0 9.4 + - + +
123A ASP* 2.8 26.6 + - + +
251A LYS* 5.1 0.7 - - - -
583B VAL* 3.8 25.8 - - + -
586B TRP* 4.1 20.9 - - + -
587B GLN* 3.9 22.9 - - + +
591B TYR* 3.8 30.5 - - + +
1695B 1TB 4.1 13.5 - - + +
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Residues in contact with PRO 120 (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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93A THR* 5.3 1.2 + - - -
95A GLY* 3.8 6.2 - - - -
116A GLY 4.1 0.2 - - - +
117A ALA 3.7 10.1 - - - +
118A ILE 3.3 4.7 - - - -
119A LEU* 1.3 94.1 - - + +
121A VAL* 1.3 58.0 + - - -
123A ASP* 4.0 3.0 + - + +
124A ALA* 3.5 18.5 + - - +
251A LYS* 3.7 24.7 - - + +
254A THR* 3.2 37.8 - - - +
255A ALA* 3.8 11.2 - - + +
591B TYR* 3.8 22.2 - - + +
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Residues in contact with VAL 121 (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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95A GLY* 4.1 10.3 - - - +
98A PHE* 3.5 41.1 - - + -
118A ILE* 3.1 30.3 + - + +
120A PRO* 1.3 75.5 - - - +
122A TYR* 1.3 67.3 + - - +
124A ALA* 3.1 4.5 + - - +
125A ILE* 3.1 21.8 + - + +
160A LEU* 3.9 16.2 - - + -
249A LEU* 4.5 5.8 - - + -
254A THR* 3.6 29.8 - - + +
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Residues in contact with TYR 122 (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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113A TYR 3.0 15.8 + - - -
114A PRO* 3.6 27.6 - - + -
118A ILE* 3.2 39.7 + - + +
119A LEU* 3.0 11.8 + - + +
121A VAL* 1.3 80.2 - - - +
123A ASP* 1.3 63.0 + - - +
125A ILE* 3.1 8.8 + - + +
126A HIS 3.0 12.5 + - - -
133A PHE* 3.1 30.6 - + - -
160A LEU* 2.7 44.3 + - + -
587B GLN* 5.2 4.0 - - - +
596B SER* 2.9 43.4 + - - +
597B HIS* 3.8 12.3 - + - -
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Residues in contact with ASP 123 (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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119A LEU* 2.8 14.9 + - + +
120A PRO 4.2 4.3 - - - +
122A TYR* 1.3 75.2 - - - +
124A ALA* 1.3 60.4 + - - +
126A HIS* 3.3 9.4 - - - +
587B GLN* 5.8 1.1 - - - +
591B TYR* 3.4 38.7 - - + +
594B ARG* 2.7 71.0 + - - +
596B SER* 4.7 4.0 - - - -
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Residues in contact with ALA 124 (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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93A THR* 5.0 0.7 - - - +
95A GLY* 3.3 37.2 - - - +
96A GLN* 3.6 18.0 - - + +
99A ASN* 3.8 16.1 + - + +
120A PRO 3.5 8.8 + - - +
121A VAL 3.1 8.0 + - - +
122A TYR 3.1 0.4 - - - -
123A ASP* 1.3 81.9 + - - +
125A ILE* 1.3 58.4 + - - +
126A HIS 3.3 3.0 + - - +
128A SER* 4.7 1.6 - - - -
594B ARG* 5.2 0.8 + - - +
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Residues in contact with ILE 125 (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 PHE* 4.4 15.3 - - + -
99A ASN* 3.5 19.7 - - + +
110A VAL* 5.7 0.2 - - + -
121A VAL* 3.4 11.4 - - + +
122A TYR* 3.1 24.2 - - + +
124A ALA* 1.3 77.4 - - + +
126A HIS* 1.3 64.5 + - - +
127A ASN 3.2 1.6 + - - -
128A SER* 3.2 16.1 + - - +
131A PHE* 3.5 33.1 - - + -
133A PHE* 4.0 24.5 - - + -
160A LEU* 3.8 27.1 - - + -
596B SER* 4.3 2.5 - - - +
597B HIS* 4.4 10.2 + - + +
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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