Contacts of the helix formed by residues 71 - 85 (chain A) in PDB entry 2Z1Z
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 PRO 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A PRO 3.6 6.7 - - - +
70A ILE* 1.4 92.0 - - + +
72A GLU* 1.3 67.4 + - - +
73A VAL* 4.0 7.6 - - + -
74A ILE* 2.9 23.5 + - + +
75A THR 3.3 6.2 + - - -
272A ALA* 4.2 11.0 - - - +
330A ALA* 3.4 36.1 - - + +
331A MET* 4.8 3.6 - - + +
334A VAL* 4.1 22.4 - - + -
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Residues in contact with GLU 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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70A ILE 3.5 1.4 + - - -
71A PRO* 1.3 70.3 - - - +
73A VAL* 1.3 54.6 + - - +
74A ILE 3.2 0.2 - - - -
75A THR* 3.5 11.2 + - - +
76A SER* 2.7 41.6 + - - +
86B SER* 3.8 22.0 + - - +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PRO* 2.9 6.0 + - + -
72A GLU* 1.3 74.6 - - - +
74A ILE* 1.3 79.9 + - + +
76A SER* 4.4 4.0 - - - -
77A ALA* 3.7 10.9 + - - +
321A ALA* 3.8 19.5 - - + +
326A GLU* 3.9 39.9 - - + +
327A GLY* 4.1 4.5 - - - +
330A ALA* 3.7 26.2 - - + -
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Residues in contact with ILE 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 ILE* 3.5 15.5 - - + -
71A PRO* 2.9 17.4 + - + +
73A VAL* 1.3 95.0 - - + +
75A THR* 1.3 64.1 + - - +
77A ALA* 3.2 6.4 + - - +
78A MET* 3.2 23.2 + - - +
272A ALA* 5.4 1.8 - - + -
274A PHE* 3.3 40.6 - - + -
318A GLY* 3.5 13.2 - - - +
321A ALA* 4.0 5.8 - - - +
322A CYS* 3.4 39.9 - - - +
327A GLY* 4.3 6.7 - - - +
331A MET* 5.4 2.0 - - + -
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Residues in contact with THR 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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70A ILE* 3.5 35.0 - - + +
71A PRO 3.3 0.4 + - - -
72A GLU* 3.5 8.8 + - - -
73A VAL 3.6 0.2 - - - -
74A ILE* 1.3 76.0 - - - +
76A SER* 1.4 51.5 + - - +
78A MET* 3.4 11.7 - - - +
79A ALA* 2.8 34.3 + - - +
82B ALA* 3.1 30.2 - - - +
83B HIS* 4.6 6.4 + - - -
85B LEU* 4.0 7.6 - - + -
86B SER* 3.2 33.1 + - - +
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Residues in contact with SER 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 2.7 26.3 + - - +
73A VAL* 4.4 5.2 - - - -
75A THR* 1.4 73.6 + - - +
77A ALA* 1.3 57.6 + - - +
79A ALA* 3.8 6.5 - - - +
80A LYS* 2.8 38.6 + - - +
83B HIS* 4.7 9.5 + - - -
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Residues in contact with ALA 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 VAL 3.7 4.2 + - - +
74A ILE 3.2 7.9 + - - +
76A SER* 1.3 79.4 - - - +
78A MET* 1.3 55.8 + - - +
80A LYS* 3.8 8.0 - - - +
81A LYS* 2.9 29.3 + - - +
317A ALA* 3.7 18.8 - - + +
321A ALA* 3.4 33.7 - - + -
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Residues in contact with MET 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 ILE* 5.7 0.4 - - - -
74A ILE* 3.2 11.4 + - - +
75A THR* 3.4 13.7 - - - +
77A ALA* 1.3 75.5 - - - +
79A ALA* 1.3 53.8 + - - +
81A LYS* 3.1 7.0 + - - +
82A ALA* 2.8 34.3 + - - +
274A PHE* 4.1 16.6 - - + -
277A VAL* 2.8 41.1 - - + -
314A ILE* 3.4 25.5 - - + +
315A SER* 3.3 27.6 - - - +
318A GLY* 3.6 13.2 - - - -
82B ALA* 4.0 12.6 - - + -
85B LEU* 5.4 2.5 - - - -
314B ILE* 4.0 13.9 - - + -
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Residues in contact with ALA 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 THR 2.8 17.0 + - - +
76A SER 3.8 3.1 - - - +
78A MET* 1.3 72.1 - - - +
80A LYS* 1.3 58.3 + - - +
82A ALA* 3.3 2.8 + - - +
83A HIS* 2.9 36.7 + - + -
79B ALA* 3.8 19.9 - - + +
82B ALA* 3.8 6.9 - - + +
83B HIS* 3.4 39.0 - - + +
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Residues in contact with LYS 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 SER* 2.8 18.9 + - - +
77A ALA* 3.8 7.4 - - - +
79A ALA* 1.3 73.6 - - - +
81A LYS* 1.3 66.9 + - - +
83A HIS* 3.5 11.1 + - - +
84A GLU* 3.1 48.4 + - + +
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Residues in contact with LYS 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 ALA 2.9 15.5 + - - +
78A MET* 3.3 9.4 - - - +
80A LYS* 1.3 76.9 - - - +
82A ALA* 1.3 64.1 + - - +
84A GLU* 3.2 30.5 + - - +
85A LEU* 3.2 21.6 + - + +
90A GLY 4.8 3.2 + - - -
92A SER* 3.5 25.6 + - - -
313A ASN* 3.6 39.3 + - - +
314A ILE* 3.9 12.3 - - + -
317A ALA* 3.7 16.7 - - + +
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Residues in contact with ALA 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 MET 2.8 16.8 + - - +
79A ALA 3.6 5.8 - - - +
81A LYS* 1.3 72.0 - - - +
83A HIS* 1.3 64.9 + - - +
85A LEU* 3.1 15.8 + - - +
314A ILE* 4.0 16.0 - - + +
75B THR* 3.3 24.6 - - - +
78B MET* 3.9 13.0 - - + -
79B ALA* 3.6 28.3 - - - +
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Residues in contact with HIS 83 (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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79A ALA* 2.9 35.7 + - + +
80A LYS* 3.8 9.4 - - + +
81A LYS 3.4 0.2 - - - -
82A ALA* 1.3 71.4 - - - +
84A GLU* 1.3 57.7 + - + +
86A SER* 2.7 32.6 + - - +
87A THR* 4.0 5.2 + - - +
75B THR* 4.6 5.5 + - - -
76B SER* 4.9 14.1 + - - -
79B ALA* 3.5 23.1 - - + +
83B HIS* 4.5 10.5 + - - -
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Residues in contact with GLU 84 (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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80A LYS* 3.1 52.8 + - + +
81A LYS* 3.2 25.8 + - + +
82A ALA 3.1 0.2 + - - -
83A HIS* 1.3 75.2 - - + +
85A LEU* 1.3 58.5 + - - +
86A SER 3.1 1.1 - - - -
87A THR* 2.8 21.2 + - + +
90A GLY* 2.8 41.3 - - - +
91A TYR 3.1 1.2 + - - -
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Residues in contact with LEU 85 (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 LYS* 3.2 19.3 + - + +
82A ALA* 3.1 10.9 + - - +
84A GLU* 1.3 77.6 - - - +
86A SER* 1.3 55.5 + - - +
87A THR 3.3 2.0 - - - -
90A GLY 4.1 2.2 - - - +
91A TYR* 3.6 15.0 - - + +
92A SER* 3.9 26.7 - - - +
313A ASN* 3.5 24.2 - - - +
314A ILE* 3.9 22.7 - - + -
69B PRO* 3.2 8.5 - - - +
70B ILE* 2.9 39.0 + - + -
75B THR* 4.2 3.8 - - + -
78B MET* 5.4 0.9 - - - -
277B VAL* 3.7 27.1 - - + -
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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