Contacts of the helix formed by residues 99 - 122 (chain u) in PDB entry 4B2Q
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 99 (chain u).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117t LEU* 4.6 22.7 + - - +
121t ARG* 4.3 13.8 - - - +
95u GLU* 2.6 39.7 + - - -
96u ASP* 4.8 0.3 - - - -
98u LYS* 1.3 78.7 - - - +
100u CYS* 1.3 83.2 + - - +
103u PHE* 3.1 22.1 + - - +
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Residues in contact with CYS 100 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117t LEU* 5.8 2.2 - - - -
95u GLU 3.7 0.6 + - - -
96u ASP* 2.9 30.4 + - + +
99u SER* 1.3 92.8 + - - +
101u ALA* 1.3 83.0 + - - +
104u LEU* 3.0 39.6 + - + +
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Residues in contact with ALA 101 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96u ASP 3.2 5.2 + - - +
97u VAL* 4.0 11.0 - - - +
100u CYS* 1.3 88.6 - - - +
102u GLU* 1.3 57.4 + - - +
104u LEU* 3.6 2.8 - - - +
105u THR* 2.5 45.1 + - - +
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Residues in contact with GLU 102 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97u VAL 3.7 6.8 + - - +
98u LYS* 3.2 29.8 + - + +
99u SER 3.5 0.4 + - - -
100u CYS 3.3 1.0 - - - -
101u ALA* 1.3 79.5 - - - +
103u PHE* 1.3 64.4 + - - +
105u THR* 3.4 6.3 + - - -
106u GLN* 3.1 50.6 + - - +
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Residues in contact with PHE 103 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110t MET* 5.2 4.5 - - - -
113t SER* 3.5 24.5 - - - -
114t GLN* 4.0 18.4 - - + -
117t LEU* 3.3 32.5 - - + -
98u LYS 3.8 1.1 + - - +
99u SER* 3.1 17.0 + - - +
102u GLU* 1.3 76.7 - - - +
104u LEU* 1.3 69.9 + - + +
106u GLN* 3.1 9.9 + - - +
107u SER* 2.8 49.9 + - - -
110u ARG* 4.9 11.2 - - - -
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Residues in contact with LEU 104 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114t GLN* 3.9 37.2 + - + +
117t LEU* 4.3 13.5 - - + -
118t VAL* 4.7 13.0 - - + +
99u SER 4.6 0.2 - - - +
100u CYS* 3.0 49.4 + - - +
101u ALA* 3.7 2.9 - - - +
103u PHE* 1.3 89.0 - - + +
105u THR* 1.3 63.4 + - - +
107u SER* 3.4 3.1 + - - -
108u LYS* 3.0 44.1 + - - +
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Residues in contact with THR 105 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101u ALA* 2.5 37.8 + - - +
102u GLU* 3.7 8.0 - - - -
104u LEU* 1.3 74.8 - - - +
106u GLN* 1.3 63.7 + - + +
108u LYS* 3.5 9.7 + - - +
109u THR* 3.2 22.5 + - - -
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Residues in contact with GLN 106 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102u GLU* 3.1 45.5 + - - +
103u PHE* 3.1 10.3 + - - +
105u THR* 1.3 77.0 - - + +
107u SER* 1.3 59.3 + - - +
109u THR* 3.0 15.6 - - + +
110u ARG* 2.8 47.9 + - - +
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Residues in contact with SER 107 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110t MET* 2.9 33.6 + - - +
114t GLN* 3.1 24.2 + - - +
103u PHE* 2.8 39.4 + - - -
104u LEU 3.7 1.8 - - - -
106u GLN* 1.3 73.5 - - - +
108u LYS* 1.3 57.4 + - - +
110u ARG* 3.3 11.3 + - - +
111u ILE* 2.9 28.2 + - - +
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Residues in contact with LYS 108 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114t GLN* 3.6 22.0 - - - +
104u LEU* 3.0 36.5 + - - +
105u THR* 3.6 7.6 - - - +
106u GLN 3.3 0.2 - - - -
107u SER* 1.3 73.5 - - - +
109u THR* 1.3 61.4 + - - +
111u ILE* 2.8 27.1 - - + +
112u GLN* 2.8 23.7 + - + +
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Residues in contact with THR 109 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105u THR 3.2 7.7 + - - +
106u GLN* 3.0 34.7 + - + +
108u LYS* 1.3 77.5 - - - +
110u ARG* 1.3 64.8 + - + +
112u GLN* 3.1 15.7 + - - +
113u GLU* 3.1 31.0 + - - +
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Residues in contact with ARG 110 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110t MET* 2.8 44.1 - - + +
103u PHE* 4.9 12.1 - - - -
106u GLN* 2.8 27.9 + - - +
107u SER* 3.7 22.2 - - - +
109u THR* 1.3 80.8 - - + +
111u ILE* 1.3 61.4 + - - +
113u GLU* 3.3 23.3 + - + +
114u TYR* 3.1 46.9 + - + -
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Residues in contact with ILE 111 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107t ALA* 4.3 21.3 - - + +
110t MET* 4.6 11.6 - - + +
111t GLU* 4.3 20.4 - - + +
114t GLN* 4.6 6.5 - - - +
107u SER 2.9 19.2 + - - +
108u LYS* 2.8 32.5 - - + +
110u ARG* 1.3 76.7 - - - +
112u GLN* 1.3 65.5 + - + +
114u TYR* 3.4 10.1 - - - +
115u GLU* 2.9 56.6 + - + +
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Residues in contact with GLN 112 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108u LYS* 2.8 21.2 + - + +
109u THR* 3.3 16.1 + - - +
111u ILE* 1.3 80.3 - - + +
113u GLU* 1.3 52.7 + - - +
115u GLU* 2.9 12.4 + - - +
116u LYS* 2.7 35.0 + - - +
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Residues in contact with GLU 113 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109u THR* 3.1 14.2 + - - +
110u ARG* 3.3 38.8 + - + +
112u GLN* 1.3 77.1 - - - +
114u TYR* 1.3 54.0 - - + +
116u LYS* 2.8 11.3 + - + +
117u GLU* 2.4 39.1 + - - +
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Residues in contact with TYR 114 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103t GLN* 4.2 27.8 - - + +
106t ASP* 2.3 40.6 + - + -
107t ALA* 4.3 18.2 - - + -
110t MET* 4.0 18.8 - - + +
110u ARG* 3.1 35.9 + - + -
111u ILE* 3.4 11.9 - - - +
113u GLU* 1.3 77.3 - - + +
115u GLU* 1.3 58.0 + - + +
117u GLU* 3.1 10.1 + - + +
118u LEU* 2.8 36.2 + - + +
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Residues in contact with GLU 115 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107t ALA* 5.4 7.0 - - + +
111u ILE* 2.9 48.6 + - + +
112u GLN* 2.9 11.6 + - - +
114u TYR* 1.3 72.3 - - + +
116u LYS* 1.3 61.3 + - - +
118u LEU* 3.0 14.8 + - + +
119u GLU* 2.9 27.4 + - - +
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Residues in contact with LYS 116 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112u GLN 2.7 15.8 + - - +
113u GLU* 2.8 13.0 + - + +
115u GLU* 1.3 71.8 - - - +
117u GLU* 1.3 58.0 + - - +
119u GLU* 2.8 35.7 + - + +
120u LYS* 3.3 26.2 + - + +
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Residues in contact with GLU 117 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103t GLN* 3.2 21.1 - - + +
113u GLU 2.4 22.6 + - - +
114u TYR* 3.3 15.9 - - + +
116u LYS* 1.3 74.9 - - - +
118u LEU* 1.3 57.5 + - - +
120u LYS* 3.4 33.7 + - - +
121u MET* 3.6 29.4 + - - +
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Residues in contact with LEU 118 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100t SER* 4.2 19.3 - - - +
103t GLN* 3.4 39.7 - - + +
104t ILE* 4.0 31.6 - - + +
107t ALA* 5.8 3.6 - - + -
114u TYR* 2.8 17.7 + - + +
115u GLU* 3.0 15.2 + - + +
117u GLU* 1.3 75.7 - - - +
119u GLU* 1.3 68.5 + - - +
121u MET* 3.4 8.1 + - + +
122u ARG* 3.1 18.9 + - - +
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Residues in contact with GLU 119 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115u GLU 2.9 11.9 + - - +
116u LYS* 2.8 26.4 + - + +
118u LEU* 1.3 71.6 - - - +
120u LYS* 1.3 69.2 + - + +
122u ARG* 2.8 48.9 + - - +
123u ASN* 3.8 10.8 + - - +
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Residues in contact with LYS 120 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116u LYS* 3.3 26.8 + - + +
117u GLU* 3.4 34.2 + - - +
119u GLU* 1.3 80.0 - - + +
121u MET* 1.3 56.5 + - + +
123u ASN* 2.6 41.7 + - - +
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Residues in contact with MET 121 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96t VAL* 3.3 57.4 - - + +
97t LYS* 5.8 0.2 + - - -
99t ALA* 3.7 6.7 - - + -
100t SER* 3.5 27.1 - - - +
103t GLN* 3.4 22.7 - - - +
117u GLU* 3.6 27.7 + - - +
118u LEU* 3.4 9.1 + - + +
119u GLU 3.1 0.8 + - - -
120u LYS* 1.3 80.1 - - + +
122u ARG* 1.3 58.6 + - - +
123u ASN 3.1 8.7 + - - +
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Residues in contact with ARG 122 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118u LEU 3.1 10.0 + - - +
119u GLU* 2.8 36.7 + - - +
121u MET* 1.3 76.2 - - - +
123u ASN* 1.3 78.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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