Contacts of the helix formed by residues 66 - 87 (chain A) in PDB entry 4U9W
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 GLU 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLY 4.2 1.0 + - - -
65A LEU* 1.3 74.7 - - - +
67A PRO* 1.3 81.9 - - + +
68A ALA* 4.1 8.5 - - + +
69A THR* 2.9 28.4 + - - +
70A VAL* 3.1 11.3 + - - +
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Residues in contact with PRO 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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65A LEU 3.6 4.5 - - - +
66A GLU* 1.3 97.5 - - + +
68A ALA* 1.3 61.7 + - - +
70A VAL* 3.5 10.5 + - + +
71A ASP* 3.1 31.3 + - - +
98A ARG* 5.0 0.2 + - - -
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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
----------------------------------------------------------
66A GLU* 3.1 7.7 - - + +
67A PRO* 1.3 79.4 - - - +
69A THR* 1.3 53.1 + - - +
71A ASP* 3.3 10.8 + - - +
72A TRP* 2.8 32.4 + - - +
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 4.4 9.2 - - + -
66A GLU* 2.9 25.6 + - - +
68A ALA* 1.3 75.1 - - - +
70A VAL* 1.3 60.3 + - - +
72A TRP* 3.0 21.8 + - + +
73A ALA* 2.9 27.0 + - + +
110A ILE* 3.6 31.0 - - + -
112A TRP* 3.7 30.1 - - + -
118A PRO* 4.9 2.4 - - + +
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Residues in contact with VAL 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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62A VAL* 4.2 18.8 - - + +
65A LEU* 4.1 24.2 - - + +
66A GLU 3.1 13.9 + - - +
67A PRO* 3.7 11.0 - - + +
69A THR* 1.3 76.3 - - - +
71A ASP* 1.3 62.4 + - - +
73A ALA* 3.2 7.0 + - + +
74A PHE* 2.9 24.4 + - + +
98A ARG* 4.1 17.9 - - - +
101A MET* 5.3 4.3 - - + +
102A THR* 3.9 26.9 - - + -
108A TYR* 5.8 4.7 - - + +
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Residues in contact with ASP 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 PRO* 3.1 22.8 + - - +
68A ALA* 3.4 11.3 - - - +
70A VAL* 1.3 76.4 - - - +
72A TRP* 1.3 59.2 + - - +
74A PHE* 3.8 3.7 - - - +
75A ASP* 2.8 44.3 + - - +
98A ARG* 2.3 37.4 + - - +
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Residues in contact with TRP 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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68A ALA 2.8 14.4 + - - +
69A THR* 3.0 20.8 + - + +
71A ASP* 1.3 77.2 - - - +
73A ALA* 1.3 70.8 + - + +
75A ASP* 3.3 7.9 + - + +
76A LEU* 2.9 45.6 + - + +
110A ILE* 4.1 8.7 - - + -
118A PRO* 3.4 49.5 + - + -
119A VAL 3.6 4.3 - - - -
120A ALA* 3.5 38.6 - - - -
121A PHE* 3.8 25.6 - + + -
143A GLU* 2.9 25.2 + - - -
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Residues in contact with ALA 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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65A LEU* 6.4 0.7 - - + -
69A THR* 2.9 13.2 + - + +
70A VAL* 3.2 10.1 + - - +
72A TRP* 1.3 82.3 - - + +
74A PHE* 1.3 66.7 + - - +
76A LEU 3.3 1.0 + - - -
77A THR* 2.9 29.7 + - - -
101A MET* 3.9 9.2 - - + -
108A TYR* 4.3 9.9 - - + -
110A ILE* 6.3 0.7 - - + -
121A PHE* 3.6 35.2 - - + -
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Residues in contact with PHE 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 VAL* 2.9 18.1 + - + +
71A ASP* 3.8 5.4 - - - +
73A ALA* 1.3 76.7 - - - +
75A ASP* 1.3 70.8 + - - +
77A THR* 3.6 1.7 - - - -
78A LYS* 2.9 41.0 + - + +
92A TRP* 3.9 7.6 - + - -
94A ASP* 3.5 53.2 - - + -
97A LYS* 3.9 12.1 - - + -
98A ARG* 3.6 42.6 - - + +
101A MET* 3.9 24.3 - - + +
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Residues in contact with ASP 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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71A ASP* 2.8 32.1 + - - +
72A TRP* 3.5 8.4 - - + +
74A PHE* 1.3 87.8 - - - +
76A LEU* 1.3 59.5 + - - +
78A LYS* 3.3 5.7 + - - +
79A THR* 2.8 38.0 + - - +
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Residues in contact with LEU 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 TRP* 2.9 46.1 + - + +
73A ALA* 3.7 3.8 - - - +
75A ASP* 1.3 76.0 - - - +
77A THR* 1.3 64.1 + - - +
79A THR* 3.6 6.5 - - + -
80A ASN* 2.9 56.5 + - - +
121A PHE* 4.3 2.7 - - + -
141A GLN* 3.7 34.8 - - + +
142A LEU 3.8 13.9 - - - +
143A GLU* 3.8 22.9 - - - +
147A ARG* 5.1 0.2 - - - +
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Residues in contact with THR 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 ALA 2.9 18.5 + - - -
74A PHE* 3.6 6.3 - - - -
76A LEU* 1.3 77.8 - - - +
78A LYS* 1.3 52.5 + - - +
81A MET* 2.7 53.2 + - + +
92A TRP* 4.5 12.6 - - + -
97A LYS* 4.8 2.0 - - + -
101A MET* 3.9 11.0 - - - +
121A PHE* 3.1 22.9 - - - -
139A GLU* 3.5 30.7 - - - +
141A GLN* 3.7 11.3 - - - +
1F SER* 4.5 1.3 - - - +
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Residues in contact with LYS 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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74A PHE* 2.9 28.5 + - + +
75A ASP* 3.7 7.2 - - - +
77A THR* 1.3 77.6 - - - +
79A THR* 1.3 59.5 + - - +
82A GLN* 2.9 60.3 + - - +
92A TRP* 3.6 29.6 - - + +
94A ASP* 3.0 39.4 + - - +
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Residues in contact with THR 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 ASP* 2.8 27.6 + - - +
76A LEU* 3.6 8.5 - - + -
78A LYS* 1.3 73.8 - - - +
80A ASN* 1.3 67.7 + - - +
82A GLN* 4.8 0.9 + - - +
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Residues in contact with ASN 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 LEU* 2.9 43.1 + - - +
77A THR 3.9 0.2 - - - +
79A THR* 1.3 84.8 - - - +
81A MET* 1.3 70.6 + - + +
82A GLN 3.8 0.4 - - - -
83A THR* 5.5 0.7 + - - -
84A MET* 4.7 9.9 - - - +
141A GLN* 2.8 28.5 + - - +
142A LEU 3.5 13.5 + - - +
147A ARG* 3.3 20.8 + - - +
301A COA 4.0 10.2 - - + +
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Residues in contact with MET 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 THR* 2.7 31.0 + - + +
80A ASN* 1.3 84.0 - - - +
82A GLN* 1.3 65.7 + - - +
83A THR 3.4 2.7 - - - -
84A MET* 3.1 13.9 + - - +
85A TYR* 2.9 36.7 + - + -
92A TRP* 4.6 1.1 - - + -
141A GLN* 3.4 31.2 - - - +
176A PHE* 4.0 21.8 - - + -
179A ASN* 3.8 19.1 - - - +
301A COA 3.8 18.6 - - - +
1F SER* 3.8 24.5 - - - +
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Residues in contact with GLN 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 LYS* 2.9 48.5 + - + +
79A THR 4.8 1.0 + - - +
80A ASN 3.8 0.6 - - - -
81A MET* 1.3 75.9 - - - +
83A THR* 1.3 65.4 + - - +
85A TYR* 3.0 5.0 + - - +
86A GLU* 2.9 42.8 + - - +
92A TRP* 3.8 37.4 - - + +
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Residues in contact with THR 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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80A ASN 5.5 0.2 + - - -
81A MET 3.4 0.6 - - - -
82A GLN* 1.3 78.5 - - - +
84A MET* 1.3 60.1 + - + +
86A GLU* 3.1 17.3 + - + +
87A GLN* 2.9 49.0 + - + +
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Residues in contact with MET 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 ASN 4.7 7.9 - - - +
81A MET* 3.1 21.8 + - + +
83A THR* 1.3 80.1 - - + +
85A TYR* 1.3 61.1 + - - +
87A GLN* 3.4 6.7 + - - +
88A SER* 3.3 9.7 + - - -
176A PHE* 3.9 16.1 - - + -
178A HIS* 2.8 55.1 + - + +
179A ASN* 3.4 45.3 - - - +
180A HIS 5.1 0.4 - - - +
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Residues in contact with TYR 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 MET* 2.9 39.6 + - + +
82A GLN 3.3 7.9 - - - +
84A MET* 1.3 76.8 - - - +
86A GLU* 1.3 61.8 + - - +
88A SER* 2.7 21.5 + - - -
90A TRP* 3.5 26.5 - + + -
91A GLY 3.0 36.9 + - - +
92A TRP* 3.5 27.6 - + + +
93A LYS 5.5 0.4 - - - -
97A LYS* 2.7 34.8 + - - -
176A PHE* 3.6 19.1 - + - -
303A GOL 3.5 13.2 + - - -
1F SER* 2.8 33.0 + - - -
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Residues in contact with GLU 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 GLN* 2.9 35.9 + - - +
83A THR* 3.5 20.6 + - + +
85A TYR* 1.3 76.7 - - - +
87A GLN* 1.3 60.6 + - + +
88A SER 3.1 8.4 + - - +
91A GLY* 4.1 7.4 - - - -
92A TRP* 4.2 14.3 - - + +
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Residues in contact with GLN 87 (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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83A THR* 2.9 36.5 + - + +
84A MET* 3.4 7.9 + - - +
85A TYR 3.2 0.2 - - - -
86A GLU* 1.3 77.1 - - + +
88A SER* 1.3 58.1 + - - +
178A HIS* 3.3 39.4 + - + +
210A SER* 4.7 3.5 + - - -
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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
------------------------------------------------------------
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