Contacts of the helix formed by residues 126 - 137 (chain I) in PDB entry 5JKL
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 ASP 126 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11I ASN* 3.2 25.8 + - - +
12I TYR* 3.6 13.2 - - - -
13I HIS 4.7 0.7 + - - +
16I SER* 4.6 3.1 + - - +
76I ARG* 2.9 31.9 + - - -
121I ALA* 2.9 18.6 + - - +
122I THR* 5.0 0.2 - - - +
124I LYS* 4.3 8.3 - - + +
125I ASN* 1.3 75.0 - - - +
127I PRO* 1.4 59.3 - - - +
128I HIS* 3.6 4.5 + - - +
129I LEU* 3.1 25.2 + - + +
130I CYS* 3.0 30.7 + - - -
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Residues in contact with PRO 127 (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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11I ASN* 4.0 8.7 - - - +
125I ASN 3.2 14.6 - - - +
126I ASP* 1.4 81.2 - - - +
128I HIS* 1.3 60.7 + - - +
130I CYS* 3.3 9.5 + - + +
131I ASP* 3.0 30.0 + - - +
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Residues in contact with HIS 128 (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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72I LEU* 3.7 28.6 - - + +
75I GLN* 5.4 5.4 - - + -
76I ARG* 3.1 40.1 + - - +
126I ASP* 3.3 2.5 + - - +
127I PRO* 1.3 81.3 - - - +
129I LEU* 1.3 57.6 + - - +
131I ASP* 3.3 11.3 + - - +
132I PHE* 2.9 30.7 + + + +
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Residues in contact with LEU 129 (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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12I TYR* 4.5 6.5 - - + -
16I SER* 3.9 29.6 - - - +
20I ILE* 3.9 29.2 - - + -
72I LEU* 4.1 17.7 - - + -
76I ARG* 4.1 3.1 - - - +
117I LEU* 5.1 5.4 - - + -
120I LEU* 6.5 0.2 - - + -
121I ALA* 3.7 20.9 - - + +
126I ASP* 3.1 28.7 + - - +
128I HIS* 1.3 76.7 + - - +
130I CYS* 1.3 65.4 + - - +
132I PHE* 3.3 11.3 + - + +
133I ILE* 3.0 39.1 + - + +
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Residues in contact with CYS 130 (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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118I HIS* 3.6 24.9 - - + +
121I ALA* 3.6 17.0 - - - -
122I THR* 3.5 30.5 - - - -
126I ASP 3.0 19.8 + - - +
127I PRO* 3.6 12.1 - - + +
128I HIS 3.3 0.4 - - - -
129I LEU* 1.3 78.5 - - - +
131I ASP* 1.3 61.0 + - - +
133I ILE* 3.3 2.1 + - - -
134I GLU* 3.0 34.6 + - - +
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Residues in contact with ASP 131 (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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203G MG 3.6 14.2 - - - -
127I PRO 3.0 17.5 + - - +
128I HIS* 3.7 12.3 - - + +
129I LEU 3.2 0.2 - - - -
130I CYS* 1.3 76.1 - - - +
132I PHE* 1.3 59.3 + - - +
134I GLU* 4.4 8.1 - - - -
135I THR* 2.7 53.3 + - - +
136I HIS* 6.1 0.2 - - - -
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Residues in contact with PHE 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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68I LYS* 3.9 23.6 - - + -
69I LEU* 3.7 17.9 - - + -
72I LEU* 3.8 44.0 - - + -
75I GLN* 5.4 2.7 - - - -
128I HIS* 2.9 21.7 + + + +
129I LEU* 3.5 12.8 - - + +
131I ASP* 1.3 80.5 + - - +
133I ILE* 1.3 69.8 + - + +
136I HIS* 3.0 54.4 + + - +
137I TYR* 3.4 34.0 - + - -
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Residues in contact with ILE 133 (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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69I LEU* 6.3 0.2 - - + -
114I LEU* 4.1 24.5 - - + +
117I LEU* 3.7 36.1 - - + +
118I HIS* 4.0 24.7 - - + -
121I ALA* 4.6 0.4 - - + -
129I LEU* 3.0 33.8 + - + +
130I CYS* 3.7 4.3 - - - +
132I PHE* 1.3 89.7 - - + +
134I GLU* 1.3 58.3 + - - +
137I TYR* 2.9 16.0 + - + +
138I LEU* 2.9 47.8 + - + -
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Residues in contact with GLU 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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127G PRO* 4.2 6.9 - - - +
130G CYS* 5.3 1.5 - - - +
131G ASP* 3.4 49.5 + - + +
134G GLU* 4.5 4.5 - - - +
203G MG 4.0 6.9 - - - -
204G MG 3.8 17.0 - - - -
118I HIS* 2.7 34.3 + - + +
130I CYS* 3.0 25.1 + - - +
131I ASP* 3.8 6.6 - - - +
133I ILE* 1.3 78.1 - - - +
135I THR* 1.3 65.1 + - - +
138I LEU* 3.8 26.6 + - + +
139I ASN* 4.1 8.7 + - - +
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Residues in contact with THR 135 (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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131G ASP* 4.8 3.2 + - - -
203G MG 4.3 6.9 - - - -
131I ASP* 2.7 40.8 + - - +
134I GLU* 1.3 80.5 - - - +
136I HIS* 1.3 85.5 + - + +
139I ASN* 5.8 2.4 + - - +
140I GLU* 5.6 2.1 - - - +
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Residues in contact with HIS 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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65I HIS* 5.4 4.0 + - - -
68I LYS* 3.2 34.7 + - + +
131I ASP* 6.1 0.2 - - - -
132I PHE* 3.0 37.6 + + - +
135I THR* 1.3 100.8 + - + +
137I TYR* 1.3 85.0 + - + +
140I GLU* 3.4 21.4 - - - +
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Residues in contact with TYR 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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27I GLU* 4.1 13.0 - - - -
65I HIS* 2.6 54.5 + + + -
68I LYS* 3.4 18.5 - - + +
69I LEU* 3.3 23.2 + - + +
114I LEU* 3.9 29.6 - - + -
132I PHE* 3.4 35.4 - + - -
133I ILE* 2.9 15.9 + - + +
135I THR 3.7 0.4 - - - -
136I HIS* 1.3 96.3 - - + +
138I LEU* 1.3 65.5 + - - +
139I ASN 3.4 2.0 - - - -
140I GLU* 3.2 6.1 + - - +
141I GLN* 3.0 29.5 + - - +
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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