Contacts of the helix formed by residues 122 - 133 (chain A) in PDB entry 1TQN
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 GLU 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A ASN* 3.2 32.0 + - + +
105A ARG 4.5 6.5 - - - +
107A PRO* 4.4 19.8 - - - +
120A ILE 3.7 10.1 - - - +
121A ALA* 1.3 81.1 - - - +
123A ASP* 1.3 83.5 + - - +
125A GLU* 3.0 14.4 + - - +
126A TRP* 2.9 11.4 + - - -
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Residues in contact with ASP 123 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A THR* 4.0 11.9 - - - +
104A ASN* 2.8 36.6 + - - -
122A GLU* 1.3 78.0 - - - +
124A GLU* 1.3 63.1 + - + +
125A GLU 4.7 0.2 - - - +
126A TRP* 2.8 28.7 + - - +
127A LYS* 3.0 15.8 + - - +
378A LYS* 3.0 32.2 + - - +
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Residues in contact with GLU 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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123A ASP* 1.3 82.5 - - + +
125A GLU* 1.3 63.0 + - - +
127A LYS* 3.4 36.4 + - - +
128A ARG* 3.0 25.1 + - - +
287A HIS* 5.8 0.3 - - - -
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Residues in contact with GLU 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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115A LYS 5.7 1.8 - - - +
116A SER* 4.9 9.5 - - - -
121A ALA* 4.0 17.7 - - + -
122A GLU 3.0 12.9 + - - +
123A ASP* 4.7 0.2 - - - +
124A GLU* 1.3 80.6 - - - +
126A TRP* 1.3 64.1 + - - +
128A ARG* 3.0 25.7 + - - +
129A LEU* 3.2 26.5 + - - +
294A GLU* 3.8 12.5 - - - +
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Residues in contact with TRP 126 (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 CYS* 4.6 2.9 - - - -
99A TYR* 3.6 36.3 - + - -
103A THR* 4.0 21.3 - - + -
118A ILE* 3.2 32.7 - - + +
121A ALA* 3.7 24.7 - - - +
122A GLU* 2.9 9.5 + - - -
123A ASP 2.8 16.4 + - - +
125A GLU* 1.3 71.0 - - - +
127A LYS* 1.3 74.6 + - + +
129A LEU* 3.1 3.4 + - - +
130A ARG* 2.8 55.8 + - + +
439A PRO* 3.6 27.6 - - + -
440A ARG* 3.2 29.7 - - + +
508A HEM 2.7 20.3 + - - -
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Residues in contact with LYS 127 (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 TYR* 3.8 55.6 + - + +
103A THR* 5.7 1.8 - - - -
123A ASP* 3.0 9.6 + - - +
124A GLU* 3.2 46.2 + - - +
126A TRP* 1.3 85.9 - - + +
128A ARG* 1.3 62.8 + - - +
130A ARG* 3.2 14.0 + - + +
131A SER* 3.3 15.2 + - - -
287A HIS* 4.1 8.5 - - + +
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Residues in contact with ARG 128 (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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124A GLU 3.0 15.5 + - - +
125A GLU* 3.0 30.0 + - - +
127A LYS* 1.3 74.3 - - - +
129A LEU* 1.3 69.2 + - - +
131A SER* 3.0 13.5 + - - -
132A LEU* 3.1 26.6 + - + +
287A HIS* 3.2 45.9 + - + +
288A LYS 3.7 15.8 + - - -
289A ALA 3.2 19.6 + - - -
294A GLU* 2.8 39.6 + - - -
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Residues in contact with LEU 129 (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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116A SER 3.1 24.7 - - - +
118A ILE* 3.9 21.5 - - + +
121A ALA* 3.5 26.0 - - + -
125A GLU* 3.2 21.3 + - - +
126A TRP 3.1 6.8 + - - +
128A ARG* 1.3 84.1 - - - +
130A ARG* 1.3 60.5 + - - +
131A SER 3.0 1.7 + - - -
132A LEU* 3.6 4.5 + - + +
133A LEU* 3.2 31.1 + - + +
290A LEU* 3.6 31.4 - - + -
294A GLU* 4.1 12.8 - - - +
298A GLN* 3.9 11.9 - - - +
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Residues in contact with ARG 130 (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 TYR* 6.0 1.3 - - - +
118A ILE* 3.9 12.1 - - - +
126A TRP* 2.8 42.6 + - + +
127A LYS* 3.5 9.0 - - + +
128A ARG 3.1 0.2 - - - -
129A LEU* 1.3 75.6 - - - +
131A SER* 1.3 51.9 + - - +
133A LEU* 4.2 2.2 - - - -
134A SER* 2.6 34.0 + - - +
439A PRO 2.9 19.3 + - - +
440A ARG* 3.8 1.2 - - - +
441A ASN* 2.7 48.5 + - - +
443A ILE* 4.1 25.8 - - - +
508A HEM 2.6 37.9 + - - +
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Residues in contact with SER 131 (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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127A LYS 3.3 5.5 + - - -
128A ARG 3.0 9.7 + - - -
130A ARG* 1.3 78.1 - - - +
132A LEU* 1.3 68.6 + - - +
133A LEU 2.8 2.7 + - - -
134A SER* 3.1 13.7 + - - -
135A PRO* 3.2 12.0 - - - +
287A HIS* 3.4 27.1 - - - -
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Residues in contact with LEU 132 (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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128A ARG* 3.1 38.3 + - + +
129A LEU* 3.6 6.9 + - + +
131A SER* 1.3 79.4 - - - +
133A LEU* 1.3 61.0 + - - +
135A PRO* 3.9 7.8 - - - +
136A THR* 3.9 7.6 + - - -
278A SER* 4.9 20.0 + - - +
287A HIS 4.1 6.3 - - - +
288A LYS* 3.6 31.9 - - + -
289A ALA 3.9 4.5 - - - +
290A LEU* 3.2 49.6 - - + +
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Residues in contact with LEU 133 (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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118A ILE* 3.9 15.9 - - + -
129A LEU* 3.2 19.3 + - + +
130A ARG 4.9 0.2 - - - -
131A SER 2.8 2.2 + - - -
132A LEU* 1.3 83.5 - - + +
134A SER* 1.3 68.7 + - - +
135A PRO 3.4 2.0 - - - -
136A THR* 3.0 30.6 + - - +
137A PHE* 3.3 9.0 - - + -
275A MET* 3.3 31.6 - - + -
290A LEU* 4.5 4.5 - - + -
298A GLN* 3.7 22.4 - - + +
302A PHE* 3.4 33.4 - - + -
443A ILE* 4.1 13.2 - - + -
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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