Contacts of the helix formed by residues 125 - 134 (chain b) in PDB entry 6QY3
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 125 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123b GLU* 4.0 5.6 + - - -
124b ILE* 1.3 76.7 - - - +
126b LEU* 1.3 62.3 + - - +
127b LEU* 3.5 8.7 - - - -
128b GLU* 4.0 15.3 - - - +
129b LEU* 3.2 24.1 + - - +
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Residues in contact with LEU 126 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84b VAL* 5.4 13.0 - - + -
87b LEU* 6.2 4.0 - - + -
125b THR* 1.3 73.8 - - - +
127b LEU* 1.3 60.0 + - - +
129b LEU* 3.1 7.7 + - - +
130b ILE* 2.9 28.6 + - - +
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Residues in contact with LEU 127 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80b HIS* 5.7 9.6 - - + +
84b VAL* 5.5 12.1 - - + +
125b THR* 4.2 5.2 - - - -
126b LEU* 1.3 78.3 - - - +
128b GLU* 1.3 57.7 + - - +
130b ILE* 3.4 6.6 + - - +
131b LYS* 2.9 29.5 + - - +
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Residues in contact with GLU 128 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124b ILE 5.2 0.2 - - - -
125b THR* 3.7 22.5 + - - +
126b LEU 3.2 0.4 - - - -
127b LEU* 1.3 76.6 - - - +
129b LEU* 1.3 58.4 + - - +
131b LYS* 3.8 7.0 - - - +
132b ALA* 2.9 29.1 + - - +
132c ALA* 4.2 29.9 - - + +
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Residues in contact with LEU 129 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125b THR 3.2 15.1 + - - +
126b LEU* 3.1 12.4 + - - +
128b GLU* 1.3 75.6 - - - +
130b ILE* 1.3 59.1 + - - +
132b ALA* 3.4 6.1 + - - +
133b LEU* 2.9 27.5 + - - +
104c ILE* 6.5 0.9 - - + -
124c ILE* 5.8 1.0 - - - +
132c ALA* 6.0 0.2 - - - -
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Residues in contact with ILE 130 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80b HIS* 4.8 20.4 - - + +
83b ILE* 5.9 5.4 - - + -
126b LEU 2.9 15.8 + - - +
127b LEU* 3.9 7.4 - - - +
129b LEU* 1.3 74.0 - - - +
131b LYS* 1.3 64.8 + - - +
133b LEU* 3.1 7.4 + - - +
134b GLY 3.0 18.9 + - - -
135b VAL* 3.7 16.2 + - + +
108c ILE* 6.6 0.2 - - + -
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Residues in contact with LYS 131 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80b HIS* 5.9 1.2 - - - +
127b LEU 2.9 17.9 + - - +
128b GLU* 3.9 7.0 - - - +
130b ILE* 1.3 77.4 - - - +
132b ALA* 1.3 62.7 + - - +
134b GLY* 3.4 11.8 + - - +
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Residues in contact with ALA 132 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128b GLU 2.9 19.8 + - - +
129b LEU* 3.7 6.7 - - - +
130b ILE 3.2 0.2 - - - -
131b LYS* 1.3 76.0 - - - +
133b LEU* 1.3 57.3 + - - +
134b GLY 3.5 0.3 + - - -
502b CA 2.7 29.5 - - - -
123c GLU 3.3 3.1 - - - +
124c ILE* 4.5 10.3 - - + -
128c GLU* 4.1 31.3 - - + +
129c LEU* 6.0 0.4 - - - -
132c ALA* 5.1 3.4 - - + -
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Residues in contact with LEU 133 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129b LEU 2.9 17.0 + - - +
130b ILE* 3.1 10.1 + - - +
132b ALA* 1.3 77.0 - - - +
134b GLY* 1.3 62.7 + - - +
135b VAL* 4.7 4.5 - - + +
502b CA 4.5 0.7 - - - -
108c ILE* 6.0 6.1 - - + -
121c TYR* 3.9 9.7 - - + +
122c ASP* 3.5 23.2 + - - +
123c GLU 3.9 15.9 + - - +
124c ILE* 5.1 5.8 - - + +
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Residues in contact with GLY 134 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130b ILE 3.0 5.8 + - - -
131b LYS* 3.4 10.7 + - - -
132b ALA 3.3 3.8 - - - -
133b LEU* 1.3 79.4 - - - +
135b VAL* 1.3 64.9 + - - +
136b ARG* 3.4 4.8 + - - +
120c GLU 3.2 12.2 - - - +
121c TYR* 3.8 3.9 - - - -
122c ASP* 4.6 3.0 + - - +
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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