Contacts of the helix formed by residues 68 - 90 (chain B) in PDB entry 5DIR
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 TRP 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY* 1.3 73.4 - - - -
69B GLN* 1.3 106.3 + - + +
70B ARG 3.2 2.1 + - - -
71B TRP* 3.4 9.6 + - - +
72B LEU* 3.4 32.0 + - + +
73B PHE* 6.4 0.4 - + - -
62D LEU* 3.4 39.3 - - + -
64D ASP* 4.2 15.8 + - - -
65D SER* 2.5 31.2 + - - -
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ASN* 5.3 6.6 + - - -
60B SER 3.9 15.0 + - - +
67B GLY* 3.4 0.8 - - - -
68B TRP* 1.3 111.7 - - + +
70B ARG* 1.3 65.9 + - - +
72B LEU* 4.6 4.0 - - - -
73B PHE* 3.0 57.4 + - + -
62D LEU* 6.0 2.4 - - - +
65D SER* 3.8 24.7 - - - +
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY* 3.3 27.6 + - - +
69B GLN* 1.3 78.9 - - - +
71B TRP* 1.3 97.7 + - + +
73B PHE* 5.1 0.2 - - - -
74B ALA* 3.2 23.7 + - - +
116B ARG* 2.9 40.1 + - + +
117B MET 2.7 26.7 + - - -
118B VAL 4.7 2.8 + - - -
119B LEU 3.8 7.1 + - - -
120B GLY* 4.2 24.7 - - - +
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Residues in contact with TRP 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLY 3.4 25.4 + - - +
68B TRP* 3.4 9.2 + - - +
69B GLN 3.1 0.2 - - - -
70B ARG* 1.3 121.2 - - + +
72B LEU* 1.3 58.9 + - - +
73B PHE 3.1 1.8 - - - -
74B ALA* 3.5 12.2 - - + +
75B LEU* 2.6 39.6 + - + +
117B MET* 4.3 29.6 - - + -
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TRP* 3.4 28.7 + - + +
69B GLN* 3.4 5.4 + - - +
71B TRP* 1.3 77.2 - - - +
73B PHE* 1.3 69.4 + - + +
75B LEU* 3.5 16.1 + - + +
76B ILE* 3.1 32.0 + - + +
205H 5BV 4.2 30.1 - - + -
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TRP* 6.4 0.4 - + - -
69B GLN* 3.0 46.0 + - + +
70B ARG* 5.1 0.2 - - - -
72B LEU* 1.3 94.0 - - + +
74B ALA* 1.3 64.6 + - - +
76B ILE* 3.1 18.9 - - + +
77B ALA* 3.2 12.3 + - - +
116B ARG* 3.3 36.5 + - - +
201H MLE 3.8 5.2 - - - -
203H SER 5.5 0.9 - - - -
204H ALO 4.4 5.4 - - - -
205H 5BV 3.5 62.8 - - + -
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG 3.2 21.0 + - - +
71B TRP* 3.0 17.8 + - + +
73B PHE* 1.3 76.1 - - - +
75B LEU* 1.3 62.6 - - - +
77B ALA* 3.3 3.9 + - - +
78B ILE* 3.2 29.2 + - - +
113B LEU* 3.5 22.2 - - + +
116B ARG* 4.2 7.3 - - + +
117B MET* 4.1 17.7 - - + +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TRP* 2.6 21.5 + - + +
72B LEU* 3.7 16.4 - - + +
74B ALA* 1.3 74.1 - - - +
76B ILE* 1.3 67.0 + - + +
77B ALA 3.3 0.2 + - - -
78B ILE* 3.3 11.4 + - - +
79B VAL* 3.2 38.2 + - + +
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Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 3.1 19.3 + - + +
73B PHE* 3.1 24.2 - - + +
75B LEU* 1.3 83.1 - - + +
77B ALA* 1.3 61.6 + - - +
79B VAL* 4.0 4.4 - - + +
80B VAL* 3.0 37.9 + - + +
201H MLE 3.5 15.3 - - + -
205H 5BV 3.6 44.4 - - + -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE 3.2 15.3 + - - +
74B ALA* 3.4 10.1 - - - +
75B LEU 3.2 0.4 - - - -
76B ILE* 1.3 79.1 - - - +
78B ILE* 1.3 51.9 + - - +
80B VAL* 3.7 0.7 - - - +
81B SER* 2.7 43.7 + - - +
109B ALA 4.4 6.1 - - - +
113B LEU* 4.0 25.6 - - + -
116B ARG* 5.9 1.6 - - - +
201H MLE 3.5 24.7 - - + +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA 3.2 14.3 + - - +
75B LEU* 3.3 9.6 + - - +
77B ALA* 1.3 75.9 - - - +
79B VAL* 1.3 64.9 + - + +
81B SER* 3.5 6.5 - - - -
82B ALA* 3.0 26.3 + - + +
113B LEU* 3.8 18.8 - - + -
117B MET* 3.5 28.0 - - + -
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.2 29.2 + - + +
76B ILE* 4.0 6.3 - - + +
78B ILE* 1.3 79.7 - - + +
80B VAL* 1.3 69.2 + - + +
82B ALA* 3.4 6.2 + - - +
83B SER* 3.1 23.1 + - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ILE* 3.0 32.9 + - + +
77B ALA 3.9 2.0 - - - +
79B VAL* 1.3 77.5 - - + +
81B SER* 1.3 65.6 + - - +
83B SER* 2.7 22.5 + - - +
84B LEU* 3.1 31.0 + - + +
105B VAL* 5.6 0.9 - - + -
109B ALA* 5.9 0.7 - - + -
201H MLE 4.2 27.4 - - + -
205H 5BV 6.3 0.4 - - + -
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Residues in contact with SER 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA* 2.7 29.5 + - - +
78B ILE* 3.5 7.2 - - - -
80B VAL* 1.3 73.4 - - - +
82B ALA* 1.3 63.9 + - - +
84B LEU* 3.1 3.0 + - - -
85B VAL* 3.1 27.7 + - - +
106B LEU* 3.4 22.2 - - - +
109B ALA* 3.9 15.1 - - - +
110B LEU* 3.6 25.7 - - - +
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 3.0 19.0 + - + +
79B VAL* 3.5 7.6 - - - +
80B VAL 3.3 0.2 - - - -
81B SER* 1.3 76.0 - - - +
83B SER* 1.3 62.8 + - - +
85B VAL* 3.1 10.6 + - - +
86B VAL* 3.0 30.2 + - + +
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Residues in contact with SER 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 3.1 8.8 + - - -
80B VAL* 2.7 29.1 + - - +
82B ALA* 1.3 79.0 - - - +
84B LEU* 1.3 63.3 + - - +
86B VAL* 3.9 7.7 - - - +
87B TRP* 3.0 31.2 + - - +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL* 3.1 38.3 + - + +
81B SER* 3.1 8.7 + - - +
83B SER* 1.3 82.1 + - - +
85B VAL* 1.3 56.5 + - - +
87B TRP* 3.6 21.7 - - + +
88B LEU* 2.8 34.0 + - - +
102B LEU* 4.2 24.1 - - + +
105B VAL* 3.6 35.9 - - + -
106B LEU* 4.0 28.0 - - + +
109B ALA* 5.7 1.1 - - + -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LEU* 6.0 0.7 - - + -
13B LEU* 5.0 15.5 - - + -
81B SER* 3.1 15.6 + - - +
82B ALA* 3.1 8.5 + - - +
84B LEU* 1.3 73.6 - - - +
86B VAL* 1.3 61.7 + - + +
88B LEU* 3.0 9.1 + - + +
89B LYS* 2.9 51.1 + - + +
106B LEU* 3.7 25.8 - - + -
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ALA* 3.0 24.0 + - + +
83B SER* 3.9 8.3 - - - +
85B VAL* 1.3 76.3 - - + +
87B TRP* 1.3 58.1 + - + +
89B LYS* 3.3 9.6 + - + +
90B ARG* 3.1 69.6 + - + +
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Residues in contact with TRP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B SER* 3.0 21.0 + - - +
84B LEU* 3.8 21.1 - - + +
86B VAL* 1.3 74.8 - - - +
88B LEU* 1.3 63.2 + - - +
90B ARG* 3.6 14.8 + - + +
91B LEU* 3.2 28.5 + - + +
98B LEU* 4.4 21.7 - - + +
102B LEU* 3.4 31.2 - - + -
153B LEU* 3.6 28.0 - - + -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ARG* 3.4 25.7 - - + +
10B LEU* 5.1 2.2 - - + -
12B TRP* 4.3 11.4 - - + -
13B LEU* 3.5 37.9 - - + -
84B LEU 2.8 17.5 + - - +
85B VAL* 3.0 8.7 + - + +
87B TRP* 1.3 76.0 - - - +
89B LYS* 1.3 65.9 + - - +
91B LEU* 3.2 26.7 + - + +
99B ALA* 4.0 35.9 - - + +
102B LEU* 4.2 15.0 - - + -
103B ALA* 5.1 5.2 - - + +
106B LEU* 5.5 2.2 - - + -
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ARG* 4.1 11.0 + - - +
10B LEU* 3.6 35.0 - - + -
85B VAL* 2.9 35.3 + - + +
86B VAL* 3.3 13.3 + - + +
88B LEU* 1.3 78.1 - - + +
90B ARG* 1.3 75.7 + - - +
91B LEU 2.9 12.8 + - - +
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B VAL* 3.1 50.7 + - + +
87B TRP* 3.9 14.6 - - + +
88B LEU 3.2 0.6 - - - -
89B LYS* 1.3 97.4 - - - +
91B LEU* 1.3 61.5 + - - +
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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
------------------------------------------------------------
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