Contacts of the helix formed by residues 116 - 130 (chain A) in PDB entry 2NBV
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A GLU* 6.2 1.6 - - + -
113A LYS 4.1 5.7 + - - +
114A THR 3.1 0.4 - - - -
115A ASP* 1.3 99.5 - - + +
117A ASP* 1.3 60.2 + - - +
118A GLU 3.5 2.0 - - - -
119A GLU* 3.5 33.0 - - + +
120A HIS* 2.9 50.1 + - + +
123A LYS* 5.8 1.8 - - - +
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Residues in contact with ASP 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLY 4.7 1.7 - - - +
92A ARG* 2.7 56.5 + - - +
94A TYR* 3.4 17.8 + - - +
109A MET* 3.4 28.0 - - - +
111A GLU* 4.7 2.6 - - - +
113A LYS 4.0 1.4 - - - +
114A THR* 3.2 27.4 + - - +
115A ASP 3.5 0.2 - - - -
116A GLN* 1.3 80.8 - - - +
118A GLU* 1.3 65.5 + - + +
120A HIS* 3.4 4.6 + - - +
121A CYS* 3.2 15.1 + - - +
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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
----------------------------------------------------------
84A ARG* 3.9 18.7 + - - +
94A TYR* 2.7 30.9 + - - +
114A THR 4.7 1.2 + - - -
115A ASP 5.4 0.4 + - - -
117A ASP* 1.3 77.9 - - + +
119A GLU* 1.3 60.5 + - - +
121A CYS* 3.1 10.5 + - - +
122A ARG* 2.8 41.4 + - - +
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP 4.8 1.7 + - - +
116A GLN* 3.5 47.7 - - + +
117A ASP 3.2 0.4 - - - -
118A GLU* 1.3 80.0 - - - +
120A HIS* 1.3 63.2 + - + +
122A ARG* 2.7 43.9 + - - +
123A LYS* 3.1 56.3 + - - +
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Residues in contact with HIS 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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24A VAL* 4.6 8.4 - - + +
25A GLU 3.8 10.6 + - - -
26A PHE* 3.5 45.5 - + + +
109A MET* 4.1 10.1 - - + -
111A GLU* 4.0 24.5 - - + +
116A GLN* 2.9 39.1 + - + +
117A ASP* 3.6 6.5 + - - +
119A GLU* 1.3 76.9 - - + +
121A CYS* 1.3 63.7 + - - +
123A LYS* 3.3 14.1 + - + +
124A VAL* 3.0 28.9 + - - +
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Residues in contact with CYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A PHE* 3.5 31.6 - - + -
83A LYS* 4.4 3.4 - - - -
84A ARG 5.0 0.4 - - - -
94A TYR* 3.5 34.5 - - + -
109A MET* 4.7 0.8 - - + +
117A ASP 3.2 4.0 + - - +
118A GLU* 3.1 17.2 + - - +
120A HIS* 1.3 79.6 - - - +
122A ARG* 1.3 62.1 + - - +
124A VAL* 3.3 1.9 + - - +
125A ASN* 2.8 47.6 + - - -
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Residues in contact with ARG 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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118A GLU* 2.8 26.2 + - - +
119A GLU* 2.7 46.7 + - - +
121A CYS* 1.3 73.4 - - - +
123A LYS* 1.3 63.9 + - + +
125A ASN* 3.4 6.2 + - - +
126A GLU* 3.0 45.3 + - + +
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Residues in contact with LYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 5.8 1.1 + - - +
24A VAL* 4.0 28.3 - - + -
116A GLN* 5.8 1.4 - - - +
119A GLU* 3.1 45.3 + - + +
120A HIS* 3.5 14.8 - - + +
122A ARG* 1.3 77.7 - - + +
124A VAL* 1.3 62.8 + - - +
126A GLU* 3.2 10.8 + - - +
127A TYR* 2.9 41.0 + - + -
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Residues in contact with VAL 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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24A VAL* 4.3 4.0 - - + -
26A PHE* 3.5 31.0 - - + -
49A ILE* 3.8 16.4 - - + -
59A PHE* 3.9 16.4 - - + -
82A PHE* 3.9 24.9 - - + -
120A HIS 3.0 19.9 + - - +
121A CYS 3.5 7.4 - - - +
123A LYS* 1.3 76.3 - - - +
125A ASN* 1.3 64.2 + - - +
127A TYR 3.4 0.5 + - - -
128A LEU* 2.9 50.5 + - + +
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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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81A GLU* 4.2 5.4 - - - +
82A PHE* 2.7 52.8 + - - +
121A CYS* 2.8 36.1 + - - +
122A ARG* 3.8 6.6 - - - +
123A LYS 3.3 0.2 - - - -
124A VAL* 1.3 76.4 - - - +
126A GLU* 1.3 63.7 + - + +
128A LEU* 4.0 4.4 - - - +
129A ASN* 3.1 36.3 + - - +
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Residues in contact with GLU 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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122A ARG* 3.0 34.1 + - + +
123A LYS* 3.5 14.4 - - - +
125A ASN* 1.3 76.4 - - + +
127A TYR* 1.3 62.2 + - + +
130A ASN* 2.8 49.8 + - + +
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Residues in contact with TYR 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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23A LEU* 3.8 42.8 + - + -
24A VAL* 3.5 21.3 - - + -
49A ILE* 3.9 20.2 - - + -
57A ILE* 4.0 21.0 - - + +
123A LYS* 2.9 41.1 + - + +
126A GLU* 1.3 81.0 - - + +
128A LEU* 1.3 62.3 + - - +
130A ASN 3.8 15.6 - - - +
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Residues in contact with LEU 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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49A ILE* 3.8 16.6 - - + -
57A ILE* 3.7 31.3 - - + +
59A PHE* 3.9 15.0 - - + -
75A ILE* 3.7 38.9 - - + +
76A PHE* 4.3 1.2 - - - -
77A PRO* 4.1 12.3 - - - +
80A CYS* 4.9 8.3 - - + -
81A GLU 6.4 0.2 - - - -
82A PHE* 5.3 1.3 - - + -
96A LEU* 4.1 20.2 - - + -
124A VAL* 2.9 41.9 + - + +
125A ASN* 4.0 4.9 - - - +
127A TYR* 1.3 80.1 - - - +
129A ASN* 1.3 64.1 + - - +
130A ASN 3.6 1.4 + - - -
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Residues in contact with ASN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A PHE 4.2 1.4 - - - +
77A PRO* 3.3 43.7 - - + +
78A ASP 3.3 9.1 + - - -
79A ASP 4.4 0.2 + - - -
80A CYS* 3.4 30.6 + - - +
125A ASN* 3.1 24.8 + - - +
128A LEU* 1.3 81.4 - - - +
130A ASN* 1.3 69.5 + - - +
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Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 6.1 2.5 - - - -
77A PRO* 5.9 1.6 - - - -
126A GLU* 2.8 28.1 + - + +
127A TYR* 3.8 18.6 - - - +
128A LEU 4.7 1.6 - - - -
129A ASN* 1.3 90.7 + - - +
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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