Contacts of the helix formed by residues 128 - 137 (chain K) in PDB entry 5HJD
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 THR 128 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93K GLU* 3.5 40.8 + - + +
126K ASN 3.9 1.1 + - - +
127K PRO* 1.3 71.9 - - - +
129K GLU* 1.3 53.0 + - - +
130K ASP* 4.0 6.8 + - - +
131K PHE* 2.8 27.2 + - - +
132K ARG 2.7 30.3 + - - -
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Residues in contact with GLU 129 (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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127K PRO 3.5 3.1 + - - -
128K THR* 1.3 72.2 - - - +
130K ASP* 1.3 61.1 + - + +
132K ARG* 3.5 18.9 - - + +
133K ARG* 3.0 39.2 + - - +
129N GLU* 3.1 25.0 - - + +
132N ARG* 6.5 0.4 - - - -
133N ARG* 2.5 40.9 + - - -
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Residues in contact with ASP 130 (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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128K THR* 3.0 7.5 + - - +
129K GLU* 1.3 83.3 - - + +
131K PHE* 1.3 62.2 + - - +
133K ARG* 2.7 31.0 + - - +
134K LYS* 3.3 35.2 + - - +
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Residues in contact with PHE 131 (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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47K PHE* 4.0 18.2 - - + -
89K PHE* 3.9 24.0 - + + -
90K LYS 3.3 26.7 - - - +
91K ASN* 3.2 33.7 - - - +
93K GLU* 5.1 0.7 - - - +
124K PHE* 3.7 20.2 - + - -
127K PRO* 3.8 13.9 - - + -
128K THR* 2.8 20.0 + - - +
130K ASP* 1.3 76.6 - - - +
132K ARG* 1.3 59.7 + - - +
134K LYS* 3.2 10.5 + - + +
135K LEU* 3.0 59.1 + - + +
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Residues in contact with ARG 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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5K CYS* 4.3 6.3 - - - -
7K VAL* 4.1 11.0 - - + -
127K PRO* 4.2 11.0 - - + +
128K THR 2.7 15.7 + - - +
129K GLU* 3.3 20.7 + - - +
131K PHE* 1.3 71.5 - - - +
133K ARG* 1.3 63.2 + - - +
135K LEU* 3.2 11.9 + - - +
136K LEU* 2.9 55.5 + - + +
5N CYS* 3.8 12.5 - - - +
126N ASN* 4.9 1.8 - - - +
127N PRO* 3.8 29.3 + - - +
128N THR 4.9 0.2 + - - -
129N GLU* 4.3 27.9 - - - +
132N ARG* 2.9 43.5 - - - +
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Residues in contact with ARG 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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129K GLU* 3.0 21.5 + - - +
130K ASP* 2.7 45.4 + - - +
131K PHE 3.3 0.2 - - - -
132K ARG* 1.3 79.4 - - - +
134K LYS* 1.3 58.4 + - + +
136K LEU* 3.3 8.7 + - + +
137K LYS* 2.9 51.4 + - + +
129N GLU* 2.2 48.5 + - - +
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Residues in contact with LYS 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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46K HIS* 3.4 44.8 + - - +
47K PHE* 4.0 10.2 - - + +
90K LYS* 3.6 37.7 - - + +
130K ASP* 3.3 29.3 + - - +
131K PHE* 3.2 12.0 + - + +
133K ARG* 1.3 78.1 - - + +
135K LEU* 1.3 62.1 + - - +
137K LYS* 3.4 16.5 + - + +
138K ALA 3.7 1.9 + - - -
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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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7K VAL* 3.6 38.1 - - + -
9K VAL* 3.7 17.1 - - + +
47K PHE* 3.7 25.8 - - + -
124K PHE* 3.9 19.1 - - + -
127K PRO* 4.3 4.3 - - + -
131K PHE* 3.0 58.1 + - + +
132K ARG* 3.5 6.7 - - - +
134K LYS* 1.3 76.6 - - - +
136K LEU* 1.3 53.9 + - - +
138K ALA* 3.6 8.8 + - - +
3N SER* 2.7 29.6 + - - -
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Residues in contact with LEU 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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7K VAL* 4.7 6.5 - - + -
132K ARG* 2.9 62.7 + - + +
133K ARG* 3.3 7.4 + - + +
134K LYS 3.2 0.2 - - - -
135K LEU* 1.3 74.3 - - - +
137K LYS* 1.3 59.7 + - - +
138K ALA 3.1 10.8 + - - +
3N SER* 3.8 24.0 - - - +
4N SER* 3.9 22.9 - - - +
5N CYS* 5.2 0.4 - - + -
126N ASN* 4.3 7.2 - - - +
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Residues in contact with LYS 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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43K ASN 5.5 0.2 + - - -
46K HIS* 2.9 49.2 + - + +
133K ARG* 2.9 40.6 + - + +
134K LYS* 3.4 8.3 + - + +
136K LEU* 1.3 77.0 - - - +
138K ALA* 1.3 62.1 + - - +
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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