Contacts of the helix formed by residues 124 - 136 (chain T) in PDB entry 5IY6
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 TYR 124 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541B ILE* 5.3 6.9 - - - +
544B PHE* 4.7 28.9 - + + -
590B LEU* 4.0 26.2 - - + -
593B GLN* 5.3 1.6 - - - +
595B ASP* 3.8 42.7 + - + +
596B ILE* 6.0 0.7 - - - +
122T GLU* 2.9 13.5 + - - -
123T ASN* 1.3 84.9 - - + +
125T MET* 1.3 65.0 + - - +
127T LEU* 3.2 14.5 + - + +
128T LYS* 2.8 68.7 + - + +
131T GLN* 4.8 7.6 + - - -
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Residues in contact with MET 125 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122T GLU* 2.8 15.4 + - - +
123T ASN* 5.2 15.5 - - + +
124T TYR* 1.3 80.6 - - - +
126T ARG* 1.3 70.8 + - + +
128T LYS* 3.3 7.9 + - - +
129T ARG* 2.9 39.7 + - - +
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Residues in contact with ARG 126 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121T SER* 2.9 22.4 + - - -
122T GLU* 2.8 52.9 + - + +
125T MET* 1.3 80.4 - - + +
127T LEU* 1.3 53.1 + - - +
129T ARG* 3.0 23.4 + - + +
130T LEU* 2.5 54.2 + - + +
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Residues in contact with LEU 127 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544B PHE* 3.6 37.0 - - + -
547B GLU* 3.6 34.8 - - - +
26T TYR* 5.0 9.0 - - + -
122T GLU* 3.9 10.0 + - + +
123T ASN 5.8 0.9 - - - +
124T TYR* 3.2 21.9 + - + +
126T ARG* 1.3 78.8 - - - +
128T LYS* 1.3 56.5 + - - +
130T LEU* 3.2 22.2 + - + +
131T GLN* 2.8 50.4 + - + +
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Residues in contact with LYS 128 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B MET 5.1 1.2 + - - -
595B ASP* 3.3 33.4 + - - +
124T TYR* 2.8 47.8 + - + +
125T MET* 3.3 11.0 - - - +
127T LEU* 1.3 74.9 - - - +
129T ARG* 1.3 57.5 + - - +
131T GLN* 3.3 15.1 + - - +
132T ILE* 2.9 47.9 + - + +
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Residues in contact with ARG 129 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125T MET* 2.9 26.1 + - - +
126T ARG* 3.2 22.1 - - + +
128T LYS* 1.3 73.0 - - - +
130T LEU* 1.3 55.0 + - + +
132T ILE* 3.2 15.6 + - + +
133T GLU* 2.6 49.0 + - + +
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Residues in contact with LEU 130 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26T TYR* 4.4 43.7 - - + -
122T GLU* 6.4 0.2 - - + -
126T ARG* 2.5 38.5 + - + +
127T LEU* 3.4 21.1 - - + +
129T ARG* 1.3 73.6 - - + +
131T GLN* 1.3 57.1 + - + +
133T GLU* 3.4 18.7 + - + +
134T GLU* 2.9 31.3 + - - +
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Residues in contact with GLN 131 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540B PRO* 3.4 32.2 + - + +
541B ILE* 6.0 1.9 - - - +
543B GLU* 4.6 13.5 + - - +
544B PHE* 4.3 19.0 - - - +
124T TYR* 4.8 7.7 + - - -
127T LEU* 2.8 35.5 + - + +
128T LYS* 3.4 19.8 - - - +
130T LEU* 1.3 72.4 - - - +
132T ILE* 1.3 62.7 + - + +
134T GLU* 3.4 11.6 + - - +
135T SER* 3.0 27.2 + - - -
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Residues in contact with ILE 132 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128T LYS* 2.9 40.7 + - + +
129T ARG* 3.3 14.8 - - + +
131T GLN* 1.3 74.8 - - + +
133T GLU* 1.3 63.1 + - - +
135T SER* 3.3 16.0 + - - -
136T SER* 3.3 13.5 + - - -
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Residues in contact with GLU 133 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129T ARG* 2.6 33.5 + - + +
130T LEU* 3.3 22.7 + - + +
132T ILE* 1.3 72.4 - - - +
134T GLU* 1.3 64.2 + - - +
136T SER* 3.4 18.3 + - - -
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Residues in contact with GLU 134 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543B GLU* 4.7 7.5 - - - +
25T LYS* 3.4 30.8 + - - +
130T LEU 2.9 19.7 + - - +
131T GLN* 3.7 11.6 - - - +
133T GLU* 1.3 74.8 - - - +
135T SER* 1.3 66.0 + - - +
136T SER* 4.5 1.0 - - - -
137T LYS* 5.6 0.7 - - - -
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Residues in contact with SER 135 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131T GLN 3.0 14.8 + - - -
132T ILE* 3.3 10.3 + - - -
134T GLU* 1.3 83.7 - - - +
136T SER* 1.3 71.0 + - - +
137T LYS* 3.1 29.7 - - - +
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Residues in contact with SER 136 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132T ILE 3.3 8.3 + - - -
133T GLU* 3.4 17.2 + - - -
134T GLU 4.5 0.9 - - - -
135T SER* 1.3 81.0 - - - +
137T LYS* 1.3 59.2 + - - +
138T PRO* 4.7 0.3 - - - +
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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