Contacts of the helix formed by residues 135 - 149 (chain A) in PDB entry 1FXT
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ARG* 5.5 1.0 + - - -
133A ASP* 2.8 16.2 + - - +
134A ARG* 1.3 77.4 - - - +
136A SER* 1.3 71.9 + - - +
137A PHE 3.5 0.6 - - - +
138A ASN* 3.4 9.1 + - - +
139A LYS* 2.7 61.7 + - - +
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Residues in contact with SER 136 (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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129A HIS* 3.6 14.8 + - - -
132A ARG* 4.8 1.8 - - - -
133A ASP* 3.1 18.3 + - - -
135A GLU* 1.3 86.6 + - - +
137A PHE* 1.3 58.7 + - - +
139A LYS* 3.6 18.3 + - - +
140A THR* 2.9 36.0 + - - -
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Residues in contact with PHE 137 (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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46A PRO* 5.2 7.2 - - + -
47A TYR* 3.1 29.6 - + - -
76A TYR* 3.3 37.0 - + - -
78A PRO* 4.0 20.2 - - + -
116A PRO* 4.5 8.5 - - + -
126A VAL* 4.3 4.3 - - + -
129A HIS* 3.2 18.1 + + + +
130A TYR* 3.7 45.5 - + + -
133A ASP* 2.8 25.0 + - + +
134A ARG* 5.1 6.7 - - - +
135A GLU 5.1 0.9 - - - +
136A SER* 1.3 68.9 - - - +
138A ASN* 1.3 60.9 + - - +
140A THR 4.5 0.2 - - - +
141A ALA* 3.0 41.5 + - + +
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Residues in contact with ASN 138 (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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46A PRO* 3.3 29.2 - - + +
134A ARG* 3.2 43.5 + - - +
135A GLU* 3.4 9.8 + - - +
137A PHE* 1.3 75.7 - - - +
139A LYS* 1.4 60.7 + - - +
142A ALA* 3.3 24.3 + - - +
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Residues in contact with LYS 139 (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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135A GLU* 2.7 60.1 + - - +
136A SER* 3.5 20.7 - - - +
137A PHE 3.5 0.2 - - - -
138A ASN* 1.4 72.6 - - - +
140A THR* 1.3 61.9 + - - +
142A ALA* 4.6 0.3 - - - +
143A LEU* 3.3 27.9 + - - +
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Residues in contact with THR 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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76A TYR* 3.7 40.1 - - + -
129A HIS* 5.1 1.9 - - - -
136A SER* 2.9 27.8 + - - -
139A LYS* 1.3 70.0 - - - +
141A ALA* 1.3 60.3 + - - +
143A LEU* 3.5 5.0 + - - +
144A TRP* 2.9 58.3 + - + +
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Residues in contact with ALA 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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46A PRO* 3.6 16.8 - - + -
47A TYR* 3.7 27.6 - - + +
76A TYR* 3.8 20.7 - - + +
137A PHE* 3.0 27.8 + - + +
140A THR* 1.3 71.5 - - - +
142A ALA* 1.3 55.3 + - - +
144A TRP* 4.0 1.9 - - - +
145A THR* 2.9 34.0 + - - -
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Residues in contact with ALA 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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46A PRO* 3.6 22.6 + - + +
138A ASN 3.3 22.9 + - - +
139A LYS 4.6 0.2 - - - +
140A THR 3.5 0.4 - - - -
141A ALA* 1.3 73.3 - - - +
143A LEU* 1.3 59.1 + - - +
145A THR* 3.7 1.6 + - - -
146A ARG* 3.2 36.3 + - + +
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Residues in contact with LEU 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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139A LYS 3.3 20.8 + - - +
140A THR* 3.8 5.6 - - + +
142A ALA* 1.3 75.2 - - - +
144A TRP* 1.3 64.5 + - + +
146A ARG* 3.3 8.7 + - + +
147A LEU* 3.0 57.6 + - + +
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Residues in contact with TRP 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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74A LYS* 3.4 30.9 - - + +
75A VAL* 5.3 0.4 - - - -
76A TYR* 3.6 28.0 - + + +
82A SER* 3.5 48.2 - - - -
83A VAL* 6.2 0.2 - - + -
140A THR* 2.9 48.3 + - + +
141A ALA* 4.0 5.6 - - - +
143A LEU* 1.3 82.4 - - + +
145A THR* 1.3 56.2 + - - +
147A LEU* 4.7 4.3 - - + +
148A TYR* 2.9 62.7 + + + +
149A ALA 3.7 0.2 + - - -
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Residues in contact with THR 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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46A PRO 2.6 24.3 + - - +
47A TYR* 3.5 32.3 - - - +
48A GLU 3.3 27.1 - - - +
49A GLY 4.9 0.7 - - - +
52A PHE* 4.0 14.3 - - + -
75A VAL* 5.6 0.3 - - - +
141A ALA 2.9 10.4 + - - -
142A ALA* 3.9 3.8 - - - -
144A TRP* 1.3 74.0 - - - +
146A ARG* 1.3 66.2 + - - +
149A ALA* 3.1 38.3 + - + +
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Residues in contact with ARG 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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48A GLU* 2.8 62.6 + - - +
49A GLY* 3.2 16.3 + - - -
142A ALA* 3.2 21.2 + - + +
143A LEU* 3.9 8.1 - - + +
145A THR* 1.3 85.9 - - - +
147A LEU* 1.3 63.7 + - + +
149A ALA 5.0 0.9 + - - -
150A SER* 4.1 10.4 + - - -
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Residues in contact with LEU 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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143A LEU* 3.0 44.3 + - + +
144A TRP* 4.3 6.1 - - + +
146A ARG* 1.3 78.4 - - + +
148A TYR* 1.3 69.9 + - + +
149A ALA 3.7 0.4 - - - -
150A SER* 2.8 23.8 + - - -
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Residues in contact with TYR 148 (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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51A LYS 4.3 0.5 - - - +
72A ASP 5.3 2.0 - - - -
73A THR* 3.1 22.9 + - + -
74A LYS* 3.3 53.0 - - + +
144A TRP* 2.9 64.1 + + + +
147A LEU* 1.3 83.4 - - + +
149A ALA* 1.3 56.1 + - - +
150A SER* 3.4 4.7 + - - -
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Residues in contact with ALA 149 (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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49A GLY 4.0 2.6 - - - +
50A GLY* 3.1 19.8 - - - -
51A LYS 3.6 12.3 - - - +
52A PHE* 3.6 40.8 - - + -
73A THR* 3.8 10.5 - - + -
144A TRP 3.7 1.4 + - - -
145A THR* 3.1 25.2 + - + +
146A ARG* 5.0 1.2 + - - +
148A TYR* 1.3 73.3 - - - +
150A SER* 1.3 60.0 + - - +
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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
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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