Contacts of the helix formed by residues 100 - 113 (chain B) in PDB entry 1NZ0
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 ASP 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B TRP* 4.0 2.2 - - - -
98B ARG 3.7 2.2 + - - -
99B VAL* 1.3 75.4 - - - +
101B PHE* 1.3 67.3 + - - +
102B TRP* 3.2 15.2 + - - +
103B THR* 2.8 49.9 + - - -
104B VAL* 3.3 12.0 + - - +
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Residues in contact with PHE 101 (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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66B TRP* 3.5 61.9 - + + -
69B GLU* 4.0 24.0 - - + -
70B ILE* 3.6 34.1 - - + -
73B ARG* 4.8 12.1 - - - -
74B ASN* 6.1 0.4 - - - -
100B ASP* 1.3 75.1 - - - +
102B TRP* 1.3 86.6 + + - +
104B VAL* 3.2 2.3 + - - +
105B ARG* 2.9 31.8 + - + -
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Residues in contact with TRP 102 (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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100B ASP* 3.2 13.5 + - - +
101B PHE* 1.3 98.9 - + - +
103B THR* 1.3 59.2 + - - +
105B ARG* 3.4 58.8 - - - +
106B GLU* 2.9 31.2 + - + +
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Residues in contact with THR 103 (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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31B TYR* 4.4 11.2 - - + +
99B VAL* 4.0 16.2 - - + -
100B ASP* 2.8 33.0 + - - -
102B TRP* 1.3 75.3 - - - +
104B VAL* 1.3 64.5 + - - +
106B GLU* 3.3 10.4 + - - +
107B LYS* 3.1 30.6 + - + +
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Residues in contact with VAL 104 (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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31B TYR* 4.3 8.3 - - + -
32B PHE* 3.7 26.9 - - + -
63B LEU* 5.4 3.4 - - + -
66B TRP* 3.8 23.3 - - + -
67B VAL* 5.5 0.9 - - + -
70B ILE* 4.0 13.5 - - + -
92B LEU* 4.2 16.8 - - + -
96B PHE* 5.5 0.4 - - + -
99B VAL* 3.8 27.1 - - + -
100B ASP 3.3 12.7 + - - +
101B PHE 3.2 7.0 + - - +
103B THR* 1.3 74.1 - - - +
105B ARG* 1.3 58.3 + - - +
107B LYS* 3.4 2.1 + - - +
108B LEU* 2.9 29.6 + - - +
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Residues in contact with ARG 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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70B ILE* 3.6 27.1 - - + +
74B ASN* 2.9 33.8 + - - +
101B PHE* 2.9 24.9 + - + +
102B TRP* 3.4 63.0 - - - +
104B VAL* 1.3 77.9 - - - +
106B GLU* 1.3 66.4 + - - +
108B LEU* 3.9 0.5 - - - +
109B LEU* 2.9 48.9 + - + +
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Residues in contact with GLU 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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102B TRP* 2.9 22.2 + - + +
103B THR* 3.3 10.2 + - + +
105B ARG* 1.3 80.0 - - - +
107B LYS* 1.3 61.0 + - + +
109B LEU* 3.9 4.6 - - - +
110B ASN* 2.9 34.6 + - + +
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Residues in contact with LYS 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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29B ASN* 2.9 41.6 + - + +
30B GLU* 5.9 5.4 - - + +
31B TYR* 4.3 29.6 - - + +
32B PHE* 4.7 1.8 - - + -
103B THR* 3.1 23.3 + - + +
104B VAL 3.9 2.9 - - - +
106B GLU* 1.3 79.3 - - + +
108B LEU* 1.3 62.3 + - - +
110B ASN* 3.5 5.6 + - + +
111B LEU* 3.4 11.4 + - - +
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Residues in contact with LEU 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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32B PHE* 3.8 21.0 - - + -
34B VAL* 4.2 9.4 - - + -
67B VAL* 4.0 32.8 - - + +
70B ILE* 3.9 29.4 - - + -
71B PHE* 5.4 1.3 - - + +
86B VAL* 4.1 26.0 - - + -
104B VAL 2.9 18.0 + - - +
105B ARG 4.0 1.8 - - - +
107B LYS* 1.3 75.0 - - - +
109B LEU* 1.3 67.2 + - - +
111B LEU* 3.1 5.6 + - + +
112B LEU* 2.9 50.3 + - + +
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Residues in contact with LEU 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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70B ILE* 3.7 22.0 - - + +
74B ASN* 3.8 36.6 - - + +
77B VAL* 4.5 13.2 - - + -
78B ILE* 4.4 8.5 - - + -
105B ARG* 2.9 44.6 + - + +
106B GLU* 4.1 3.6 - - - +
108B LEU* 1.3 76.2 - - - +
110B ASN* 1.3 62.8 + - - +
112B LEU* 4.3 15.0 - - + +
113B LYS* 3.0 46.0 + - + +
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Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B ASN* 5.0 4.1 + - - +
106B GLU* 2.9 23.3 + - + +
107B LYS* 3.6 10.8 - - + +
108B LEU 3.2 0.2 - - - -
109B LEU* 1.3 77.0 - - - +
111B LEU* 1.3 62.1 + - - +
113B LYS* 3.7 10.9 + - - +
114B ARG* 3.5 37.1 + - - +
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Residues in contact with LEU 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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27B LEU* 3.5 34.1 - - + +
28B GLN 3.5 18.4 - - - +
29B ASN* 4.0 13.0 - - - +
32B PHE* 3.8 31.0 - - + +
34B VAL* 3.3 35.4 - - + -
107B LYS 3.4 5.3 + - - +
108B LEU* 3.1 9.8 + - + +
110B ASN* 1.3 80.9 + - - +
112B LEU* 1.3 67.6 + - - +
114B ARG* 2.9 37.8 + - - +
115B ILE* 3.7 4.7 + - - +
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Residues in contact with LEU 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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34B VAL* 3.9 15.9 - - + -
70B ILE* 5.4 1.1 - - + -
71B PHE* 4.3 12.3 - - + -
78B ILE* 4.0 35.9 - - + -
79B PRO* 3.2 17.6 - - - +
84B ILE* 3.8 31.0 - - + -
86B VAL* 4.7 2.5 - - + -
108B LEU* 2.9 48.5 + - + +
109B LEU* 4.0 11.9 - - + +
111B LEU* 1.3 77.1 - - - +
113B LYS* 1.3 62.8 + - + +
114B ARG 3.2 0.9 + - - -
115B ILE* 3.2 22.5 + - + +
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Residues in contact with LYS 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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77B VAL* 3.9 45.5 - - + +
78B ILE* 5.9 0.4 - - + -
79B PRO* 4.2 11.8 - - - +
109B LEU* 3.0 37.4 + - + +
110B ASN* 4.0 7.8 - - - +
111B LEU 3.1 0.4 - - - -
112B LEU* 1.3 77.3 - - + +
114B ARG* 1.3 56.3 + - + +
115B ILE 3.3 5.7 + - - +
116B GLU* 4.7 3.8 - - - +
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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