Contacts of the helix formed by residues 123 - 131 (chain b) in PDB entry 5JPQ
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 123 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116b THR* 3.9 7.9 - - - -
121b ALA* 3.3 3.8 - - - +
122b GLU* 1.3 80.8 - - - +
124b VAL* 1.3 58.2 + - - +
125b GLN* 3.0 9.9 - - - -
126b ALA* 3.3 20.2 - - - +
127b ALA* 3.0 30.0 + - - +
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Residues in contact with VAL 124 (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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34b ARG 5.3 2.9 - - - +
35b ARG 4.5 16.2 - - - +
36b TYR* 4.8 1.8 - - - -
37b MET* 3.0 29.7 - - + +
112b PRO* 5.4 7.3 - - - +
116b THR* 4.1 15.3 - - - -
123b THR* 1.3 72.5 - - - +
125b GLN* 1.3 57.7 - - - +
127b ALA* 3.8 9.4 - - - +
128b THR* 3.9 5.4 + - - -
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Residues in contact with GLN 125 (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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37b MET* 4.1 10.1 - - + -
123b THR* 3.0 7.7 - - - -
124b VAL* 1.3 77.6 - - + +
126b ALA* 1.3 60.2 + - - +
127b ALA 3.0 1.6 - - - -
128b THR* 2.7 31.9 + - - -
129b LYS* 3.4 4.2 + - - +
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Residues in contact with ALA 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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121b ALA* 4.4 1.6 - - + -
122b GLU* 3.8 17.0 - - + +
123b THR* 3.3 31.0 - - - +
125b GLN* 1.3 77.3 - - - +
127b ALA* 1.3 65.5 + - - +
129b LYS* 3.2 13.4 + - - +
130b LEU* 3.3 10.9 + - - +
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Residues in contact with ALA 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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112b PRO* 4.5 10.8 - - + +
115b MET* 4.6 8.5 - - + +
116b THR* 4.3 16.6 - - - +
121b ALA* 3.6 19.0 - - + +
123b THR 3.0 17.5 - - - +
124b VAL 3.8 8.5 - - - +
126b ALA* 1.3 76.3 - - - +
128b THR* 1.3 55.2 + - - +
130b LEU* 2.8 34.5 + - - +
131b ILE* 3.2 9.4 + - - +
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Residues in contact with THR 128 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37b MET* 4.9 11.9 - - - -
112b PRO* 5.7 6.7 - - - +
124b VAL 3.9 7.9 + - - -
125b GLN* 2.7 23.8 + - - -
127b ALA* 1.3 75.1 - - - +
129b LYS* 1.3 57.4 + - - -
131b ILE* 4.4 1.4 + - - -
132b GLU* 3.5 17.2 + - - +
146b PRO* 4.9 17.8 - - - +
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Residues in contact with LYS 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 GLN 3.4 3.2 + - - +
126b ALA* 3.2 9.5 + - - +
128b THR* 1.3 77.9 - - - +
130b LEU* 1.3 57.8 + - - +
132b GLU* 2.9 23.9 - - - +
133b GLN* 3.0 13.4 + - - +
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Residues in contact with LEU 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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115b MET* 6.5 0.7 - - + -
120b MET 5.9 2.7 - - - +
121b ALA* 6.0 0.9 - - + -
126b ALA 3.3 9.4 + - - +
127b ALA* 2.8 15.9 + - - +
129b LYS* 1.3 72.7 - - - +
131b ILE* 1.3 54.7 + - - +
132b GLU 2.8 4.4 + - - -
133b GLN* 2.8 25.6 + - - -
135b HIS* 3.3 34.3 + - + +
136b VAL* 6.1 0.4 - - + -
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Residues in contact with ILE 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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111b LEU* 5.4 12.6 - - + +
112b PRO* 6.0 1.6 - - + -
115b MET* 5.9 5.4 - - + -
127b ALA 3.2 9.2 + - - +
128b THR* 5.0 1.6 - - - +
130b LEU* 1.3 76.5 - - - +
132b GLU* 1.3 54.0 + - - +
134b GLY 4.0 2.8 + - - -
136b VAL* 4.3 21.9 - - + +
143b VAL* 3.3 9.2 - - + +
144b ARG* 2.7 39.4 - - - +
145b ASP 5.3 0.7 - - - -
146b PRO* 4.6 19.1 - - + -
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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