Contacts of the helix formed by residues 114 - 123 (chain A) in PDB entry 1TFF
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 SER 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.0 3.6 - - - +
108A LEU* 4.4 2.8 - - - +
112A ASP* 2.9 19.3 + - - -
113A GLY* 1.3 81.7 - - - +
115A VAL* 1.3 63.1 + - - +
116A SER* 3.4 10.0 + - - -
117A SER* 3.1 22.0 + - - -
118A LEU* 3.2 20.6 + - - +
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Residues in contact with VAL 115 (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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43A ARG* 4.2 6.5 - - - +
58A TYR* 3.3 22.7 - - - +
62A GLU* 3.9 15.3 - - + +
65A LEU* 3.2 26.6 - - + +
114A SER* 1.3 73.2 - - - +
116A SER* 1.3 64.9 + - - +
118A LEU* 3.2 5.2 + - - +
119A LEU* 3.0 30.7 + - + +
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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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114A SER* 3.4 11.3 + - - -
115A VAL* 1.3 80.4 - - - +
117A SER* 1.3 64.0 + - - +
119A LEU* 3.9 7.5 - - - +
120A LYS* 3.0 22.7 + - - +
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Residues in contact with SER 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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108A LEU* 3.8 13.6 - - - +
112A ASP* 2.7 32.4 + - - -
114A SER* 3.1 15.3 + - - -
115A VAL 3.3 0.2 - - - -
116A SER* 1.3 79.7 + - - +
118A LEU* 1.3 58.2 + - - +
120A LYS* 3.3 10.9 + - - +
121A VAL* 3.0 31.9 + - - +
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Residues in contact with LEU 118 (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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58A TYR* 3.6 24.2 - - + +
61A LEU* 3.8 13.2 - - + +
62A GLU* 3.4 40.2 - - + +
65A LEU* 4.5 11.2 - - + -
105A VAL* 3.7 27.8 - - + -
108A LEU* 3.8 16.1 - - + +
109A VAL* 4.2 4.7 - - + -
114A SER 3.2 9.7 + - - +
115A VAL 3.2 9.4 + - - +
117A SER* 1.3 78.3 - - - +
119A LEU* 1.3 57.1 + - - +
121A VAL* 3.0 4.5 + - - +
122A PHE* 2.9 45.2 + - + -
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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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9A ILE* 3.5 37.5 - - + +
10A SER 4.8 1.3 - - - +
11A GLU* 5.7 1.1 - - - -
43A ARG* 3.4 24.0 - - - +
58A TYR* 3.6 27.4 - - + +
115A VAL* 3.0 20.0 + - + +
116A SER* 3.9 6.7 - - - +
118A LEU* 1.3 81.2 - - - +
120A LYS* 1.3 57.7 + - - +
122A PHE* 3.6 1.4 - - - +
123A ASN* 2.8 53.8 + - - +
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Residues in contact with LYS 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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116A SER 3.0 15.4 + - - +
117A SER* 3.3 14.1 - - - +
119A LEU* 1.3 75.7 - - - +
121A VAL* 1.3 70.2 + - + +
123A ASN* 3.4 5.5 + - - +
124A ASP* 3.2 20.0 + - + +
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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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105A VAL* 4.1 13.2 - - + -
108A LEU* 3.5 22.0 - - + -
117A SER 3.0 15.7 + - - +
118A LEU 3.0 6.5 + - - +
120A LYS* 1.3 75.6 - - + +
122A PHE* 1.3 58.3 + - + +
124A ASP* 2.9 31.2 + - - +
127A ALA* 4.0 15.0 - - + -
128A SER* 3.8 3.5 + - - -
131A ILE* 3.5 30.1 - - + -
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Residues in contact with PHE 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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8A LEU* 3.5 14.2 - - - +
9A ILE* 4.2 11.4 - - + +
54A ARG* 3.8 17.9 - - + -
57A GLY* 3.8 7.4 - - - -
58A TYR* 3.6 54.3 - + + -
61A LEU* 3.9 14.4 - - + -
105A VAL* 4.0 10.3 - - + -
118A LEU* 2.9 42.9 + - + +
119A LEU* 4.0 3.4 - - - +
121A VAL* 1.3 77.8 - - + +
123A ASN* 1.3 59.6 + - - +
124A ASP 3.4 0.2 - - - -
128A SER* 2.8 34.0 + - - -
131A ILE* 3.7 35.0 - - + -
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Residues in contact with ASN 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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7A ASN* 3.4 26.2 + - - +
8A LEU* 2.8 23.3 + - - +
9A ILE 2.8 47.4 + - - -
119A LEU* 2.8 37.1 + - - +
120A LYS* 3.8 5.8 - - - +
121A VAL 3.1 0.4 - - - -
122A PHE* 1.3 79.4 - - - +
124A ASP* 1.3 60.1 + - - +
125A GLN 3.4 3.2 + - - -
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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