Contacts of the helix formed by residues 123 - 134 (chain A) in PDB entry 2B4J
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 SER 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLY* 3.7 25.6 - - - -
119A SER 2.9 19.0 + - - -
120A ASN 4.0 4.0 - - - -
121A PHE 3.3 0.4 - - - -
122A THR* 1.3 80.5 + - - +
124A THR* 1.3 57.7 + - - +
125A THR* 3.1 25.1 + - - +
126A VAL* 3.1 5.7 + - - +
127A LYS* 3.0 23.4 + - - +
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Residues in contact with THR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A THR 3.4 2.2 + - - +
123A SER* 1.3 73.6 + - - +
125A THR* 1.3 61.5 + - - +
126A VAL 3.4 0.2 - - - -
127A LYS* 3.7 17.7 - - + +
128A ALA* 2.9 28.1 + - - +
368D LEU* 3.8 24.3 - - + +
370D VAL* 5.9 2.0 - - + -
408D VAL* 4.0 16.4 - - + +
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Residues in contact with THR 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY 3.6 18.9 + - - -
95A GLN* 3.8 18.9 + - + +
98A ALA* 3.7 9.5 - - - +
123A SER* 3.1 12.6 + - - +
124A THR* 1.3 79.1 + - - +
126A VAL* 1.3 64.0 + - - +
128A ALA* 3.7 2.6 - - - +
129A ALA* 3.1 23.2 + - - +
365D ILE 3.9 18.6 + - - +
366D ASP 5.6 3.1 - - - -
367D ASN* 6.2 0.2 - - - -
368D LEU* 5.1 13.2 - - + +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLY* 3.5 19.3 - - - +
97A THR* 3.6 15.3 - - + -
98A ALA* 3.8 9.4 - - - +
101A LEU* 4.0 20.0 - - + -
113A VAL* 6.1 0.2 - - + -
120A ASN 3.1 25.4 - - - +
121A PHE* 3.5 23.6 - - + +
123A SER* 3.1 10.5 + - - +
125A THR* 1.3 72.9 + - - +
127A LYS* 1.3 60.0 + - - +
129A ALA* 3.3 2.6 + - - +
130A CYS* 2.9 28.6 + - - -
137A GLN* 3.5 15.5 - - - +
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Residues in contact with LYS 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A THR* 2.6 39.8 + - - +
123A SER 3.0 13.9 + - - +
124A THR* 3.7 21.2 - - + +
126A VAL* 1.3 77.0 - - - +
128A ALA* 1.3 56.9 + - - +
130A CYS* 3.4 1.6 + - - +
131A TRP* 2.8 30.7 + - - +
137A GLN* 3.5 20.9 - - - +
139A PHE* 4.5 14.9 - - - -
408D VAL* 3.8 23.0 - - + +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A THR 2.9 18.1 + - - +
125A THR 3.7 4.5 - - - +
126A VAL 3.2 0.4 - - - -
127A LYS* 1.3 73.3 - - - +
129A ALA* 1.3 60.5 + - - +
131A TRP* 3.4 7.3 + - - +
132A TRP* 2.8 29.8 + - - +
365D ILE* 4.0 29.2 - - + +
368D LEU* 4.3 14.6 - - + -
406D PHE* 4.8 4.3 - - + -
408D VAL* 3.7 16.1 - - + +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ALA* 3.9 23.3 - - + +
101A LEU* 5.3 5.4 - - + -
102A LEU* 4.0 21.7 - - + +
125A THR 3.1 16.9 + - - +
126A VAL 3.7 3.6 - - - +
128A ALA* 1.3 76.8 - - - +
130A CYS* 1.3 57.0 + - - +
132A TRP* 3.2 2.8 + - - +
133A ALA* 2.9 31.8 + - - +
135A ILE* 5.4 1.3 - - - -
365D ILE* 4.1 17.1 - - + +
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Residues in contact with CYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.8 25.1 - - - -
113A VAL* 4.5 0.2 - - - -
126A VAL* 2.9 21.7 + - - +
127A LYS 3.7 4.0 - - - +
129A ALA* 1.3 72.6 - - - +
131A TRP* 1.3 64.9 + - - +
133A ALA 3.3 0.3 + - - -
134A GLY 2.9 5.0 + - - -
135A ILE* 2.8 63.3 + - + +
137A GLN* 3.6 33.9 - - + +
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Residues in contact with TRP 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LYS 2.8 20.5 + - - +
128A ALA* 3.5 11.4 - - - +
130A CYS* 1.3 70.5 - - - +
132A TRP* 1.3 96.6 + + + +
134A GLY* 3.2 12.1 + - - -
135A ILE 5.1 0.7 - - - -
363D LEU* 5.4 5.6 - - + -
365D ILE* 4.4 9.2 - - + -
402D LYS* 4.4 35.6 + - + -
403D ILE* 5.0 9.2 - - + -
405D ARG* 3.0 31.3 + - - +
406D PHE* 3.5 39.3 - + + +
407D LYS* 3.9 19.1 - - + +
408D VAL* 4.3 7.6 - - + +
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Residues in contact with TRP 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 4.2 12.6 - - + -
128A ALA 2.8 18.1 + - - +
129A ALA 3.2 4.0 + - - +
131A TRP* 1.3 103.3 - + + +
133A ALA* 1.3 69.7 + - + +
134A GLY 3.4 0.7 + - - -
165B VAL* 4.7 2.5 - - + -
168B GLN* 2.9 28.4 + - + -
178B MET* 3.5 63.6 - - + +
181B PHE* 3.6 40.6 - + + -
182B ILE* 4.0 16.8 - - + -
365D ILE* 4.1 13.2 - - + -
402D LYS* 5.2 2.5 - - - +
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A LEU* 4.4 7.4 - - + -
105A ALA* 4.0 10.3 - - + +
110A VAL 4.9 2.1 - - - +
129A ALA 2.9 16.4 + - - +
132A TRP* 1.3 88.8 - - + +
134A GLY* 1.3 62.2 + - - +
135A ILE* 3.5 19.8 - - + +
181B PHE* 3.5 37.2 - - + -
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Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A VAL 4.3 4.3 - - - +
111A LYS* 4.3 9.9 - - - +
130A CYS 2.9 4.8 + - - -
131A TRP* 3.2 10.2 + - - -
132A TRP 3.2 1.6 + - - -
133A ALA* 1.3 79.1 - - - +
135A ILE* 1.3 59.3 + - - +
136A LYS 4.1 0.7 + - - -
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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