Contacts of the helix formed by residues 112 - 131 (chain A) in PDB entry 3N4U
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 PRO 112 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASN 3.8 4.0 - - - +
111A LEU* 1.3 102.8 - - + +
113A LYS* 1.3 60.2 + - - +
114A GLN* 4.5 5.2 - - + +
115A SER* 3.4 18.1 + - - +
116A GLN* 3.0 21.8 + - - +
210A ASN* 4.2 15.7 - - - +
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Residues in contact with LYS 113 (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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111A LEU 3.6 0.4 + - - -
112A PRO* 1.3 70.6 - - - +
114A GLN* 1.3 68.4 + - + +
116A GLN* 3.1 25.8 + - - +
117A ASN* 3.1 40.9 + - - +
247A LYS* 5.9 2.0 - - - -
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Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PRO* 3.5 4.6 - - + +
113A LYS* 1.3 78.2 - - + +
115A SER* 1.3 58.7 + - - +
117A ASN* 3.4 9.5 + - - +
118A GLN* 3.1 26.0 + - - +
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A LEU* 5.2 0.2 - - - +
111A LEU* 4.3 18.6 - - - +
112A PRO* 3.4 22.7 + - - +
113A LYS 3.1 0.6 - - - -
114A GLN* 1.3 78.0 - - - +
116A GLN* 1.3 65.1 + - - +
117A ASN 3.2 1.3 - - - -
118A GLN* 3.9 7.1 - - - +
119A ALA* 3.2 22.9 + - - +
205A PHE* 5.5 0.7 - - - -
210A ASN* 3.8 35.0 + - - +
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Residues in contact with GLN 116 (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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108A LEU* 3.1 38.1 - - + +
109A ASN* 2.8 32.8 - - - +
111A LEU* 2.8 12.5 - - + +
112A PRO 3.0 15.9 + - - +
113A LYS* 3.1 29.8 + - + +
115A SER* 1.3 76.0 - - - +
117A ASN* 1.3 64.7 + - - +
119A ALA* 3.4 1.9 + - - +
120A ALA* 3.3 16.5 + - - +
243A GLU* 5.0 9.3 + - - -
244A PHE* 3.3 18.3 - - + -
247A LYS* 6.2 1.5 - - - +
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Residues in contact with ASN 117 (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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113A LYS* 3.1 31.3 + - - +
114A GLN* 3.6 10.4 - - - +
116A GLN* 1.3 76.9 - - - +
118A GLN* 1.3 66.1 + - - +
120A ALA* 3.3 7.8 + - - +
121A LYS* 3.1 37.4 + - - +
247A LYS* 3.4 29.8 - - - +
251A HIS* 4.7 3.3 - - + -
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Residues in contact with GLN 118 (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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114A GLN 3.1 16.5 + - - +
115A SER* 3.9 8.1 - - - +
116A GLN 3.4 0.4 - - - -
117A ASN* 1.3 76.3 - - - +
119A ALA* 1.3 58.2 + - - +
121A LYS* 3.2 28.6 + - - +
122A ASP* 2.8 67.0 + - - +
210A ASN 5.7 0.9 - - - +
211A THR* 5.0 14.4 - - + -
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Residues in contact with ALA 119 (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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103A LEU* 4.3 10.5 - - + -
108A LEU* 4.6 5.2 - - + -
115A SER 3.2 17.5 + - - +
116A GLN 3.6 5.6 - - - +
117A ASN 3.2 0.2 - - - -
118A GLN* 1.3 74.9 - - - +
120A ALA* 1.3 66.6 + - - +
122A ASP* 3.4 2.4 + - - -
123A LEU* 3.0 28.6 + - - +
205A PHE* 5.2 5.6 - - + -
211A THR* 6.5 0.2 - - - -
212A ILE* 3.7 27.3 - - + +
244A PHE* 3.9 13.2 - - + -
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Residues in contact with ALA 120 (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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116A GLN 3.3 5.6 + - - +
117A ASN* 3.6 8.3 - - - +
118A GLN 3.3 0.2 - - - -
119A ALA* 1.3 79.1 - - - +
121A LYS* 1.3 57.8 + - - +
123A LEU* 3.5 2.4 + - - +
124A ALA* 3.0 28.4 + - - +
244A PHE* 3.5 26.8 - - + -
247A LYS* 3.7 31.0 - - + -
248A ILE* 3.7 16.0 - - + +
251A HIS* 4.5 4.7 - - + +
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 3.1 22.7 + - - +
118A GLN* 3.2 32.5 + - - +
120A ALA* 1.3 74.3 - - - +
122A ASP* 1.3 66.5 + - - +
124A ALA* 3.2 2.6 + - - +
125A ARG* 3.0 24.3 + - - +
251A HIS* 3.4 48.2 - - + +
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Residues in contact with ASP 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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72A PRO* 5.6 0.7 - - - +
73A LEU* 4.2 23.3 - - + +
118A GLN* 2.8 54.2 + - - +
119A ALA* 4.0 4.3 - - - +
121A LYS* 1.3 72.3 - - - +
123A LEU* 1.3 57.4 - - - +
125A ARG* 3.5 22.9 + - - +
126A PHE* 2.9 28.6 + - - +
211A THR* 4.7 7.3 - - - +
212A ILE* 4.5 21.1 + - + +
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Residues in contact with LEU 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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73A LEU* 4.5 3.6 - - + -
103A LEU* 5.1 2.2 - - + -
119A ALA 3.0 18.7 + - - +
120A ALA 3.6 4.0 - - - +
122A ASP* 1.3 75.3 - - - +
124A ALA* 1.3 64.2 + - - +
126A PHE* 3.3 3.9 + - - +
127A LEU* 3.0 30.1 + - - +
198A PHE* 3.9 24.9 - - + -
203A ILE* 3.9 33.9 - - + -
212A ILE* 3.7 23.6 - - + -
215A ILE* 4.2 8.5 - - + -
233A LEU* 5.3 0.7 - - + -
240A TYR* 4.9 1.8 - - + -
244A PHE* 3.8 28.3 - - + -
248A ILE* 3.8 16.6 - - + -
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Residues in contact with ALA 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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120A ALA 3.0 14.7 + - - +
121A LYS 3.5 7.6 - - - +
123A LEU* 1.3 77.0 - - - +
125A ARG* 1.3 57.4 + - - +
127A LEU* 3.3 1.5 + - - -
128A SER* 2.9 30.2 + - - -
248A ILE* 3.4 33.5 - - + +
251A HIS* 3.6 19.1 - - + +
252A TYR* 3.6 17.1 - - + +
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Residues in contact with ARG 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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72A PRO* 3.6 44.2 + - + +
73A LEU* 5.9 1.8 - - - +
121A LYS 3.0 17.1 + - - +
122A ASP* 3.9 19.5 + - - +
124A ALA* 1.3 73.1 - - - +
126A PHE* 1.3 67.3 + - - +
128A SER* 3.5 6.5 + - - -
129A GLU* 3.2 24.1 + - + +
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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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71A LEU* 3.5 35.8 - - + +
72A PRO* 3.9 13.5 - - + +
73A LEU* 3.6 43.3 - - + -
75A ILE* 4.1 2.5 - - + -
122A ASP 2.9 18.6 + - - +
123A LEU* 3.5 5.8 - - - +
124A ALA 3.2 0.2 - - - -
125A ARG* 1.3 76.9 - - - +
127A LEU* 1.3 66.8 + - + +
129A GLU* 3.4 2.3 + - - +
130A LEU* 3.0 38.2 + - + +
195A HIS* 5.4 1.1 - + - -
198A PHE* 4.0 26.9 - + + -
215A ILE* 3.6 29.8 - - + -
218A PHE* 4.2 9.6 - + - -
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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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123A LEU 3.0 19.4 + - - +
124A ALA 3.9 2.5 - - - +
126A PHE* 1.3 84.2 - - + +
128A SER* 1.3 58.1 + - - +
130A LEU* 4.2 5.8 - - + -
131A HIS* 2.8 45.7 + - + +
198A PHE* 3.3 50.3 - - + -
229A ASP* 3.8 33.7 - - + +
230A PHE* 3.8 26.9 - - + -
233A LEU* 4.8 1.3 - - + -
248A ILE* 4.7 6.3 - - + -
252A TYR* 3.8 7.9 - - + -
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Residues in contact with SER 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 ALA 2.9 18.2 + - - -
125A ARG* 3.7 9.4 - - - -
126A PHE 3.2 0.2 - - - -
127A LEU* 1.3 78.2 - - - +
129A GLU* 1.3 64.0 + - - +
131A HIS* 3.8 2.3 - - - +
132A SER* 3.2 24.4 + - - -
252A TYR* 3.5 26.1 + - - -
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Residues in contact with GLU 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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70A LYS 4.3 10.5 - - - +
71A LEU* 4.3 7.7 - - + +
72A PRO* 3.8 24.7 - - + -
125A ARG* 3.2 21.8 + - + +
126A PHE 3.9 2.5 - - - +
128A SER* 1.3 75.0 - - - +
130A LEU* 1.3 66.0 + - - +
132A SER* 3.2 16.1 + - - -
133A ILE* 3.3 15.9 + - - +
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Residues in contact with LEU 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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67A ILE* 4.7 6.5 - - + -
71A LEU* 4.0 26.8 - - + +
126A PHE* 3.0 33.0 + - + +
127A LEU* 3.3 8.0 + - + +
129A GLU* 1.3 78.5 - - - +
131A HIS* 1.3 62.1 + - + +
132A SER 3.2 1.4 + - - -
133A ILE* 3.2 21.4 + - + +
193A LEU* 3.7 37.0 - - + +
194A ILE* 3.9 3.1 - - - -
195A HIS* 3.4 36.3 - - + +
218A PHE* 5.2 6.5 - - + -
229A ASP* 3.9 10.3 - - - +
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Residues in contact with HIS 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 2.8 35.8 + - + +
128A SER 3.8 3.4 - - - +
130A LEU* 1.3 80.0 - - + +
132A SER* 1.3 58.9 + - - +
133A ILE 3.4 1.9 - - - +
192A CYS* 3.5 34.8 - - - +
193A LEU 3.2 23.1 - - - -
194A ILE* 4.1 0.9 - - + -
226A PRO* 3.4 29.4 + - + +
229A ASP* 3.0 29.1 + - + -
230A PHE* 4.3 2.9 - + - -
252A TYR* 2.7 32.0 + + - +
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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
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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