Contacts of the helix formed by residues 130 - 148 (chain A) in PDB entry 1TF5
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 ASN 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A THR* 3.1 19.1 + - - +
129A VAL* 1.3 93.3 - - - +
131A GLU* 1.3 62.5 + - - +
132A TYR* 3.1 10.3 + - - +
133A LEU* 2.9 31.9 + - - +
134A ALA 3.1 3.5 + - - -
176A THR* 3.4 9.4 - - - -
464A HIS* 3.6 48.1 + - + +
489A ARG* 5.2 3.2 + - - +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASN* 1.3 71.4 - - - +
132A TYR* 1.3 65.5 + - - +
133A LEU 3.3 0.2 - - - -
134A ALA* 3.7 5.1 - - - +
135A SER* 2.9 31.1 + - - +
155A ASN 5.5 0.4 - - - +
156A LEU* 3.5 30.2 - - + +
157A ASN* 2.8 38.6 + - - +
158A SER* 5.3 1.7 + - - -
176A THR* 3.8 19.1 - - + +
179A GLU* 4.0 6.8 - - - +
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Residues in contact with TYR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ASN* 3.1 10.5 + - - +
131A GLU* 1.3 75.7 - - - +
133A LEU* 1.3 84.6 + - + +
135A SER* 3.8 3.5 - - - -
136A ARG* 2.9 55.8 + - + +
464A HIS* 3.9 22.6 - - + -
465A GLU* 3.7 43.0 + - + +
468A ALA* 3.6 30.5 - - + +
469A GLN* 6.1 0.3 - - - +
491A THR* 4.6 2.5 + - - +
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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
----------------------------------------------------------
128A THR* 3.0 25.1 - - - +
129A VAL* 3.6 25.6 - - + -
130A ASN* 2.9 18.7 + - - +
132A TYR* 1.3 97.2 - - + +
134A ALA* 1.3 64.1 + - - +
136A ARG* 3.7 30.7 - - - +
137A ASP* 2.9 32.3 + - - +
207A ASP* 5.0 6.7 - - - +
208A GLU* 6.2 0.7 - - + +
489A ARG 3.7 24.5 - - - +
490A GLY* 4.2 9.9 - - - +
491A THR* 4.8 0.7 - - - +
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Residues in contact with ALA 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A THR* 3.1 26.4 - - + +
130A ASN 3.1 8.2 + - - +
131A GLU* 3.7 12.1 - - + +
132A TYR 3.3 0.2 - - - -
133A LEU* 1.3 77.7 - - - +
135A SER* 1.3 57.5 + - - +
138A ALA* 2.9 31.0 + - - +
154A LEU* 4.0 15.3 - - + -
156A LEU* 5.1 1.6 - - + -
174A TYR* 3.7 10.4 - - + +
175A SER* 4.1 18.4 - - - +
176A THR* 4.5 1.1 - - + -
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLU* 2.9 20.1 + - - +
132A TYR* 3.8 4.0 - - - -
134A ALA* 1.3 74.4 - - - +
136A ARG* 1.3 65.3 + - - +
138A ALA* 4.0 0.9 - - - +
139A GLU* 3.1 25.5 + - - +
154A LEU* 3.4 29.9 - - - +
156A LEU* 3.9 14.4 - - - +
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Residues in contact with ARG 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 4.4 10.5 + - - +
132A TYR* 2.9 42.5 + - + +
133A LEU* 3.7 22.2 - - - +
135A SER* 1.3 77.1 - - - +
137A ASP* 1.3 85.3 + - - +
139A GLU* 3.2 6.8 + - + +
140A GLN* 2.9 60.1 + - + +
490A GLY* 2.8 29.5 + - - -
491A THR* 3.7 16.8 + - - +
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Residues in contact with ASP 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A THR* 3.8 27.2 + - + +
126A VAL* 5.9 0.7 - - - +
128A THR* 4.8 5.9 + - - -
133A LEU* 2.9 24.0 + - - +
136A ARG* 1.3 106.2 + - - +
138A ALA* 1.3 59.8 + - - +
140A GLN* 4.5 5.1 - - - +
141A MET* 2.6 39.4 + - - +
174A TYR* 3.3 25.5 - - + +
207A ASP* 5.7 1.6 - - - +
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Residues in contact with ALA 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ALA 2.9 19.4 + - - +
135A SER* 4.0 3.4 - - - +
137A ASP* 1.3 75.3 - - - +
139A GLU* 1.3 58.2 + - - +
142A GLY* 2.9 28.4 + - - -
152A VAL* 4.2 11.3 - - + +
154A LEU* 4.3 19.5 - - + -
174A TYR* 3.7 32.8 - - + -
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER 3.1 19.4 + - - +
136A ARG* 3.4 7.2 - - - +
137A ASP 3.1 0.2 - - - -
138A ALA* 1.3 80.3 - - - +
140A GLN* 1.3 72.3 + - + +
143A LYS* 3.0 55.0 + - - +
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Residues in contact with GLN 140 (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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77A THR* 4.9 5.2 - - - +
107A THR* 6.0 0.7 - - - +
136A ARG* 2.9 50.6 + - + +
137A ASP* 4.2 4.2 - - - +
139A GLU* 1.3 85.3 - - + +
141A MET* 1.3 81.4 + - + +
143A LYS* 3.6 22.1 + - - +
144A ILE* 4.4 4.3 + - - +
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Residues in contact with MET 141 (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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77A THR* 5.0 3.6 - - + -
79A MET* 4.8 12.3 - - + -
107A THR* 3.7 26.5 - - + +
108A LEU* 4.0 27.6 - - + +
111A THR* 3.6 29.4 - - + -
137A ASP* 2.6 18.9 + - - +
140A GLN* 1.3 91.4 - - + +
142A GLY* 1.3 63.0 + - - -
143A LYS 3.1 1.8 - - - -
144A ILE* 2.9 26.9 + - + +
145A PHE* 3.4 11.3 + - + -
174A TYR* 3.2 24.5 - - - +
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Residues in contact with GLY 142 (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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137A ASP 3.6 0.4 + - - -
138A ALA* 2.9 24.3 + - - +
140A GLN 3.3 0.2 - - - -
141A MET* 1.3 78.7 - - - +
143A LYS* 1.3 56.6 + - - +
144A ILE 3.1 0.2 + - - -
145A PHE* 3.2 4.1 + - - +
146A GLU* 2.8 39.5 + - - +
152A VAL* 3.7 23.3 - - - -
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Residues in contact with LYS 143 (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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76A VAL* 3.7 22.0 - - + +
77A THR* 6.5 0.2 - - + -
139A GLU* 3.0 40.0 + - - +
140A GLN* 3.6 15.0 + - - +
141A MET 3.1 0.4 - - - -
142A GLY* 1.3 75.8 - - - +
144A ILE* 1.3 57.2 + - - +
146A GLU* 4.0 9.1 + - - +
147A PHE* 3.0 27.5 + - - +
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Residues in contact with ILE 144 (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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69A VAL* 4.5 17.0 - - + -
72A ALA* 4.5 18.8 - - + -
73A SER* 4.1 12.1 - - - +
76A VAL* 4.1 20.9 - - + -
77A THR* 4.0 15.3 - - + -
108A LEU* 3.6 31.2 - - + -
111A THR* 4.4 13.2 - - + +
140A GLN 4.7 1.3 - - - +
141A MET* 2.9 18.1 + - + +
143A LYS* 1.3 75.6 - - - +
145A PHE* 1.3 75.2 + - + +
147A PHE* 3.0 17.8 + - - +
148A LEU* 3.2 16.6 + - + +
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Residues in contact with PHE 145 (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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69A VAL* 5.9 0.4 - - + -
110A SER* 5.2 0.4 - - - -
111A THR* 3.4 50.9 - - + -
114A VAL* 3.8 13.9 - - + -
115A TYR* 4.1 18.8 - + + -
141A MET* 3.5 17.5 - - + -
142A GLY* 3.2 2.6 + - - -
144A ILE* 1.3 79.3 - - + +
146A GLU* 1.3 61.6 + - - +
148A LEU* 3.2 13.7 + - - +
149A GLY 3.4 0.3 + - - -
150A LEU* 3.0 30.6 + - + +
152A VAL* 3.7 25.6 - - + -
172A ILE* 3.3 31.6 - - + -
174A TYR* 3.6 30.5 - + - -
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Residues in contact with GLU 146 (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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42A LYS* 4.6 5.7 + - - -
142A GLY* 2.8 26.2 + - - +
143A LYS* 4.1 7.7 + - - +
145A PHE* 1.3 71.6 - - - +
147A PHE* 1.3 66.4 + - - +
148A LEU 3.0 1.8 - - - -
149A GLY* 3.1 12.5 + - - -
150A LEU 3.4 19.0 - - - +
151A THR* 4.9 1.4 - - - -
152A VAL* 4.0 26.0 + - + +
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Residues in contact with PHE 147 (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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38A ASP* 3.4 50.7 - - + -
41A LEU* 4.0 26.0 - - + -
42A LYS* 3.5 24.0 - - + +
72A ALA* 4.0 12.1 - - + -
75A ARG* 4.3 14.1 - - + -
76A VAL* 3.7 22.0 - - + -
143A LYS 3.0 15.3 + - - +
144A ILE 3.0 10.0 + - - +
146A GLU* 1.3 76.6 - - - +
148A LEU* 1.3 69.8 + - + +
149A GLY 3.3 0.2 - - - -
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Residues in contact with LEU 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.1 16.8 - - + +
42A LYS* 3.8 11.4 - - - +
45A THR* 2.5 36.9 + - - +
68A VAL* 3.9 22.9 - - + -
69A VAL* 4.2 11.4 - - + -
72A ALA* 3.8 30.5 - - + -
115A TYR* 3.5 32.3 - - + -
144A ILE* 3.2 15.7 + - + +
145A PHE* 3.2 8.4 + - + +
146A GLU 3.0 1.0 - - - -
147A PHE* 1.3 86.1 - - + +
149A GLY* 1.3 60.3 + - - +
150A LEU* 3.5 3.0 + - - +
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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
------------------------------------------------------------
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