Contacts of the helix formed by residues 108 - 122 (chain B) in PDB entry 1TAR
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 GLY 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B SER* 1.3 70.5 + - - +
109B THR* 1.3 63.7 + - - +
111B SER 3.3 0.3 + - - -
112B LEU* 2.9 26.7 + - - +
222B ASP* 5.8 0.7 - - - -
253B SER* 3.3 11.4 + - - -
254B GLN 3.7 15.5 - - - -
255B SER* 3.8 7.6 - - - -
411B PLP 2.8 32.6 + - - -
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Residues in contact with THR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ARG 3.6 4.3 - - - +
294A MET 4.1 2.0 - - - -
295A TYR* 3.6 16.4 - - - +
296A SER* 3.3 28.5 + - - +
108B GLY* 1.3 72.7 - - - +
110B GLY* 1.3 56.3 + - - +
112B LEU* 3.2 12.0 + - - +
113B ARG* 3.0 26.9 + - - +
140B TRP* 3.5 16.4 - - - -
142B ASN* 3.4 23.3 - - - +
146B ILE* 4.2 10.2 - - + +
411B PLP 2.5 29.4 + - - -
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Residues in contact with GLY 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A MET 3.5 15.4 + - - -
295A TYR* 4.0 5.0 - - - +
105B GLY* 4.8 0.7 - - - -
106B ILE* 3.0 32.0 + - - -
109B THR* 1.3 75.0 - - - +
111B SER* 1.3 56.4 + - - +
113B ARG* 3.2 3.3 + - - +
114B VAL* 2.9 34.5 + - - +
294B MET* 5.4 0.9 - - - +
295B TYR* 6.3 2.2 - - - -
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLY* 3.4 12.3 - - - -
106B ILE 4.2 1.4 - - - +
107B SER 2.9 18.7 + - - -
108B GLY* 3.5 1.1 - - - -
110B GLY* 1.3 73.3 - - - +
112B LEU* 1.3 59.1 + - - +
114B VAL* 3.3 3.7 + - - +
115B GLY* 2.9 24.8 + - - -
220B TYR* 4.3 0.2 - - - -
253B SER* 3.2 20.2 - - - -
269B ALA 3.3 36.5 + - - -
270B PHE* 3.7 17.0 - - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY 2.9 19.2 + - - +
109B THR* 3.5 7.2 - - - +
111B SER* 1.3 75.0 - - - +
113B ARG* 1.4 54.0 + - - +
116B ALA* 2.7 36.0 + - - +
140B TRP* 3.8 19.5 - - + -
143B HIS* 3.8 20.6 - - + +
146B ILE* 4.3 14.5 - - + +
147B PHE* 4.6 3.9 - - + -
187B LEU* 4.5 7.4 - - + -
220B TYR* 3.0 35.8 + - + +
222B ASP* 3.7 31.9 - - + +
253B SER* 3.7 15.7 + - - +
411B PLP 3.9 6.3 - - + -
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 5.5 3.6 - - - +
117A ASN* 5.0 9.7 - - - +
290A LEU 5.2 0.2 + - - -
293A PRO 3.0 33.5 + - - +
294A MET* 3.4 42.8 - - + +
109B THR 3.0 9.1 + - - +
110B GLY 3.2 3.8 + - - +
112B LEU* 1.4 73.4 - - - +
114B VAL* 1.3 60.3 + - - +
116B ALA* 3.2 1.1 + - - -
117B ASN* 2.8 70.2 + - - +
146B ILE* 3.8 20.3 + - + +
149B ASP* 3.8 40.6 + - - +
150B ALA* 4.1 3.9 - - - +
294B MET* 4.6 13.5 - - + -
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Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL* 4.6 4.7 - - + -
104B GLN 6.1 0.2 - - - +
105B GLY* 5.9 1.6 - - - -
110B GLY 2.9 19.3 + - - +
111B SER* 3.8 6.1 - - - +
113B ARG* 1.3 75.2 - - - +
115B GLY* 1.3 64.6 + - - +
117B ASN* 3.2 5.6 + - - -
118B PHE* 2.8 22.3 + - - +
270B PHE* 4.1 9.9 - - + -
287B LEU* 4.1 23.1 - - + -
290B LEU* 3.7 9.4 - - + +
291B ILE* 4.1 24.7 - - + -
294B MET* 3.9 28.7 - - + -
295B TYR* 4.3 14.1 - - + +
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B SER 2.9 11.1 + - - -
114B VAL* 1.3 77.7 - - - +
116B ALA* 1.4 61.3 + - - +
118B PHE* 3.0 4.7 + - - +
119B LEU* 2.9 26.2 + - - +
220B TYR* 3.4 17.3 - - - -
270B PHE* 3.2 31.6 - - - -
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU 2.7 20.6 + - - +
113B ARG* 3.2 8.9 + - - +
115B GLY* 1.4 71.1 - - - +
117B ASN* 1.3 58.1 + - - +
119B LEU* 3.3 3.9 + - - +
120B GLN* 3.1 24.8 + - - +
146B ILE* 4.2 6.5 - - + +
147B PHE* 3.6 34.1 - - + -
150B ALA* 3.7 18.2 - - + -
152B LEU* 3.6 11.1 - - - +
220B TYR* 3.8 1.6 + - - -
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Residues in contact with ASN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 4.7 10.7 - - - +
113B ARG* 2.8 56.9 + - - +
114B VAL* 3.8 4.5 - - - +
116B ALA* 1.3 71.9 - - - +
118B PHE* 1.3 60.6 + - - +
120B GLN* 3.5 10.1 + - - +
121B ARG* 3.3 21.5 + - - +
150B ALA* 3.1 16.0 - - - +
290B LEU* 4.0 24.4 - - + +
294B MET* 4.1 19.1 - - - +
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Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TRP* 3.6 42.8 - + - -
9A VAL* 5.1 1.8 - - + -
114B VAL 2.8 13.6 + - - +
115B GLY* 3.0 9.2 + - - +
117B ASN* 1.3 73.6 - - - +
119B LEU* 1.3 71.4 + - + +
121B ARG* 3.1 4.6 + - - +
122B PHE* 2.9 58.3 + + + -
251B VAL* 5.8 0.2 - - + -
270B PHE* 4.5 11.2 - + + -
272B VAL* 4.5 6.5 - - + -
283B VAL* 3.6 39.0 - - + -
286B GLN* 4.6 4.7 - - + -
287B LEU* 3.5 30.5 - - + -
290B LEU* 3.8 6.9 - - + +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TRP* 3.6 31.2 - - + -
115B GLY* 2.9 13.6 + - - +
116B ALA* 3.7 8.3 - - - +
118B PHE* 1.3 84.4 - - + +
120B GLN* 1.3 59.1 + - - +
123B PHE* 2.9 35.4 + - + +
129B ARG* 3.0 11.0 + - - -
133B VAL* 5.6 0.4 - - + -
147B PHE* 5.2 3.4 - - + -
152B LEU* 4.3 10.8 - - + -
185B ILE* 4.3 17.5 - - + -
218B LEU* 3.8 25.1 - - + -
220B TYR* 3.8 33.7 - - + -
251B VAL* 4.7 7.0 - - + -
270B PHE* 5.8 0.9 - - + -
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Residues in contact with GLN 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B ALA 3.1 12.6 + - - +
117B ASN* 3.6 11.6 - - - +
119B LEU* 1.3 76.2 - - - +
121B ARG* 1.3 72.5 + - - +
129B ARG* 2.7 43.1 + - - +
150B ALA 3.1 27.8 - - - +
151B GLY* 4.3 14.2 + - - -
152B LEU* 4.1 8.2 - - + +
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Residues in contact with ARG 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ASP* 3.3 33.5 + - - +
117B ASN 3.3 12.0 + - - +
118B PHE* 3.1 2.5 + - - -
120B GLN* 1.3 92.1 + - - +
122B PHE* 1.3 97.2 + - + +
123B PHE 5.4 0.2 - - - -
286B GLN 5.4 0.2 + - - -
289B ILE* 4.2 23.0 + - - +
290B LEU* 3.8 31.8 - - + +
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TRP* 4.2 11.2 - - + -
8A HIS* 2.8 37.0 + + - -
9A VAL* 3.9 38.6 - - + -
10A GLU 5.4 1.3 - - - -
118B PHE* 2.9 38.4 + + + +
121B ARG* 1.3 109.9 - - + +
123B PHE* 1.3 58.3 + - - +
124B LYS* 3.0 3.3 + - - +
286B GLN* 3.2 48.2 - - + -
290B LEU* 6.1 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
------------------------------------------------------------
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