Contacts of the helix formed by residues 110 - 127 (chain F) in PDB entry 1NZB
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 110 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F PRO* 3.8 31.4 - - - +
106F ARG 4.2 1.1 + - - -
107F PRO* 3.1 10.8 + - - -
109F ASP* 1.3 79.6 - - - +
111F ASN* 1.3 67.2 + - - +
112F ALA* 3.0 6.4 + - - -
113F VAL* 3.1 4.5 + - - +
114F SER* 2.9 23.3 + - - -
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Residues in contact with ASN 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E ASN* 4.6 16.1 + - - +
29E ASP* 5.2 7.6 - - + +
30E MET* 4.5 4.6 - - - +
100E ARG* 3.3 19.1 - - - +
101E ARG* 2.8 59.4 + - - +
103E GLY* 5.0 1.9 + - - -
109F ASP 4.0 2.0 + - - -
110F SER* 1.3 69.8 + - - +
112F ALA* 1.3 67.0 + - - +
114F SER* 4.2 6.5 - - - -
115F LEU* 2.9 40.2 + - + +
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Residues in contact with ALA 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E LYS* 6.0 2.0 - - - +
29E ASP* 4.7 9.4 - - + +
32E ARG* 3.7 24.7 + - - +
33E ASP* 5.3 0.7 - - - -
68F PRO* 4.7 17.0 - - + +
69F GLU* 4.0 17.7 - - - +
72F ARG* 3.6 12.1 - - - -
110F SER* 3.0 3.4 + - - +
111F ASN* 1.3 82.7 - - - +
113F VAL* 1.3 63.2 + - + +
115F LEU* 4.1 2.1 - - - +
116F VAL* 3.3 20.4 + - - +
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Residues in contact with VAL 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F PRO* 3.4 34.8 - - + +
71F VAL* 3.7 20.9 - - + -
72F ARG* 4.2 2.7 - - - +
75F LEU* 4.4 4.3 - - + -
92F LEU* 3.7 32.5 - - + -
107F PRO* 3.0 30.7 - - + +
108F SER* 3.9 4.9 - - - +
110F SER 3.1 1.8 + - - -
112F ALA* 1.3 78.3 - - - +
114F SER* 1.3 68.7 + - - +
116F VAL* 2.8 23.8 - - - +
117F MET* 3.3 5.5 + - - +
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Residues in contact with SER 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E ARG* 3.3 28.7 + - - -
107F PRO 4.6 0.4 + - - -
108F SER* 4.2 20.0 - - - +
109F ASP 5.6 0.4 - - - -
110F SER 2.9 20.8 + - - -
111F ASN* 3.6 5.4 - - - -
113F VAL* 1.3 77.7 - - - +
115F LEU* 1.3 64.3 + - - +
117F MET* 3.3 16.8 - - - +
118F ARG* 3.5 9.3 + - - +
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Residues in contact with LEU 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ASP 3.9 7.9 - - - +
30E MET* 3.8 35.2 - - + +
33E ASP* 4.3 9.2 - - + +
36E ALA* 3.8 15.4 - - + +
37E PHE* 3.8 24.7 - - + -
101E ARG* 3.5 35.7 - - + +
111F ASN* 2.9 38.1 + - - +
112F ALA* 4.1 1.8 - - - +
114F SER* 1.3 67.6 - - - +
116F VAL* 1.3 66.9 + - - +
117F MET 3.0 1.8 - - - -
118F ARG* 2.7 20.0 + - - +
119F ARG* 2.8 11.0 + - - +
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Residues in contact with VAL 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33E ASP* 4.3 6.8 + - - +
72F ARG* 3.3 53.6 - - + +
75F LEU* 4.5 7.6 - - + -
76F LEU* 3.9 17.7 - - + -
112F ALA 3.3 5.5 + - - +
113F VAL* 2.8 30.5 - - - +
115F LEU* 1.3 75.4 - - - +
117F MET* 1.3 52.5 + - - +
119F ARG* 3.3 10.0 - - + +
120F ILE* 2.7 59.3 + - + +
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Residues in contact with MET 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F LEU* 4.1 5.8 - - + -
85F VAL* 4.5 6.5 - - + +
88F ILE* 3.7 34.3 - - + -
89F GLN* 4.0 33.4 - - + +
92F LEU* 3.8 30.7 - - + -
113F VAL 3.8 6.1 - - - +
114F SER* 3.3 12.7 + - - +
115F LEU 2.8 1.2 + - - -
116F VAL* 1.3 85.7 - - - +
118F ARG* 1.3 64.5 + - + +
120F ILE* 3.1 14.9 + - + -
121F ARG* 2.9 26.5 + - + +
119H A 5.7 2.5 - - - +
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Residues in contact with ARG 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36E ALA* 3.6 31.5 + - + +
37E PHE* 4.7 4.6 - - - -
101E ARG* 4.1 22.2 - - - +
114F SER* 4.0 9.6 + - - +
115F LEU* 2.7 15.6 + - - +
117F MET* 1.3 75.9 - - + +
119F ARG* 1.3 51.4 + - - +
121F ARG* 2.9 29.0 + - - +
122F LYS* 2.7 38.1 + - + +
121G G 5.4 0.8 + - - -
122G C 4.2 36.8 + - - -
123G T 4.5 5.3 + - - -
118H T 4.5 10.9 + - - -
119H A 3.5 36.7 + - - +
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Residues in contact with ARG 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E ARG* 3.9 9.7 + - - +
33E ASP* 2.8 45.5 + - + +
35E GLN* 4.0 21.3 - - + +
36E ALA* 4.1 16.7 - - + +
72F ARG* 4.0 8.2 - - - +
76F LEU* 4.3 24.8 - - - +
79F GLN* 5.2 0.2 + - - -
115F LEU 2.8 11.2 + - - +
116F VAL* 3.3 12.8 - - - +
118F ARG* 1.3 74.6 - - - +
120F ILE* 1.3 66.0 + - - +
121F ARG 2.8 1.4 + - - -
122F LYS* 2.9 4.5 + - - +
123F GLU* 2.8 56.5 + - - +
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Residues in contact with ILE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F LEU* 3.4 40.4 - - + +
76F LEU* 4.1 7.9 - - + +
79F GLN* 3.3 33.7 - - + +
85F VAL* 4.5 2.4 - - + +
88F ILE* 3.7 31.9 - - + -
116F VAL* 2.7 40.5 + - + +
117F MET* 3.5 13.0 - - + +
119F ARG* 1.3 74.0 - - + +
121F ARG* 1.3 62.4 + - - +
123F GLU* 4.1 1.3 - - - +
124F ASN* 2.8 30.7 + - - +
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Residues in contact with ARG 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E LEU* 4.1 22.1 - - + +
85F VAL* 3.6 31.4 - - + +
89F GLN* 4.0 7.2 - - - +
117F MET* 2.9 16.0 + - + +
118F ARG* 3.1 33.8 + - - +
119F ARG 2.8 1.4 + - - -
120F ILE* 1.3 76.6 - - - +
122F LYS* 1.3 79.2 + - - +
124F ASN* 3.8 1.6 - - - +
125F VAL* 3.1 35.9 + - + +
123G T 5.4 3.2 + - - -
118H T 3.8 29.5 + - - -
119H A 2.6 43.4 + - - -
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Residues in contact with LYS 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLN* 3.7 20.8 + - + +
36E ALA 4.9 2.9 - - - -
37E PHE* 3.5 4.2 + - - +
38E SER* 3.1 35.3 - - - +
201E LYS* 5.8 11.4 - - + -
118F ARG* 2.7 20.2 + - + +
119F ARG* 3.6 3.1 - - - +
121F ARG* 1.3 87.1 - - - +
123F GLU* 1.3 65.4 + - + +
125F VAL* 3.3 13.4 + - + +
126F ASP* 3.2 24.7 + - - +
123G T 3.0 32.8 + - - +
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Residues in contact with GLU 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E GLN* 4.8 13.4 - - + +
79F GLN* 3.1 27.3 + - - +
119F ARG* 2.8 60.2 + - + +
122F LYS* 1.3 75.8 - - - +
124F ASN* 1.3 69.4 + - - +
125F VAL 2.9 2.1 + - - -
126F ASP* 3.0 6.7 + - - +
127F ALA* 3.0 21.5 + - - +
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Residues in contact with ASN 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F GLN* 2.5 44.0 + - - +
82F GLY 6.1 0.2 - - - -
83F LEU 4.2 11.9 + - - -
85F VAL* 3.6 16.3 - - + +
88F ILE* 5.1 0.4 - - - +
120F ILE* 2.8 17.7 + - - +
123F GLU* 1.3 73.4 - - - +
125F VAL* 1.3 58.6 + - - +
127F ALA* 3.8 10.4 - - - +
128F GLY 3.6 2.4 + - - -
129F GLU* 2.9 57.8 + - + +
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Residues in contact with VAL 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E THR 3.1 29.4 - - - +
201E LYS* 4.4 4.5 - - - -
202E THR 4.1 13.0 - - - +
203E LEU* 4.1 29.4 - - + +
85F VAL* 5.2 0.9 - - + -
121F ARG* 3.1 27.1 + - + +
122F LYS* 3.6 9.4 - - + +
123F GLU 2.9 1.4 + - - -
124F ASN* 1.3 74.5 - - - +
126F ASP* 1.3 60.4 + - - +
128F GLY 2.9 7.1 + - - -
129F GLU 3.6 5.6 - - - -
130F ARG* 2.7 41.3 + - - +
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Residues in contact with ASP 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199E ARG* 3.5 34.5 - - - +
201E LYS* 3.0 41.0 + - - +
122F LYS* 3.2 20.8 - - - +
123F GLU* 3.0 7.6 + - - +
125F VAL* 1.3 75.1 - - - +
127F ALA* 1.3 54.5 + - - +
128F GLY 2.7 15.5 + - - -
130F ARG* 4.6 2.0 - - - +
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Residues in contact with ALA 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F GLU 3.0 16.2 + - - +
124F ASN* 3.8 13.5 - - - +
125F VAL 3.2 0.4 - - - -
126F ASP* 1.3 75.6 - - - +
128F GLY* 1.3 57.9 + - - +
129F GLU* 3.6 1.6 - - + -
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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