Contacts of the helix formed by residues 111 - 117 (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 VAL 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A PHE* 5.2 4.5 - - + -
109A GLY 4.0 9.0 - - - +
110A PRO* 1.3 73.4 - - - +
112A GLY* 1.3 65.6 + - - +
113A PHE 3.4 0.2 + - - -
114A MET* 3.1 24.2 + - + +
115A LYS* 3.2 38.4 - - + +
120A ILE* 3.8 23.3 - - + -
234A GLU* 3.0 11.6 + - - +
239A CYS* 3.3 21.3 - - - -
240A VAL* 4.4 4.9 - - + -
241A PHE* 4.3 3.4 - - + -
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Residues in contact with GLY 112 (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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110A PRO 3.9 0.4 - - - -
111A VAL* 1.3 77.8 - - - +
113A PHE* 1.3 58.0 + - - -
115A LYS* 2.9 34.8 + - - +
234A GLU* 3.1 15.8 + - - -
239A CYS* 4.1 8.6 - - - +
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Residues in contact with PHE 113 (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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111A VAL 3.4 0.8 + - - -
112A GLY* 1.3 66.3 - - - -
114A MET* 1.3 67.7 + - + +
115A LYS* 2.8 21.8 + - - +
116A SER* 2.7 31.1 + - - -
239A CYS* 6.2 2.5 - - - -
246A THR* 4.0 20.0 - - + -
250A ARG* 3.7 40.4 - - - +
293A LEU* 3.8 39.5 - - + -
296A VAL* 4.4 0.4 - - + -
297A ALA* 3.9 29.8 - - + -
300A ILE* 4.0 21.3 - - + -
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Residues in contact with MET 114 (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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111A VAL* 3.1 22.8 + - + +
112A GLY 3.1 0.8 + - - -
113A PHE* 1.3 93.4 - - + +
115A LYS* 1.3 53.8 + - - +
116A SER* 2.8 6.7 - - - -
117A ALA* 2.7 56.2 + - + +
120A ILE* 3.6 7.4 - - + +
239A CYS* 5.2 1.3 - - - -
241A PHE* 3.7 33.9 - - + -
246A THR* 5.1 1.6 - - + -
297A ALA* 3.6 32.8 - - - +
300A ILE* 3.9 21.1 - - + -
301A ILE* 3.6 19.3 - - + -
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Residues in contact with LYS 115 (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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111A VAL* 3.2 20.2 - - + +
112A GLY 2.9 21.2 + - - +
113A PHE* 3.7 12.1 - - - +
114A MET* 1.3 78.5 - - - +
116A SER* 1.3 63.3 + - - +
117A ALA 3.4 0.2 - - - -
120A ILE* 3.9 10.9 - - + +
121A ALA* 3.7 22.9 + - - +
125A GLU* 5.7 0.9 - - - +
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Residues in contact with SER 116 (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 PHE* 2.7 22.0 + - - -
114A MET 2.8 1.6 - - - -
115A LYS* 1.3 83.4 - - - +
117A ALA* 1.3 64.8 + - - -
121A ALA* 4.6 1.3 - - - -
125A GLU* 4.9 9.2 - - - -
129A LEU* 3.1 16.3 - - - +
293A LEU* 4.9 1.4 - - - +
294A GLU* 4.0 26.9 + - - -
297A ALA* 3.4 13.7 - - - +
298A GLN* 3.0 15.5 + - - -
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Residues in contact with ALA 117 (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 MET* 2.7 50.7 + - + +
116A SER* 1.3 70.8 + - - +
118A ILE* 1.3 67.3 + - - +
119A SER 4.4 0.7 - - - +
120A ILE* 2.9 10.0 + - + -
121A ALA* 2.9 20.1 + - - +
297A ALA* 4.0 5.2 - - - +
298A GLN* 3.9 8.3 - - - +
301A ILE* 3.7 22.7 - - + -
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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