Contacts of the helix formed by residues 64 - 72 (chain A) in PDB entry 2NZ2
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 VAL 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A TYR* 4.9 3.8 - - - +
36A ALA* 5.2 5.6 - - + -
37A ASN 2.8 12.2 + - - +
38A ILE* 3.7 19.3 - - + -
62A GLU* 4.0 22.7 - - + +
63A ASP* 1.3 76.7 - - - +
65A SER* 1.3 59.9 + - - +
66A ARG 3.5 2.5 - - - -
67A GLU* 3.2 19.0 - - + +
68A PHE* 2.9 25.5 + - - +
97A CYS* 3.3 30.1 - - + +
98A ILE* 5.3 0.4 - - - +
101A LYS* 4.2 26.9 - - + -
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Residues in contact with SER 65 (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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37A ASN* 3.5 5.2 + - - -
38A ILE* 4.6 2.9 - - - +
39A GLY* 3.4 25.7 + - - -
63A ASP* 3.2 16.0 + - - -
64A VAL* 1.3 78.3 - - - +
66A ARG* 1.3 57.8 + - - +
68A PHE* 3.2 7.9 + - - +
69A VAL* 3.0 33.1 + - - +
185A LEU* 3.7 17.6 - - - +
248A LEU* 4.0 17.0 - - - -
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Residues in contact with ARG 66 (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 ASP* 4.9 1.4 + - - -
64A VAL 3.5 1.0 - - - -
65A SER* 1.3 77.5 - - - +
67A GLU* 1.3 59.4 + - - +
69A VAL* 3.3 4.0 + - - +
70A GLU* 3.0 49.1 + - - +
246A THR* 4.8 10.5 + - - -
247A SER* 3.7 8.7 + - - +
248A LEU* 3.4 55.3 - - + +
249A GLU* 4.9 1.6 - - - +
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Residues in contact with GLU 67 (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 ASP 4.4 5.0 - - - +
64A VAL* 3.2 36.5 - - - +
66A ARG* 1.3 77.1 - - - +
68A PHE* 1.3 58.1 + - - +
70A GLU* 4.4 5.2 - - - +
71A GLU* 2.9 52.1 + - - +
72A PHE* 3.7 3.1 - - - -
97A CYS* 4.2 7.4 - - - +
100A ARG* 3.1 24.5 + - - +
101A LYS* 4.5 15.7 + - - +
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Residues in contact with PHE 68 (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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38A ILE* 3.5 33.7 - - + -
64A VAL 2.9 19.7 + - - +
65A SER* 3.2 6.0 + - - +
67A GLU* 1.3 77.0 - - - +
69A VAL* 1.3 61.2 + - - +
72A PHE* 3.2 15.0 + - + -
73A ILE* 3.0 48.6 + - + +
90A GLY 3.9 20.0 - - - -
93A LEU* 3.6 19.3 - - + -
94A ALA* 3.6 23.1 - - + -
97A CYS* 3.9 11.2 - - + -
184A ASN* 3.9 15.5 - - - -
185A LEU* 4.1 14.4 - - + -
186A MET* 4.0 9.6 - - + -
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Residues in contact with VAL 69 (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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65A SER 3.0 18.6 + - - +
66A ARG* 3.6 7.4 - - - +
68A PHE* 1.3 75.8 - - - +
70A GLU* 1.3 60.7 + - + +
73A ILE* 3.4 15.0 + - + -
74A TRP* 3.0 69.7 + - + -
185A LEU* 3.5 22.0 - - + -
247A SER* 4.1 15.0 - - - +
248A LEU* 4.0 15.5 - - + -
251A PHE* 4.4 10.8 - - + -
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Residues in contact with GLU 70 (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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66A ARG* 3.0 34.3 + - - +
67A GLU* 4.5 3.4 - - - +
69A VAL* 1.3 77.8 - - - +
71A GLU* 1.3 62.6 + - + +
74A TRP* 3.4 29.6 - - + +
75A PRO* 4.1 2.3 - - - +
247A SER* 2.7 38.8 + - - +
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Residues in contact with GLU 71 (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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67A GLU* 2.9 27.1 + - + +
70A GLU* 1.3 80.4 - - + +
72A PHE* 1.3 69.0 + - + +
75A PRO* 3.4 15.0 - - - +
100A ARG* 2.8 41.2 + - - -
326A TRP* 3.3 20.7 - - + -
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Residues in contact with PHE 72 (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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67A GLU 3.7 10.5 - - - -
68A PHE* 3.2 19.3 + - + +
70A GLU 3.6 0.4 - - - -
71A GLU* 1.3 86.4 - - + +
73A ILE* 1.3 66.8 + - - +
74A TRP 3.3 0.9 - - - -
75A PRO* 3.3 4.9 - - - +
76A ALA* 3.2 21.1 + - - +
93A LEU* 3.6 29.4 - - + +
96A PRO* 3.7 20.4 - - + -
97A CYS* 3.8 30.5 - - + -
100A ARG* 3.5 41.5 - - - -
326A TRP* 3.4 48.7 - + + -
327A HIS* 5.0 0.4 - + - -
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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