Contacts of the helix formed by residues 73 - 82 (chain A) in PDB entry 1NTZ
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 ASN 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A PRO 3.4 0.2 - - - -
72A GLY* 1.3 75.0 - - - +
74A ALA* 1.3 70.3 + - - +
75A LEU* 3.2 3.1 - - - -
76A GLU* 3.1 32.8 + - - +
77A LYS* 3.2 30.7 + - - +
289B SER* 4.9 9.3 - - - +
291B ALA* 3.4 29.7 - - - +
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Residues in contact with ALA 74 (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 ARG* 4.2 10.1 - - + -
71A PRO* 3.3 29.7 + - + +
73A ASN* 1.3 82.5 + - - +
75A LEU* 1.3 61.5 + - - +
77A LYS* 3.3 13.3 + - - +
78A GLU* 3.1 26.4 + - - +
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Residues in contact with LEU 75 (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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63A ALA 4.6 1.1 - - - +
64A PHE* 4.0 31.0 - - - +
66A GLY 5.4 2.9 - - - +
67A THR* 4.9 8.7 - - + -
70A ARG* 4.3 22.9 - - + +
71A PRO 4.4 2.5 + - - +
73A ASN* 3.2 1.3 - - - -
74A ALA* 1.3 73.8 - - - +
76A GLU* 1.3 69.7 + - + +
78A GLU* 2.9 14.0 + - - +
79A VAL* 3.0 27.8 + - + +
86A LEU* 4.1 7.9 - - + -
112A LEU* 3.8 33.4 - - + -
116A ILE* 3.8 32.1 - - + -
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Residues in contact with GLU 76 (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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64A PHE* 4.0 19.8 - - - +
65A LYS* 5.0 6.9 - - - +
72A GLY 5.4 1.2 - - - +
73A ASN* 3.1 18.0 + - - +
75A LEU* 1.3 81.5 - - + +
77A LYS* 1.3 63.9 + - - +
79A VAL* 3.2 0.7 + - - +
80A GLU* 2.9 40.6 + - - +
285B VAL* 4.2 24.7 - - + +
287B ARG 4.5 0.7 - - - +
288B GLY* 3.2 12.9 - - - -
289B SER* 3.1 44.9 + - - -
290B ASN* 3.5 7.2 + - - -
291B ALA* 4.0 8.1 + - + +
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Residues in contact with LYS 77 (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 ASN* 3.2 33.4 + - - +
74A ALA* 3.4 13.0 - - - +
75A LEU 3.2 0.6 - - - -
76A GLU* 1.3 80.1 - - - +
78A GLU* 1.3 59.4 + - + +
80A GLU* 4.8 0.2 - - - -
81A SER* 2.9 31.3 + - - +
291B ALA* 3.6 25.4 - - + -
292B THR* 4.3 14.3 - - + +
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Residues in contact with GLU 78 (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 ARG* 3.2 31.9 + - - +
74A ALA* 3.1 16.6 + - + +
75A LEU* 2.9 10.0 + - - +
77A LYS* 1.3 74.7 - - + +
79A VAL* 1.3 65.8 + - - +
81A SER* 3.4 5.3 + - - -
82A MET* 3.3 28.5 + - + +
108A LYS* 3.5 33.1 + - + +
112A LEU* 4.0 11.7 - - + +
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Residues in contact with VAL 79 (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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75A LEU* 3.0 23.3 + - + +
76A GLU* 3.8 5.2 - - - +
78A GLU* 1.3 75.8 - - - +
80A GLU* 1.3 61.0 + - - +
82A MET* 3.3 12.5 + - + +
83A GLY 3.3 2.6 + - - -
84A ALA* 2.9 54.7 + - + +
85A HIS 4.1 0.7 - - - +
86A LEU* 4.0 32.5 - - + +
99A ILE* 5.0 6.5 - - + -
112A LEU* 3.7 22.2 - - + -
284B HIS* 4.8 0.2 - - + -
285B VAL* 4.2 10.3 - - + -
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Residues in contact with GLU 80 (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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76A GLU* 2.9 31.9 + - - +
79A VAL* 1.3 71.2 - - - +
81A SER* 1.3 58.1 + - - +
83A GLY* 2.8 17.8 + - - -
284B HIS* 3.8 36.8 + - + +
285B VAL* 4.3 11.9 - - + +
290B ASN* 3.5 25.0 + - - -
291B ALA* 3.5 6.6 + - - +
292B THR* 2.7 54.7 + - + +
363B LYS* 3.2 21.2 - - + +
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Residues in contact with SER 81 (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 LYS* 2.9 25.5 + - - +
78A GLU* 4.0 4.0 - - - -
79A VAL 3.3 0.4 - - - -
80A GLU* 1.3 75.6 - - - +
82A MET* 1.3 57.9 + - - +
83A GLY 3.3 0.9 - - - -
292B THR* 3.8 13.8 - - - +
359B ALA* 4.3 22.9 - - - +
362B ASN* 3.5 21.8 - - - +
363B LYS* 5.2 0.2 - - - -
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Residues in contact with MET 82 (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 GLU* 3.3 12.8 + - - +
79A VAL* 3.4 20.4 - - + +
81A SER* 1.3 77.2 - - - +
83A GLY* 1.3 59.1 + - - +
84A ALA* 3.5 15.0 + - + +
99A ILE* 5.3 2.0 - - + -
101A ALA* 5.5 0.2 - - + -
102A LEU* 4.7 6.2 + - - +
105A ASP* 3.5 41.5 - - + +
108A LYS* 3.9 24.2 - - + -
109A ALA* 4.9 8.3 - - + +
112A LEU* 3.8 28.9 - - + -
362B ASN* 4.1 15.5 - - - +
366B ALA* 4.1 6.1 - - - +
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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