Contacts of the helix formed by residues 131 - 145 (chain K) in PDB entry 5AKM
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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129K ASN* 2.6 23.6 + - - +
130K LYS* 1.3 75.3 - - + +
132K LYS* 1.3 63.8 + - - +
133K ALA* 3.1 20.0 + - - +
134K LEU* 3.1 35.3 + - + +
135K LEU* 3.2 12.4 + - - +
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Residues in contact with LYS 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K LYS 3.6 4.9 + - - -
131K ASN* 1.3 72.6 + - - +
133K ALA* 1.3 57.0 + - - +
135K LEU* 3.0 8.0 + - - +
136K GLU* 2.9 53.8 + - - +
151K ILE* 4.5 17.7 - - + -
152K HIS* 6.4 0.2 - - - +
161K TYR* 3.4 56.4 + - + +
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Residues in contact with ALA 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K ARG* 5.0 10.5 + - - +
131K ASN* 3.1 10.6 + - - +
132K LYS* 1.3 77.5 - - - +
134K LEU* 1.3 61.2 + - - +
136K GLU* 3.4 18.8 + - - +
137K ILE* 3.2 28.1 + - + +
140K ARG* 5.1 0.2 + - - -
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Residues in contact with LEU 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K ILE* 3.4 29.4 - - + -
95K LEU* 5.7 3.8 - - + -
98K ILE* 3.9 28.9 - - + -
109K PHE* 4.1 11.2 - - + -
113K LEU* 4.7 6.1 - - + -
129K ASN* 3.7 23.1 - - - +
131K ASN* 3.1 30.1 + - + +
132K LYS 3.1 0.4 - - - -
133K ALA* 1.3 77.7 - - - +
135K LEU* 1.3 65.8 + - + +
137K ILE* 3.2 16.6 + - + +
138K VAL* 3.1 25.1 + - + +
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Residues in contact with LEU 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113K LEU* 5.0 5.4 - - + -
127K ILE* 4.2 16.2 - - + +
129K ASN* 3.9 23.1 - - + +
131K ASN 3.2 8.9 + - - +
132K LYS* 3.0 9.7 + - - +
134K LEU* 1.3 80.2 - - + +
136K GLU* 1.3 53.0 + - - +
138K VAL* 3.3 9.1 + - + -
139K SER* 2.7 36.0 + - - -
151K ILE* 3.5 15.2 - - + +
161K TYR* 3.8 39.9 - - + +
162K VAL 4.1 1.6 - - - +
163K LEU* 3.6 39.2 - - + +
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Residues in contact with GLU 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K LYS* 2.9 42.1 + - + +
133K ALA* 3.6 19.3 - - - +
134K LEU 3.1 0.2 - - - -
135K LEU* 1.3 74.3 - - - +
137K ILE* 1.3 63.8 + - - +
139K SER* 3.4 3.2 + - - -
140K ARG* 3.1 46.0 + - - +
151K ILE* 3.8 17.5 - - + -
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Residues in contact with ILE 137 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K ILE* 4.4 16.4 - - + +
99K ARG* 3.9 43.7 - - + +
133K ALA* 3.2 16.2 + - + +
134K LEU* 3.2 18.9 + - + +
136K GLU* 1.3 76.5 - - - +
138K VAL* 1.3 63.9 + - + +
140K ARG* 3.2 25.7 + - - +
141K TRP* 3.1 61.9 + - + +
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Residues in contact with VAL 138 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109K PHE* 4.4 11.7 - - + -
110K ILE* 3.8 21.5 - - + -
113K LEU* 3.6 30.7 - - + -
127K ILE* 4.9 4.9 - - + -
134K LEU* 3.1 16.4 + - + +
135K LEU* 3.6 9.6 - - + +
137K ILE* 1.3 75.6 - - + +
139K SER* 1.3 63.5 + - - +
141K TRP* 3.2 17.7 + - + +
142K LEU* 2.9 34.8 + - + +
163K LEU* 3.8 17.3 - - + -
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Residues in contact with SER 139 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135K LEU 2.7 20.6 + - - -
136K GLU* 3.5 7.6 - - - -
137K ILE 3.2 0.2 - - - -
138K VAL* 1.3 74.0 - - - +
140K ARG* 1.3 62.4 + - - +
142K LEU* 3.3 0.9 + - - -
143K ASN* 3.1 33.2 + - - -
149K ASN* 2.6 36.0 + - - +
151K ILE* 3.9 15.6 - - - +
163K LEU* 4.1 3.6 - - - -
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Residues in contact with ARG 140 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K ARG* 4.9 9.9 - - - +
133K ALA 5.1 0.2 + - - -
136K GLU* 3.1 33.0 + - - +
137K ILE* 3.5 36.1 - - - +
139K SER* 1.3 79.2 - - - +
141K TRP* 1.3 67.4 + - + +
143K ASN* 3.4 10.1 + - - +
144K ASN* 3.1 22.3 + - - +
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Residues in contact with TRP 141 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98K ILE* 3.2 39.0 - - + -
99K ARG* 4.7 9.4 + - - +
101K PHE* 3.6 22.4 + + + -
106K GLN* 3.6 50.4 - - + +
109K PHE* 3.8 25.4 - + - -
110K ILE* 4.1 20.2 - - + -
137K ILE* 3.1 38.5 + - + +
138K VAL* 3.5 16.6 - - + +
140K ARG* 1.3 79.6 - - + +
142K LEU* 1.3 61.3 + - - +
144K ASN* 3.3 8.9 + - + +
145K LEU* 3.2 29.3 + - + +
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Residues in contact with LEU 142 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K ILE* 4.1 20.9 - - + -
127K ILE* 5.5 0.9 - - + -
138K VAL* 2.9 35.2 + - + +
139K SER 3.7 3.4 - - - +
140K ARG 3.3 0.4 - - - -
141K TRP* 1.3 72.8 - - - +
143K ASN* 1.3 61.4 + - - +
145K LEU* 3.0 8.7 + - + +
146K GLY 3.0 5.4 + - - -
147K VAL* 2.7 51.1 + - + +
149K ASN* 3.8 4.9 - - + +
163K LEU* 3.9 25.4 - - + -
165K ILE* 4.3 12.1 - - + -
173K PHE* 4.0 28.5 - - + -
177K ILE* 4.5 7.6 - - + -
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Residues in contact with ASN 143 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139K SER* 3.1 29.6 + - - -
140K ARG* 3.7 11.9 - - - +
142K LEU* 1.3 75.8 - - - +
144K ASN* 1.3 58.6 + - - +
146K GLY* 2.8 20.5 + - - +
147K VAL 3.7 11.4 - - - +
148K ARG* 3.8 17.7 - - - +
149K ASN* 3.7 11.0 + - - +
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Residues in contact with ASN 144 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K MET* 6.2 1.4 - - - -
106K GLN* 5.3 6.4 + - - +
140K ARG 3.1 13.6 + - - +
141K TRP* 3.4 13.0 - - + +
142K LEU 3.2 0.2 - - - -
143K ASN* 1.3 76.4 - - - +
145K LEU* 1.3 66.6 + - + +
146K GLY 3.3 1.0 + - - -
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Residues in contact with LEU 145 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K MET* 4.0 37.2 - - + -
106K GLN* 4.6 11.2 - - + +
107K ILE* 4.2 22.7 - - + -
110K ILE* 4.8 7.0 - - + -
141K TRP 3.2 19.5 + - - +
142K LEU* 3.0 13.9 + - + +
144K ASN* 1.3 85.4 - - + +
146K GLY* 1.3 61.3 + - - +
147K VAL* 3.4 7.0 + - + +
172K LYS* 3.2 19.2 - - - +
176K THR* 4.8 12.7 + - + +
177K ILE* 4.7 12.8 - - + -
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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