Contacts of the helix formed by residues 67 - 88 (chain A) in PDB entry 4OTZ
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 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ALA* 3.5 20.6 - - + +
65A SER* 3.0 15.1 + - - +
66A ASN* 1.3 79.2 - - + +
68A ALA* 1.3 54.7 + - - +
69A LEU 3.1 0.4 - - - -
70A LEU* 3.0 25.5 + - + +
71A GLY 3.0 8.8 + - - -
105A GLY* 3.7 23.3 - - - +
130A THR* 4.0 8.5 - - + -
131A LEU* 3.6 40.8 - - + -
134A GLN* 4.3 3.6 - - - +
256A LEU* 4.8 9.2 - - + -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA* 3.3 22.6 - - - +
63A GLN* 3.5 24.9 - - - +
64A THR* 3.7 4.7 + - - +
65A SER 2.9 16.8 + - - +
67A VAL* 1.3 73.7 - - - +
69A LEU* 1.3 56.5 + - - +
70A LEU 3.0 5.8 - - - -
71A GLY 3.5 0.4 - - - -
72A GLN* 2.9 34.6 + - + +
286A ASN* 4.8 0.5 + - - -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A SER 4.3 0.6 + - - +
66A ASN* 3.4 29.8 - - - +
67A VAL 3.1 0.8 - - - -
68A ALA* 1.3 76.4 - - - +
70A LEU* 1.3 58.7 + - + +
73A GLU* 4.7 3.5 - - - +
257A ALA* 4.1 15.5 - - + -
258A ALA* 3.8 35.4 - - + +
284A THR* 3.5 13.0 + - - +
286A ASN* 2.9 50.3 + - + +
290A VAL* 6.0 3.1 - - + -
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN 4.6 4.5 - - - +
67A VAL* 3.0 16.7 + - + +
69A LEU* 1.3 82.9 - - + +
71A GLY* 1.3 63.7 + - - +
72A GLN 3.3 1.8 - - - -
73A GLU* 3.3 17.3 + - - +
74A GLN* 3.6 13.4 + - - +
130A THR* 4.1 9.2 - - + -
131A LEU* 4.6 3.4 - - + -
256A LEU* 4.5 13.5 - - + -
257A ALA* 4.0 26.0 - - + +
281A GLY* 4.1 17.7 - - - +
284A THR* 5.0 1.6 - - + -
331A PHE* 3.7 33.5 - - + -
501A CYS* 3.7 33.9 - - + -
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.5 0.7 - - - +
62A ALA 3.3 22.4 - - - -
67A VAL 3.0 10.0 + - - -
68A ALA 3.4 0.2 + - - -
70A LEU* 1.3 78.4 - - - +
72A GLN* 1.3 61.4 + - - +
74A GLN* 3.0 21.0 + - - +
75A VAL* 2.9 24.9 + - - +
130A THR* 3.8 8.5 - - - +
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA 3.8 2.4 + - - -
63A GLN* 4.9 17.2 + - - +
68A ALA* 2.9 21.3 + - + +
69A LEU 5.6 0.2 - - - -
71A GLY* 1.3 77.0 - - - +
73A GLU* 1.3 57.6 + - + +
75A VAL* 3.3 28.0 + - - +
76A ALA* 3.0 31.5 + - - +
79A LYS* 5.7 0.2 + - - -
286A ASN* 5.8 3.4 - - - +
324A TYR* 5.6 0.9 + - - -
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Residues in contact with GLU 73 (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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68A ALA 4.8 0.2 + - - -
69A LEU 4.7 5.2 - - - +
70A LEU 3.3 9.9 + - - +
71A GLY 3.2 0.6 - - - -
72A GLN* 1.3 78.5 - - + +
74A GLN* 1.3 61.7 + - - +
76A ALA* 3.4 4.8 + - - +
77A GLY 3.2 10.6 + - - -
283A ASN 4.1 1.6 - - - +
284A THR* 2.7 34.2 + - - +
285A SER* 3.9 10.9 + - - -
286A ASN* 4.4 6.0 + - - +
320A TYR* 5.6 1.3 - - - +
326A LYS* 4.7 2.1 + - - +
329A PRO* 3.3 34.3 - - + +
331A PHE* 3.4 25.5 - - + -
332A SER* 2.7 31.0 + - - +
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.5 21.1 - - + +
70A LEU 3.8 9.6 - - - +
71A GLY* 3.0 8.7 + - - +
73A GLU* 1.3 75.9 - - - +
75A VAL* 1.3 65.8 + - - +
77A GLY 3.1 1.0 + - - -
78A ALA* 2.9 21.0 + - - +
130A THR* 2.8 44.0 + - - +
152A PRO* 3.5 14.3 - - - +
153A SER* 2.9 33.7 + - - +
331A PHE* 3.7 21.8 - - + +
335A ALA* 3.1 21.6 - - + +
501A CYS* 4.9 0.2 - - - -
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 4.0 17.5 - - + -
63A GLN* 3.8 35.2 - - + +
71A GLY 2.9 17.8 + - - +
72A GLN* 3.5 27.8 - - - +
74A GLN* 1.3 75.9 - - - +
76A ALA* 1.3 62.6 + - - +
78A ALA* 3.2 5.4 + - - +
79A LYS* 2.9 53.6 + - + +
100A PHE* 4.0 11.2 - - + -
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Residues in contact with ALA 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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72A GLN* 3.0 18.3 + - + +
73A GLU* 3.5 11.4 - - - +
74A GLN 3.2 0.2 - - - -
75A VAL* 1.3 79.3 - - - +
77A GLY* 1.3 61.4 + - - +
79A LYS* 3.4 6.8 + - - +
80A ILE* 3.1 30.4 + - - +
320A TYR* 4.7 4.7 - - + +
324A TYR* 3.6 34.6 + - + +
332A SER* 4.3 5.6 - - - +
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Residues in contact with GLY 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLU 3.2 5.3 + - - -
74A GLN 3.1 5.6 + - - -
76A ALA* 1.3 76.4 - - - +
78A ALA* 1.3 65.5 + - - +
80A ILE* 3.4 7.5 + - - +
81A ALA* 3.0 23.2 + - - +
316A PHE* 4.6 4.7 - - - -
332A SER* 3.3 30.4 - - - -
336A PHE* 3.8 12.3 - - - +
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 4.5 11.2 - - + -
61A LEU* 5.1 0.4 - - + -
74A GLN 2.9 15.8 + - - +
75A VAL* 3.2 6.3 + - - +
77A GLY* 1.3 77.7 - - - +
79A LYS* 1.3 56.1 + - - +
81A ALA* 3.2 3.0 + - - +
82A GLU 2.9 24.1 + - - -
98A LEU* 3.3 24.0 - - + +
100A PHE* 4.3 12.6 - - + -
127A VAL* 6.1 0.9 - - + -
335A ALA* 3.9 7.7 - - + +
339A VAL* 4.1 18.4 - - + -
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Residues in contact with LYS 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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63A GLN* 5.5 3.6 - - - +
72A GLN* 5.7 0.4 + - - -
75A VAL* 2.9 40.3 + - + +
76A ALA* 3.8 6.1 - - - +
78A ALA* 1.3 74.1 - - - +
80A ILE* 1.3 64.5 + - + +
82A GLU* 3.3 11.5 + - - +
83A LYS* 3.2 21.7 + - - +
98A LEU* 4.9 0.9 - - - -
100A PHE* 3.7 28.3 - - + -
324A TYR* 6.1 0.4 - - - +
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Residues in contact with ILE 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA 3.1 20.0 + - - +
77A GLY* 3.7 4.9 - - - +
79A LYS* 1.3 76.1 - - + +
81A ALA* 1.3 58.1 + - - +
83A LYS* 3.4 6.8 + - - +
84A TYR* 2.9 28.2 + - + +
316A PHE* 3.9 26.9 - - + -
319A ALA* 4.3 20.6 - - + -
320A TYR* 3.6 45.3 - - + +
323A GLN* 4.6 11.7 - - - +
324A TYR* 4.2 10.3 - - + -
336A PHE* 4.1 5.6 - - + -
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Residues in contact with ALA 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 GLY 3.0 13.8 + - - +
78A ALA 3.2 9.2 + - - +
80A ILE* 1.3 78.1 - - - +
82A GLU* 1.3 63.7 + - - +
85A PHE* 2.9 35.8 + - + +
336A PHE* 3.5 30.5 - - + +
339A VAL* 3.7 28.7 - - + -
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Residues in contact with GLU 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 ALA 2.9 6.8 + - - +
79A LYS* 3.3 13.1 + - - +
81A ALA* 1.3 76.5 - - - +
83A LYS* 1.3 57.2 + - - +
85A PHE* 4.4 0.2 - - - +
86A ASN* 2.9 49.5 + - - +
96A ILE* 3.9 16.4 - - + +
97A LYS* 3.6 19.9 + - - +
98A LEU* 2.9 55.9 + - + +
100A PHE* 4.6 7.1 - - - -
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Residues in contact with LYS 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 LYS 3.2 10.1 + - - +
80A ILE* 3.8 8.1 - - - +
82A GLU* 1.3 76.1 - - - +
84A TYR* 1.3 67.2 + - - +
86A ASN* 4.8 2.7 - - - -
87A ASP* 2.7 61.5 + - - +
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Residues in contact with TYR 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 ILE* 2.9 20.5 + - + +
81A ALA 3.2 2.9 + - - +
83A LYS* 1.3 79.5 - - - +
85A PHE* 1.3 98.4 + + - +
87A ASP* 3.8 6.1 - - - +
88A LYS* 3.3 54.0 + - + +
312A ILE* 3.8 27.6 - - + +
315A ALA* 3.9 29.2 - - + +
316A PHE* 5.6 0.7 - - - -
336A PHE* 3.8 16.4 - + + -
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Residues in contact with PHE 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 ALA* 2.9 33.8 + - + +
82A GLU 4.4 0.7 - - - +
84A TYR* 1.3 99.2 - + - +
86A ASN* 1.3 65.6 + - - +
88A LYS* 3.1 16.4 + - + +
89A GLY 3.4 0.5 + - - -
90A GLY* 2.9 22.7 + - - +
96A ILE* 4.9 4.7 - - + -
312A ILE* 4.2 1.1 - - + -
336A PHE* 3.8 21.3 - + - -
339A VAL* 4.4 1.3 - - + -
340A GLN* 3.4 51.1 - - + -
343A VAL* 3.9 42.0 - - + -
344A GLU* 4.2 11.0 - - + -
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Residues in contact with ASN 86 (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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82A GLU* 2.9 34.5 + - - +
83A LYS* 4.3 2.9 - - - +
85A PHE* 1.3 76.7 - - - +
87A ASP* 1.3 60.7 + - - +
89A GLY* 3.0 19.1 + - - -
90A GLY* 3.7 7.2 + - - +
95A PRO* 3.4 16.0 - - + +
96A ILE* 2.9 51.7 + - - +
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LYS* 2.7 60.5 + - - +
84A TYR* 3.8 6.3 - - - +
85A PHE 3.3 0.2 - - - -
86A ASN* 1.3 77.4 - - - +
88A LYS* 1.3 60.4 + - + +
89A GLY 3.3 1.5 + - - -
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Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 3.3 55.3 + - + +
85A PHE* 3.1 13.6 + - + +
86A ASN 3.0 1.2 - - - -
87A ASP* 1.3 78.7 - - + +
89A GLY* 1.3 59.5 + - - +
90A GLY 3.5 4.1 + - - +
347A LYS* 5.9 1.0 + - - -
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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