Contacts of the helix formed by residues 131 - 145 (chain I) in PDB entry 5AKF
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 131 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129I ASN* 2.7 19.3 + - - +
130I LYS* 1.3 77.4 - - - +
132I LYS* 1.3 62.1 + - - +
133I ALA* 3.1 12.1 + - - +
134I LEU* 2.7 40.5 + - + +
135I LEU* 3.1 22.5 + - - +
1181I CL 3.6 18.2 - - - +
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Residues in contact with LYS 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I LYS 3.3 6.7 + - - -
131I ASN* 1.3 73.0 + - - +
133I ALA* 1.3 53.8 + - - +
135I LEU* 2.8 10.4 + - - +
136I GLU* 2.7 59.4 + - - +
151I ILE* 4.6 14.4 - - + -
152I HIS* 6.4 0.4 - - - +
161I TYR* 3.6 55.6 + - + +
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Residues in contact with ALA 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I ARG* 5.1 11.4 - - - +
131I ASN* 3.1 7.9 + - - +
132I LYS* 1.3 78.9 - - - +
134I LEU* 1.3 63.1 + - - +
136I GLU* 3.3 16.3 + - - +
137I ILE* 3.1 29.4 + - - +
140I ARG* 4.8 0.5 + - - -
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Residues in contact with LEU 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I ILE* 3.9 28.7 - - + -
95I LEU* 5.7 3.6 - - + -
98I ILE* 4.1 26.7 - - + -
109I PHE* 4.2 13.7 - - + -
113I LEU* 4.7 11.4 - - + -
129I ASN* 4.2 20.4 - - + +
131I ASN* 2.7 32.2 + - + +
133I ALA* 1.3 74.5 - - - +
135I LEU* 1.3 64.0 + - + +
137I ILE* 3.4 14.4 + - + +
138I VAL* 3.1 25.1 + - + +
1181I CL 4.4 5.2 - - + +
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Residues in contact with LEU 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113I LEU* 4.7 10.1 - - + -
127I ILE* 4.2 17.9 - - + +
129I ASN* 3.9 25.4 - - + +
131I ASN 3.1 13.8 + - - +
132I LYS* 2.8 16.0 + - - +
134I LEU* 1.3 75.3 - - + +
136I GLU* 1.3 48.9 + - - +
138I VAL* 3.2 4.1 + - + +
139I SER* 2.7 35.5 + - - -
151I ILE* 3.7 17.0 - - + -
161I TYR* 3.8 33.4 - - + +
162I VAL 4.1 1.1 - - - -
163I LEU* 3.6 40.4 - - + +
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Residues in contact with GLU 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132I LYS* 2.7 47.4 + - + +
133I ALA* 3.7 19.6 - - - +
134I LEU 3.3 0.2 - - - -
135I LEU* 1.3 73.0 - - - +
137I ILE* 1.3 61.4 + - - +
139I SER* 3.4 3.7 + - - -
140I ARG* 3.1 51.1 + - - +
151I ILE* 4.0 17.3 - - + -
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Residues in contact with ILE 137 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I ILE* 4.1 16.6 - - + -
99I ARG* 3.8 48.0 - - + +
133I ALA 3.1 16.4 + - - +
134I LEU* 3.4 17.0 - - + +
135I LEU 3.3 0.2 - - - -
136I GLU* 1.3 73.0 - - - +
138I VAL* 1.3 66.3 + - + +
140I ARG* 3.3 24.8 + - - +
141I TRP* 3.2 58.3 + - + +
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Residues in contact with VAL 138 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I PHE* 4.4 16.2 - - + -
110I ILE* 4.0 19.5 - - + -
113I LEU* 4.1 22.2 - - + -
127I ILE* 4.7 12.8 - - + -
134I LEU* 3.1 17.7 + - + +
135I LEU* 3.6 8.7 - - + +
137I ILE* 1.3 76.3 - - + +
139I SER* 1.3 64.5 + - - +
141I TRP* 3.2 17.3 + - + +
142I LEU* 2.9 33.5 + - + +
163I LEU* 3.9 15.9 - - + -
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Residues in contact with SER 139 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135I LEU 2.7 20.1 + - - -
136I GLU* 3.4 8.3 - - - -
137I ILE 3.3 0.2 - - - -
138I VAL* 1.3 72.5 - - - +
140I ARG* 1.3 57.7 + - - +
142I LEU* 3.3 1.3 + - - -
143I ASN* 2.8 37.1 + - - -
149I ASN* 2.6 34.6 + - - +
151I ILE* 3.9 17.3 - - - +
163I LEU* 3.6 6.5 - - - +
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Residues in contact with ARG 140 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99I ARG* 5.5 4.0 - - - +
133I ALA 4.8 0.6 + - - -
136I GLU* 3.1 37.3 + - - +
137I ILE* 3.7 33.8 - - - +
138I VAL 3.2 0.2 - - - -
139I SER* 1.3 76.1 - - - +
141I TRP* 1.3 69.8 + - + +
143I ASN* 3.3 8.2 + - - +
144I ASN* 2.9 37.3 + - - +
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Residues in contact with TRP 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I ILE* 3.4 43.3 - - + -
99I ARG* 4.5 11.9 + - - +
101I PHE* 3.9 17.0 + + + -
106I GLN* 3.3 50.3 - - + +
109I PHE* 3.9 25.6 - + - -
110I ILE* 4.0 23.1 - - + -
137I ILE* 3.2 32.0 + - + +
138I VAL* 3.2 16.0 + - + +
140I ARG* 1.3 77.9 - - + +
142I LEU* 1.3 58.6 + - - +
144I ASN* 3.2 8.7 + - - +
145I LEU* 3.0 35.2 + - + +
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Residues in contact with LEU 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I ILE* 4.1 6.5 - - + -
127I ILE* 5.4 1.1 - - + -
138I VAL* 2.9 33.2 + - + +
139I SER 3.5 7.2 - - - +
141I TRP* 1.3 72.8 - - - +
143I ASN* 1.3 67.4 + - - +
145I LEU* 2.8 16.8 + - + +
146I GLY 3.1 0.2 + - - -
147I VAL* 3.0 32.0 + - + +
149I ASN* 3.5 11.7 - - - +
163I LEU* 4.2 13.2 - - + -
165I ILE* 4.1 28.0 - - + -
173I PHE* 4.3 11.9 - - + -
177I ILE* 3.4 33.9 - - + -
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Residues in contact with ASN 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I SER* 2.8 36.1 + - - +
140I ARG* 3.3 8.9 + - - +
142I LEU* 1.3 72.5 - - - +
144I ASN* 1.3 63.2 + - - +
146I GLY* 3.0 18.7 + - - -
147I VAL 3.5 12.7 + - - +
148I ARG* 3.7 18.2 - - - +
149I ASN* 3.9 10.5 + - - +
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Residues in contact with ASN 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I ARG* 2.9 28.6 + - - +
141I TRP* 3.6 7.1 - - - +
142I LEU 3.0 0.2 - - - -
143I ASN* 1.3 81.7 - - - +
145I LEU* 1.3 62.5 + - - +
146I GLY 3.3 1.3 + - - -
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Residues in contact with LEU 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I MET* 4.1 31.9 - - + -
106I GLN* 4.8 11.0 - - + +
107I ILE* 4.3 26.0 - - + -
110I ILE* 4.8 5.4 - - + -
141I TRP 3.0 20.1 + - - +
142I LEU* 2.8 11.7 + - + +
144I ASN* 1.3 82.5 - - + +
146I GLY* 1.3 61.0 + - - +
147I VAL* 4.1 6.3 - - + +
172I LYS* 3.8 18.0 + - - +
176I THR* 4.9 12.6 + - + +
177I ILE* 4.5 17.5 - - + -
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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