Contacts of the helix formed by residues 66 - 87 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLY 4.3 1.4 + - - +
65D LEU* 1.3 77.5 - - - +
67D PRO* 1.3 80.6 - - + +
68D ALA* 4.3 7.9 - - + +
69D THR* 3.0 28.5 + - - +
70D VAL* 3.3 9.5 + - - +
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Residues in contact with PRO 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LEU 3.5 6.3 - - - +
66D GLU* 1.3 96.7 - - + +
68D ALA* 1.3 60.4 + - - +
70D VAL* 3.2 12.8 + - + +
71D ASP* 3.1 29.5 + - - +
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Residues in contact with ALA 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D GLU* 3.1 7.0 + - + +
67D PRO* 1.3 75.9 - - - +
69D THR* 1.3 64.4 + - - +
71D ASP* 3.2 13.0 + - - +
72D TRP* 3.0 22.5 + - - +
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Residues in contact with THR 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LEU* 4.3 12.0 - - + +
66D GLU* 3.0 25.6 + - - +
68D ALA* 1.3 77.6 - - - +
70D VAL* 1.3 62.5 + - - +
72D TRP* 3.2 19.4 + - + -
73D ALA* 3.1 19.1 + - - +
110D ILE* 4.1 24.0 - - + -
112D TRP* 3.6 37.6 - - + -
118D PRO* 5.0 2.7 - - + -
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D VAL* 4.0 22.4 - - + +
65D LEU* 3.9 23.8 - - + +
66D GLU 3.3 11.9 + - - +
67D PRO* 3.2 13.4 + - + +
69D THR* 1.3 74.9 - - - +
71D ASP* 1.3 68.3 + - - +
73D ALA* 3.2 8.5 + - - +
74D PHE* 3.1 21.9 + - + +
98D ARG* 6.2 1.8 - - + +
101D MET* 4.9 5.2 - - + +
102D THR* 3.7 29.8 - - + -
108D TYR* 5.1 5.2 - - + +
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Residues in contact with ASP 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D PRO* 3.1 22.3 + - - +
68D ALA* 3.4 13.5 - - - +
70D VAL* 1.3 80.2 - - - +
72D TRP* 1.3 58.5 + - - +
74D PHE* 3.3 7.1 + - - +
75D ASP* 2.8 41.9 + - - +
98D ARG* 4.5 18.2 + - - +
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Residues in contact with TRP 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ALA 3.0 13.3 + - - +
69D THR* 3.2 18.4 + - + +
71D ASP* 1.3 77.9 - - - +
73D ALA* 1.3 73.0 + - + +
75D ASP* 3.8 7.6 - - + +
76D LEU* 2.8 40.6 + - + +
110D ILE* 4.4 9.0 - - + -
118D PRO* 3.2 56.4 + - + -
119D VAL 3.8 3.4 - - - -
120D ALA 3.5 35.9 - - - -
121D PHE* 3.8 26.9 - + + -
143D GLU* 3.0 23.8 + - - -
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Residues in contact with ALA 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LEU* 6.6 0.2 - - + -
69D THR 3.1 11.5 + - - +
70D VAL* 3.2 10.5 + - - +
72D TRP* 1.3 85.5 - - + +
74D PHE* 1.3 60.0 + - - +
76D LEU* 3.3 0.9 + - - +
77D THR* 2.8 32.9 + - - -
101D MET* 3.6 14.1 - - + -
108D TYR* 4.2 10.8 - - + -
110D ILE* 5.7 1.1 - - + -
121D PHE* 3.4 31.0 - - + -
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Residues in contact with PHE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D VAL* 3.1 13.6 + - + +
71D ASP* 3.6 6.7 - - - +
73D ALA* 1.3 77.0 - - - +
75D ASP* 1.3 67.3 + - - +
77D THR* 3.3 1.9 + - - -
78D LYS* 2.9 44.8 + - + +
92D TRP* 4.0 8.5 - + - -
94D ASP* 3.6 44.9 - - - -
97D LYS* 4.0 11.2 - - + -
98D ARG* 3.1 64.2 - - + +
101D MET* 3.6 23.6 - - + +
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Residues in contact with ASP 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D ASP* 2.8 31.4 + - - +
72D TRP* 3.8 7.5 - - + +
74D PHE* 1.3 88.1 - - - +
76D LEU* 1.3 54.8 + - - +
78D LYS* 3.5 4.9 + - - +
79D THR* 2.6 40.7 + - - +
98D ARG* 4.5 3.5 + - - -
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D TRP* 2.8 42.6 + - + +
73D ALA* 3.6 4.9 - - - +
75D ASP* 1.3 74.1 - - - +
77D THR* 1.3 66.6 + - - +
79D THR* 3.3 6.1 + - + -
80D ASN* 2.9 56.8 + - - +
119D VAL 4.7 0.2 - - - +
121D PHE* 4.2 2.9 - - + -
141D GLN* 3.6 38.1 - - + +
142D LEU 3.8 12.8 - - - +
143D GLU* 3.7 28.7 - - + +
144D SER 5.3 0.4 - - - +
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Residues in contact with THR 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ALA 2.8 20.8 + - - -
74D PHE 3.6 4.3 - - - -
76D LEU* 1.3 74.5 - - - +
78D LYS* 1.3 54.3 + - - +
80D ASN 3.2 0.9 + - - -
81D MET* 2.6 54.9 + - + +
92D TRP* 4.6 12.6 - - + -
97D LYS* 4.8 3.1 - - - -
101D MET* 3.7 13.2 - - - +
121D PHE* 3.2 21.8 - - - -
139D GLU* 3.6 29.2 + - - +
141D GLN* 3.7 11.1 - - - +
1H SER* 4.6 0.9 - - - +
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Residues in contact with LYS 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D PHE* 2.9 29.1 + - + +
75D ASP* 3.8 6.3 - - - +
77D THR* 1.3 73.4 - - - +
79D THR* 1.3 66.8 + - - +
82D GLN* 3.1 63.3 + - - +
92D TRP* 3.6 26.2 - - + -
94D ASP* 3.3 34.3 + - - +
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Residues in contact with THR 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ASP* 2.6 27.6 + - - +
76D LEU* 3.6 10.4 - - + -
78D LYS* 1.3 75.6 - - - +
80D ASN* 1.3 66.8 + - - +
82D GLN* 4.9 1.3 + - - +
83D THR* 5.8 0.7 + - - -
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Residues in contact with ASN 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D LEU* 2.9 40.8 + - - +
79D THR* 1.3 85.6 - - - +
81D MET* 1.3 63.3 + - + +
82D GLN 3.8 0.2 - - - -
83D THR* 5.4 1.4 + - - -
84D MET* 4.8 9.7 + - - +
141D GLN* 2.8 31.2 + - - +
142D LEU 3.4 13.1 + - - -
147D ARG* 3.0 22.4 + - - +
301D COA 4.0 14.5 - - + +
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Residues in contact with MET 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D THR* 2.6 29.4 + - + +
80D ASN* 1.3 80.6 - - - +
82D GLN* 1.3 59.1 + - - +
83D THR 3.4 2.0 - - - -
84D MET* 3.2 20.3 + - - +
85D TYR* 2.9 44.1 + - + -
92D TRP* 4.6 1.1 - - + -
141D GLN* 3.3 31.4 - - - +
176D PHE* 3.9 25.8 - - + -
179D ASN* 4.2 7.4 - - - +
301D COA 4.0 19.3 - - + +
1H SER* 3.7 29.4 - - - +
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Residues in contact with GLN 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D LYS* 3.1 51.0 + - + +
79D THR 4.9 0.6 + - - +
80D ASN 3.8 0.8 - - - -
81D MET* 1.3 76.7 - - - +
83D THR* 1.3 53.2 + - - +
85D TYR* 2.9 4.9 + - - +
86D GLU* 2.8 55.2 + - - +
92D TRP* 3.5 43.0 - - + +
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Residues in contact with THR 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D THR 5.9 0.2 + - - -
80D ASN 5.4 1.3 + - - -
81D MET 3.4 0.2 - - - -
82D GLN* 1.3 77.5 - - - +
84D MET* 1.3 59.0 + - + +
86D GLU* 3.1 19.9 + - - +
87D GLN* 3.0 49.3 + - + +
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Residues in contact with MET 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D ASN 4.8 8.3 + - - +
81D MET* 3.2 23.4 + - + +
83D THR* 1.3 80.6 - - + +
85D TYR* 1.3 60.5 + - - +
87D GLN* 3.6 12.3 + - - +
88D SER* 3.5 6.8 + - - -
176D PHE* 3.7 17.9 - - + -
178D HIS* 2.8 38.2 + - + +
179D ASN* 3.2 57.0 - - + +
301D COA 5.3 0.7 - - - +
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Residues in contact with TYR 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D THR* 5.5 0.2 - - + -
81D MET* 2.9 39.2 + - + +
82D GLN 2.9 10.1 + - - +
84D MET* 1.3 76.1 - - - +
86D GLU* 1.3 60.3 + - - +
87D GLN 3.2 0.4 - - - -
88D SER* 3.0 20.9 + - - -
90D TRP* 3.5 26.0 - + + -
91D GLY* 3.0 33.4 + - - -
92D TRP* 3.6 28.9 - + + -
93D LYS 5.4 0.7 - - - -
97D LYS* 3.0 32.4 + - - -
176D PHE* 3.6 21.1 - + - -
1H SER* 2.8 31.7 + - - -
2H GLY* 3.4 9.9 + - - -
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Residues in contact with GLU 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLN* 2.8 43.6 + - - +
83D THR* 3.1 24.1 + - + +
85D TYR* 1.3 73.2 - - - +
87D GLN* 1.3 62.7 + - + +
88D SER 3.3 5.6 + - - +
91D GLY* 4.3 3.4 - - - -
92D TRP* 4.2 16.1 - - + +
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Residues in contact with GLN 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D THR* 3.0 35.8 + - + +
84D MET* 3.9 13.1 - - - +
85D TYR 3.2 0.6 - - - -
86D GLU* 1.3 79.1 - - + +
88D SER* 1.3 57.1 + - - +
178D HIS* 3.8 28.2 + - + +
210D SER* 4.9 2.6 + - - -
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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