Contacts of the helix formed by residues 104 - 120 (chain A) in PDB entry 3N9Z
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 LYS 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A GLU* 3.9 33.5 + - + +
83A LEU* 6.5 1.3 - - + -
102A LEU 5.6 0.9 - - - +
103A LYS* 1.3 76.0 - - - +
105A SER* 1.3 82.0 + - - +
107A ALA* 3.4 8.2 + - - +
108A TRP* 3.1 15.5 + - - -
421A ARG* 4.5 4.3 - - - +
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Residues in contact with SER 105 (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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78A ASN* 3.5 41.1 + - - +
79A PRO 5.9 0.2 + - - -
80A GLU* 5.4 1.4 - - - +
104A LYS* 1.3 86.7 + - - +
106A ALA* 1.3 71.4 + - - +
107A ALA* 4.3 1.4 + - - +
108A TRP* 3.1 4.5 + - - +
109A LYS 3.0 18.2 + - - -
421A ARG* 5.6 0.4 - - - +
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Residues in contact with ALA 106 (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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78A ASN* 4.4 4.7 - - - +
105A SER* 1.3 84.4 + - - +
107A ALA* 1.3 59.5 + - - +
109A LYS* 3.4 8.8 + - - +
110A LYS* 3.1 24.9 + - - +
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A LYS* 3.7 26.5 + - + +
104A LYS 3.4 7.4 + - - +
105A SER* 3.3 1.8 + - - +
106A ALA* 1.3 76.3 - - - +
108A TRP* 1.3 64.5 + - - +
110A LYS* 3.7 7.3 + - - +
111A ASP* 3.5 17.5 + - - +
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Residues in contact with TRP 108 (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 PRO 4.0 11.2 - - - -
78A ASN* 3.7 24.9 - - + -
79A PRO* 4.2 6.1 - - + -
100A VAL* 3.2 40.1 - - + +
103A LYS* 3.8 9.1 - - - +
104A LYS* 3.1 27.9 + - - +
105A SER 3.1 8.5 + - - +
107A ALA* 1.3 77.2 - - - +
109A LYS* 1.3 85.9 + - + +
111A ASP* 3.3 4.5 + - - +
112A ARG* 2.9 49.9 + - + +
420A VAL* 3.6 37.0 - - + -
421A ARG* 3.2 34.9 - - + +
601A HEM 2.9 19.6 + - - -
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Residues in contact with LYS 109 (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 PRO* 4.8 9.0 + - - +
78A ASN* 3.7 17.9 - - - +
105A SER 3.0 6.3 + - - +
106A ALA* 3.6 11.4 - - - +
108A TRP* 1.3 98.0 - - + +
110A LYS* 1.3 56.1 + - - +
112A ARG* 4.4 2.5 - - + -
113A VAL* 2.9 50.0 + - + +
420A VAL* 4.9 4.9 - - - +
45C ALA* 2.5 43.6 + - - +
46C CYS* 4.8 1.0 - - - +
47C GLU* 3.9 9.4 - - - -
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Residues in contact with LYS 110 (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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106A ALA 3.1 16.6 + - - +
107A ALA* 4.0 7.4 - - - +
108A TRP 3.3 0.2 - - - -
109A LYS* 1.3 75.5 - - - +
111A ASP* 1.3 65.7 + - - +
113A VAL* 4.3 3.8 - - - +
114A ALA* 3.3 23.0 + - - +
271A LYS* 4.3 28.4 + - + -
272A MET* 5.2 4.4 - - + +
273A SER 6.2 0.2 - - - +
276A ASP* 5.4 9.7 + - - +
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Residues in contact with ASP 111 (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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99A GLY 4.3 0.2 - - - -
100A VAL* 4.1 15.6 + - + -
103A LYS* 2.8 36.6 + - + +
107A ALA 3.5 7.3 + - - +
108A TRP 3.3 8.1 + - - +
110A LYS* 1.3 81.9 - - - +
112A ARG* 1.3 60.7 + - - +
114A ALA 3.3 1.7 + - - -
115A LEU* 2.9 34.7 + - - +
272A MET* 3.3 24.7 - - + +
276A ASP* 3.8 12.9 - - - +
280A ASN* 2.8 23.1 + - - +
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Residues in contact with ARG 112 (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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100A VAL* 4.0 7.8 - - + +
108A TRP* 2.9 46.9 + - + +
109A LYS* 3.3 4.7 + - + +
111A ASP* 1.3 73.1 - - - +
113A VAL* 1.3 55.9 + - + +
115A LEU* 3.2 3.0 + - - -
116A ASN* 2.8 73.1 + - - +
120A MET* 3.9 13.3 - - - +
420A VAL* 3.4 21.9 + - + +
421A ARG* 3.7 3.4 - - - +
422A GLN* 2.9 32.3 + - - +
423A CYS 3.7 11.5 + - - -
424A LEU* 3.6 19.9 - - - +
601A HEM 2.9 32.9 + - - +
51C ALA* 5.0 1.4 - - - +
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Residues in contact with VAL 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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109A LYS* 2.9 47.8 + - + +
110A LYS* 4.3 4.0 - - - +
112A ARG* 1.3 76.9 - - + +
114A ALA* 1.3 63.7 + - - +
116A ASN* 3.7 8.0 + - - +
117A GLN* 3.2 30.7 + - + +
45C ALA 4.8 0.2 - - - +
46C CYS* 4.7 10.5 - - - +
47C GLU* 3.4 31.4 - - + +
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Residues in contact with ALA 114 (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 LYS 3.3 16.5 + - - +
111A ASP 3.3 4.9 + - - +
113A VAL* 1.3 80.8 - - - +
115A LEU* 1.3 63.4 + - - +
117A GLN* 3.7 16.9 + - - +
118A GLU* 4.1 2.1 + - - +
266A LEU* 3.9 14.0 - - + +
270A SER* 4.9 11.4 - - - +
271A LYS* 5.1 7.2 - - + +
272A MET* 4.0 29.6 - - + +
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Residues in contact with LEU 115 (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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100A VAL* 4.2 10.3 - - + -
111A ASP 2.9 21.0 + - - +
112A ARG 3.2 3.3 + - - +
114A ALA* 1.3 74.4 - - - +
116A ASN* 1.3 60.1 + - - +
117A GLN 3.2 0.2 - - - -
118A GLU* 2.9 19.9 + - - +
119A VAL* 3.0 20.5 + - + +
266A LEU* 3.9 28.7 - - + -
272A MET* 3.5 16.6 - - + -
280A ASN* 3.5 37.9 - - + +
284A MET* 4.7 12.6 - - - -
424A LEU* 3.7 34.3 - - + -
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Residues in contact with ASN 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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112A ARG* 2.8 57.7 + - - +
113A VAL* 4.0 7.8 - - - +
115A LEU* 1.3 70.9 - - - +
117A GLN* 1.3 59.2 + - - +
120A MET* 3.0 28.5 + - + +
121A ALA* 3.0 30.0 + - - +
420A VAL 5.0 2.0 + - - -
424A LEU* 3.5 3.5 - - - +
46C CYS* 4.3 14.4 + - - +
49C THR* 3.6 20.2 + - + +
51C ALA* 3.9 17.4 - - - +
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Residues in contact with GLN 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 VAL* 3.2 25.5 - - + +
114A ALA* 3.7 11.2 - - - +
115A LEU 3.2 0.8 - - - -
116A ASN* 1.3 77.9 - - - +
118A GLU* 1.3 71.8 + - + +
121A ALA* 4.0 9.8 - - - +
124A ALA* 3.3 16.6 - - - +
265A ARG* 5.4 0.3 + - - -
47C GLU* 4.6 6.5 + - - +
49C THR* 3.2 26.4 - - - +
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Residues in contact with GLU 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 ALA 4.4 3.8 - - - +
115A LEU 2.9 7.3 + - - +
117A GLN* 1.3 91.2 - - + +
119A VAL* 1.3 62.0 + - + +
124A ALA* 3.4 13.6 - - - +
128A PHE* 3.3 20.4 - - - -
259A TYR* 4.7 2.8 + - - -
262A ILE* 4.1 21.7 - - + +
265A ARG* 3.1 59.8 + - + +
266A LEU* 3.8 25.4 - - + +
269A ASP 4.8 7.0 - - - +
270A SER* 6.0 0.7 - - - -
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Residues in contact with VAL 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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115A LEU* 3.0 20.8 + - + +
118A GLU* 1.3 82.6 - - + +
120A MET* 1.3 64.9 + - + +
125A THR* 3.5 16.3 - - - +
128A PHE* 3.9 8.8 - - - -
262A ILE* 3.9 18.4 - - + -
284A MET* 3.8 28.9 - - + -
424A LEU* 3.5 44.5 - - + +
427A ARG* 3.8 10.0 - - - +
428A ILE* 4.2 16.5 - - + +
601A HEM 6.1 0.2 - - + -
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Residues in contact with MET 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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112A ARG* 3.9 8.3 - - - +
116A ASN* 3.0 33.4 + - + +
119A VAL* 1.3 81.0 - - + +
121A ALA* 1.3 67.3 + - - +
122A PRO* 3.6 3.1 - - - +
125A THR* 3.6 3.4 + - - +
422A GLN* 3.9 20.4 - - - +
423A CYS 3.8 17.5 - - - +
424A LEU* 3.5 26.2 - - + +
426A ARG* 4.3 1.8 - - + -
427A ARG* 3.5 50.0 + - - +
49C THR 3.6 14.3 - - - +
50C LEU* 4.9 0.7 - - - +
51C ALA* 3.6 26.0 - - + -
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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
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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