Contacts of the helix formed by residues 121 - 134 (chain A) in PDB entry 1B0K
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 GLN 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A LYS 3.5 17.3 + - - +
118A ASP* 3.3 18.1 + - - +
119A ILE 3.5 0.8 - - - -
120A ASN* 1.3 75.6 - - - +
122A GLU* 1.3 54.9 + - - +
124A TYR* 4.1 7.8 - - + +
125A ASN* 2.8 49.7 + - - +
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Residues in contact with GLU 122 (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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119A ILE 5.2 1.8 + - - +
120A ASN* 3.1 2.0 + - - -
121A GLN* 1.3 78.0 - - - +
123A VAL* 1.3 59.3 + - + +
125A ASN* 3.5 5.3 - - - +
126A PHE* 3.1 25.5 + - - +
532A SER* 5.0 5.0 + - - -
535A SER* 2.6 30.3 + - - -
536A GLN 5.1 1.2 + - - -
537A ARG* 3.8 31.9 + - - +
538A LEU* 4.0 17.1 - - + +
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Residues in contact with VAL 123 (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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77A GLN* 3.6 40.4 - - - +
102A LEU* 3.7 20.0 - - + -
120A ASN* 2.9 13.1 + - + +
122A GLU* 1.3 76.3 - - - +
124A TYR* 1.4 67.9 - - + +
125A ASN 3.1 1.3 - - - -
126A PHE* 3.1 8.8 + - - +
127A LEU* 3.0 34.7 + - + +
537A ARG* 3.7 39.0 - - + +
538A LEU* 4.7 6.3 - - + -
578A LYS 5.7 0.4 - - - +
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Residues in contact with TYR 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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73A ASP* 3.5 22.2 - - - -
99A CYS* 4.1 21.3 - - + -
102A LEU* 4.0 9.0 - - + +
103A ILE* 3.7 25.6 - - - +
116A ALA* 3.4 22.7 - - - +
117A LYS* 3.9 12.6 - - + -
120A ASN* 3.2 39.1 + - + +
121A GLN* 4.1 7.2 - - + +
123A VAL* 1.4 79.3 - - + +
125A ASN* 1.3 58.6 + - - +
127A LEU* 3.9 6.6 - - + +
128A ALA* 2.8 32.6 + - - +
138A PHE* 3.9 10.8 - - + -
141A PRO* 3.8 27.0 - - + +
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Residues in contact with ASN 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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121A GLN* 2.8 35.8 + - - +
122A GLU* 3.5 7.9 - - - +
124A TYR* 1.3 76.5 - - - +
126A PHE* 1.3 63.8 + - - +
128A ALA* 4.0 4.4 - - - +
129A THR* 2.8 41.4 + - - -
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Residues in contact with PHE 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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77A GLN* 4.0 21.3 - - + -
80A MET* 4.4 10.3 - - + -
81A LEU* 4.2 20.6 - - + -
84A ILE* 4.2 16.8 - - + -
122A GLU 3.1 11.9 + - - +
123A VAL* 3.1 8.5 + - - +
125A ASN* 1.3 81.1 - - - +
127A LEU* 1.4 78.8 + - + +
129A THR* 3.8 1.8 - - - -
130A ALA* 2.9 35.8 + - + +
529A VAL* 3.6 30.6 - - + +
530A ASP 4.7 4.5 - - - +
531A VAL* 4.0 18.6 - - + -
538A LEU* 3.7 35.9 - - + -
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Residues in contact with LEU 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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73A ASP* 3.6 38.4 - - + +
76A ALA* 3.9 28.7 - - + +
77A GLN* 4.2 8.3 - - + -
80A MET* 4.6 2.9 - - + -
97A ILE* 4.1 24.7 - - + +
99A CYS* 4.8 5.4 - - - -
123A VAL* 3.0 25.8 + - + +
124A TYR* 3.9 2.5 - - + +
126A PHE* 1.4 93.3 - - + +
128A ALA* 1.3 56.7 + - - +
130A ALA* 3.4 2.4 + - - +
131A GLY* 2.8 30.5 + - - -
138A PHE* 3.8 16.3 - - + -
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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 TYR 2.8 23.7 + - - +
125A ASN* 4.0 6.5 - - - +
127A LEU* 1.3 73.0 - - - +
129A THR* 1.3 57.8 + - - +
131A GLY* 3.3 1.4 + - - -
132A ALA* 2.9 27.6 + - - +
138A PHE* 3.5 29.5 - - + +
518A GLN* 4.4 16.8 + - - +
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Residues in contact with THR 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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125A ASN* 2.8 30.9 + - - -
126A PHE 3.9 2.0 - - - -
128A ALA* 1.3 72.3 - - - +
130A ALA* 1.3 65.4 + - - +
131A GLY 3.2 1.1 - - - -
132A ALA* 3.6 6.2 + - - +
133A LYS* 3.2 23.4 + - - +
527A GLN* 4.0 18.2 - - + +
528A ARG 3.2 26.7 - - - +
529A VAL* 4.1 12.3 - - + +
530A ASP 5.3 0.9 - - - +
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Residues in contact with ALA 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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80A MET* 4.1 24.4 - - + +
84A ILE* 5.3 2.0 - - + -
126A PHE* 2.9 30.6 + - + +
127A LEU* 3.9 4.7 - - - +
129A THR* 1.3 74.6 - - - +
131A GLY* 1.3 67.6 + - - +
133A LYS* 3.4 0.7 + - - -
134A TYR* 3.1 37.3 + - + +
136A VAL* 5.3 0.2 - - - +
529A VAL* 4.2 18.8 - - + +
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Residues in contact with GLY 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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97A ILE* 4.8 7.1 - - - +
127A LEU 2.8 17.8 + - - -
128A ALA* 3.5 2.2 - - - -
130A ALA* 1.3 79.9 - - - +
132A ALA* 1.4 61.1 + - - +
135A GLY 3.2 3.8 + - - -
136A VAL* 3.1 48.7 + - - -
138A PHE* 5.7 4.3 - - - -
520A PRO* 4.5 0.2 - - - +
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Residues in contact with ALA 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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128A ALA 2.9 18.7 + - - +
129A THR* 4.1 6.1 - - - +
130A ALA 3.5 0.2 - - - -
131A GLY* 1.4 70.6 - - - +
133A LYS* 1.3 56.4 + - - +
518A GLN* 6.1 2.7 - - - +
520A PRO* 4.5 4.5 - - - -
521A PRO* 3.6 33.0 - - + +
522A LYS* 3.0 26.3 + - - -
525A SER* 3.4 6.9 + - - -
527A GLN* 3.9 18.2 - - + +
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Residues in contact with LYS 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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89A PRO 4.0 8.2 - - - +
90A LYS* 5.7 0.5 - - - +
129A THR 3.2 16.6 + - - +
130A ALA 3.8 3.1 - - - +
131A GLY 3.2 0.4 + - - -
132A ALA* 1.3 79.1 - - - +
134A TYR* 1.3 95.1 + - + +
135A GLY 3.5 0.4 + - - -
522A LYS* 4.5 1.4 + - - -
525A SER* 3.2 36.6 + - - +
526A GLY* 4.8 1.6 - - - -
527A GLN* 3.0 32.5 + - + +
528A ARG* 5.6 0.9 - - - +
529A VAL* 4.0 14.4 - - + +
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Residues in contact with TYR 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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80A MET* 3.6 18.8 - - + -
83A PHE* 3.5 21.3 - + + -
84A ILE* 3.6 39.4 + - + +
88A LEU 3.5 15.7 - - - -
89A PRO* 3.4 23.3 - - + +
90A LYS* 3.3 8.7 - - - +
91A VAL* 2.9 47.8 + - + +
130A ALA* 3.1 35.1 + - + +
133A LYS* 1.3 108.5 - - + +
135A GLY* 1.3 58.1 + - - +
136A VAL* 3.8 2.0 - - + -
529A VAL* 4.5 4.4 - - + +
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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