Contacts of the helix formed by residues 104 - 122 (chain B) in PDB entry 1N33
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 ASN 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1073A U 3.2 31.4 + - - -
1074A G 3.3 39.9 + - - +
1101A A 6.0 0.2 - - + -
1102A A 4.2 9.7 - - - +
1103A C 5.9 0.8 - - - -
99B GLY 5.4 0.4 - - - +
100B GLY* 2.4 33.4 + - - +
103B THR* 1.3 71.1 - - - +
105B PHE* 1.3 61.2 + - - +
106B LYS* 4.4 2.6 + - - +
107B THR* 3.4 27.0 + - - +
108B ILE* 3.3 15.4 + - + +
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Residues in contact with PHE 105 (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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101B MET 2.8 27.5 + - - +
102B LEU* 3.1 12.2 + - + +
103B THR 3.4 1.6 + - - -
104B ASN* 1.3 73.1 - - - +
106B LYS* 1.3 72.9 + - - +
107B THR 2.7 2.8 + - - -
108B ILE 2.7 14.6 + - - -
109B SER* 2.7 30.5 + - - -
152B PHE* 3.3 28.5 - + - -
155B LEU* 3.3 40.8 - - + -
156B LYS* 4.0 20.4 - - - -
157B ARG* 4.4 0.9 - - - -
158B LEU* 3.6 28.9 - - + -
159B PRO* 5.5 0.9 - - + -
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Residues in contact with LYS 106 (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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104B ASN* 3.7 2.7 - - - +
105B PHE* 1.3 80.0 - - - +
107B THR* 1.3 64.6 + - - +
109B SER* 2.8 25.0 - - - -
110B GLN* 3.0 16.5 + - + +
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Residues in contact with THR 107 (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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1072A G 3.6 12.7 + - - +
1073A U 4.0 10.4 + - - -
1103A C 3.6 35.6 + - - +
1104A G 5.2 2.7 - - - +
104B ASN* 3.4 24.1 + - - +
105B PHE 2.7 5.1 + - - -
106B LYS* 1.3 74.2 - - - +
108B ILE* 1.3 54.6 + - + +
109B SER 2.4 16.3 + - - -
110B GLN* 2.6 44.2 + - + +
111B ARG* 3.5 2.8 + - - +
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Residues in contact with ILE 108 (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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1103A C 4.7 23.6 - - - +
98B LEU* 4.2 23.1 - - + -
99B GLY 3.5 15.0 - - - +
100B GLY* 3.2 5.2 - - - -
101B MET* 3.0 45.5 - - + +
104B ASN* 3.3 18.7 + - + +
105B PHE 2.7 8.7 + - - +
107B THR* 1.3 72.1 - - - +
109B SER* 1.3 56.3 + - - +
111B ARG* 4.2 14.6 - - + +
112B VAL* 4.5 4.2 - - - +
149B LEU* 5.0 2.8 - - + +
152B PHE* 3.6 30.5 - - + -
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Residues in contact with SER 109 (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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105B PHE* 2.7 46.9 + - - -
106B LYS* 2.8 16.2 - - - -
107B THR 2.4 5.7 + - - -
108B ILE* 1.3 76.2 + - - +
110B GLN* 1.3 51.4 + - - -
111B ARG 2.5 17.2 + - - -
112B VAL* 2.7 36.0 + - - +
113B HIS* 3.3 8.1 + - - -
152B PHE* 5.5 0.8 - - - -
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Residues in contact with GLN 110 (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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1072A G 4.7 2.6 + - - -
1104A G 5.3 5.2 + - - +
106B LYS* 3.0 24.1 + - + +
107B THR* 2.6 44.7 + - + +
109B SER* 1.3 70.1 - - - +
111B ARG* 1.3 68.1 + - - +
113B HIS* 3.9 14.0 + - - +
114B ARG* 3.6 17.3 - - - +
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Residues in contact with ARG 111 (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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1103A C 4.0 15.7 - - - +
1104A G 2.9 73.3 + - - +
1105A A 3.8 8.9 + - - -
107B THR 3.5 4.4 + - - +
108B ILE* 4.2 10.8 - - + +
109B SER 2.5 5.3 + - - -
110B GLN* 1.3 76.3 + - - +
112B VAL* 1.3 55.7 + - - +
113B HIS 3.1 1.1 - - - -
114B ARG* 2.6 53.5 + - - +
115B LEU* 3.2 5.1 + - - +
141B GLU* 4.9 19.4 + - - +
145B LEU* 4.9 14.6 - - + +
149B LEU* 3.7 22.0 - - + -
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Residues in contact with VAL 112 (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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108B ILE 4.5 8.5 - - - +
109B SER* 2.7 35.5 + - - +
111B ARG* 1.3 71.7 - - - +
113B HIS* 1.3 74.1 + - + +
114B ARG 2.6 12.5 + - - -
115B LEU* 2.8 17.3 + - - +
116B GLU* 3.0 21.0 + - - +
149B LEU* 4.1 14.6 - - + -
152B PHE* 4.4 8.1 - - + +
153B ARG* 3.3 50.3 - - + +
155B LEU 6.0 0.9 - - - +
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Residues in contact with HIS 113 (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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109B SER* 4.0 8.9 + - - +
110B GLN* 3.9 14.4 - - - +
111B ARG 3.0 1.2 + - - -
112B VAL* 1.3 90.8 - - + +
114B ARG* 1.3 63.8 + - + +
116B GLU* 3.1 25.5 + - - +
117B GLU* 3.7 11.4 - - - +
156B LYS* 5.6 11.2 - - + -
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Residues in contact with ARG 114 (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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110B GLN 3.6 13.9 - - - +
111B ARG* 2.6 33.3 + - - +
112B VAL 2.6 5.7 + - - -
113B HIS* 1.3 77.7 - - + +
115B LEU* 1.3 52.7 + - - -
117B GLU* 3.2 28.1 + - - +
118B LEU* 2.7 55.2 + - - +
137B ARG* 6.0 0.6 - - - +
138B LEU* 6.2 0.4 - - - +
141B GLU* 2.5 39.8 + - - +
145B LEU* 4.6 4.7 - - + -
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Residues in contact with LEU 115 (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 ARG 3.2 4.8 + - - +
112B VAL* 2.8 8.5 + - - +
114B ARG* 1.3 75.8 - - - +
116B GLU* 1.3 69.4 + - - +
117B GLU 2.8 1.1 - - - -
118B LEU* 2.7 14.4 + - - +
119B GLU* 3.0 35.9 + - - +
142B LEU* 3.6 21.3 - - + -
145B LEU* 3.5 37.2 - - + +
146B GLN* 4.1 8.1 - - + +
149B LEU* 4.4 12.8 - - + +
150B SER* 5.7 1.6 - - - -
153B ARG* 3.7 36.1 - - + +
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Residues in contact with GLU 116 (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 VAL* 3.0 13.6 + - - +
113B HIS* 3.1 43.9 + - - -
115B LEU* 1.3 81.0 - - - +
117B GLU* 1.3 64.5 + - + +
119B GLU* 3.6 6.8 + - - +
120B ALA* 3.4 18.0 + - - +
153B ARG* 3.1 43.5 + - - +
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Residues in contact with GLU 117 (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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113B HIS 3.7 20.9 - - - +
114B ARG* 3.2 32.4 + - - +
115B LEU 2.8 0.8 - - - -
116B GLU* 1.3 81.3 - - + +
118B LEU* 1.3 83.0 + - - +
119B GLU 3.0 1.8 - - - -
120B ALA* 3.1 22.3 + - + +
121B LEU* 3.4 12.9 + - - +
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Residues in contact with LEU 118 (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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114B ARG* 2.7 50.1 + - - +
115B LEU* 2.7 12.2 + - - +
117B GLU* 1.3 83.5 + - - +
119B GLU* 1.3 58.2 + - - +
121B LEU* 3.9 9.9 + - + +
122B PHE* 3.6 16.9 - - + -
138B LEU* 3.6 46.0 - - + +
141B GLU* 3.3 13.2 - - - +
142B LEU* 3.7 31.4 - - + +
145B LEU* 5.1 0.4 - - + -
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Residues in contact with GLU 119 (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 LEU* 3.0 31.2 + - + +
116B GLU* 3.6 9.3 - - - +
118B LEU* 1.3 76.4 - - - +
120B ALA* 1.3 55.5 + - - +
121B LEU 3.0 5.4 - - - -
122B PHE* 2.8 35.3 + - + +
123B ALA* 5.2 1.4 - - - +
142B LEU* 4.1 13.7 - - + -
146B GLN* 3.8 17.2 + - - +
153B ARG* 3.1 27.4 + - - -
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Residues in contact with ALA 120 (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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116B GLU 3.4 12.4 + - - +
117B GLU* 3.1 16.4 + - + +
119B GLU* 1.3 78.1 - - - +
121B LEU* 1.3 57.3 + - + +
122B PHE 3.2 2.2 + - - -
123B ALA* 4.4 3.3 + - - +
124B SER* 3.6 16.6 + - - -
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Residues in contact with LEU 121 (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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117B GLU* 3.4 15.6 + - - +
118B LEU* 4.3 8.5 - - + +
119B GLU 3.0 1.0 - - - -
120B ALA* 1.3 76.5 - - - +
122B PHE* 1.3 66.3 + - - +
123B ALA 3.4 5.2 + - - -
124B SER* 3.4 16.2 - - - +
126B GLU* 3.3 50.3 - - + +
127B ILE* 4.1 13.4 - - - +
138B LEU* 5.4 17.7 - - + +
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Residues in contact with PHE 122 (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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118B LEU* 3.6 15.9 - - + -
119B GLU* 2.8 22.4 + - + +
120B ALA 3.2 0.2 - - - -
121B LEU* 1.3 85.5 - - + +
123B ALA* 1.3 64.1 + - - +
127B ILE* 4.3 11.9 - - + -
138B LEU* 4.5 19.7 - - + -
139B LYS* 3.4 45.5 - - + -
142B LEU* 4.2 17.3 - - + -
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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