Contacts of the helix formed by residues 79 - 95 (chain B) in PDB entry 3BLR
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 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B PHE* 4.0 10.1 - - + +
76B THR 5.7 1.6 - - - +
77B ARG 3.3 11.7 - - - +
78B PHE* 1.3 86.7 - - + +
80B GLY* 1.3 60.0 + - - +
81B ASN* 3.0 7.6 - - + +
82B SER* 2.8 38.5 + - - +
83B VAL* 3.1 9.4 + - - +
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Residues in contact with GLY 80 (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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37B TYR 5.6 0.9 - - - -
41B ALA* 4.6 15.1 - - - +
44B LEU* 4.4 0.8 - - - +
70B TYR* 3.5 17.4 + - - -
75B PHE* 4.4 14.8 - - - -
78B PHE 3.5 0.8 + - - -
79B PRO* 1.3 72.3 - - - +
81B ASN* 1.3 58.9 + - - +
82B SER 3.1 0.2 - - - -
83B VAL* 4.4 2.0 - - - -
84B ALA* 2.9 35.5 + - - +
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Residues in contact with ASN 81 (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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40B GLN* 5.6 5.9 - - - +
41B ALA* 5.8 1.4 - - - -
44B LEU* 3.6 17.9 - - - +
79B PRO* 3.0 6.1 + - + +
80B GLY* 1.3 78.1 - - - +
82B SER* 1.3 58.0 + - - +
85B PRO* 3.3 20.8 - - - +
112B LEU* 3.7 39.5 - - + +
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PHE* 6.4 0.2 - - - -
79B PRO* 2.8 26.4 + - - +
81B ASN* 1.3 80.5 - - - +
83B VAL* 1.3 64.0 + - - +
84B ALA 3.5 0.2 - - - -
85B PRO* 3.6 8.9 - - - +
86B ALA* 3.8 6.9 + - - +
133B LEU* 5.7 1.0 - - - +
136B LEU* 3.2 30.6 - - - +
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Residues in contact with VAL 83 (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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66B MET* 4.9 9.9 - - + -
69B PHE* 3.8 32.3 - - + -
70B TYR* 3.0 33.9 - - + +
78B PHE* 3.8 11.7 - - + -
79B PRO 3.1 7.5 + - - +
80B GLY* 4.1 2.2 - - - +
82B SER* 1.3 76.7 - - - +
84B ALA* 1.3 62.0 + - - +
86B ALA* 3.1 5.7 + - - +
87B ALA* 2.8 30.9 + - + -
136B LEU* 4.1 17.9 - - + -
140B ILE* 3.9 13.6 - - + +
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA* 4.1 15.9 - - + +
44B LEU* 4.1 11.4 - - + -
45B LEU* 3.2 34.1 - - + +
48B MET* 4.0 1.8 - - + -
66B MET* 5.7 2.0 - - + +
80B GLY 2.9 20.1 + - - +
83B VAL* 1.3 77.2 - - - +
85B PRO* 1.3 62.6 - - + +
87B ALA* 3.1 6.1 + - - +
88B LEU 2.8 27.0 + - - -
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Residues in contact with PRO 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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44B LEU* 4.4 3.8 - - + -
48B MET* 3.8 25.8 - - + -
81B ASN 3.3 26.7 - - - +
82B SER 3.6 8.5 - - - +
84B ALA* 1.3 93.2 - - + +
86B ALA* 1.3 56.0 - - - +
88B LEU* 3.4 3.0 + - + +
89B PHE* 3.0 28.3 + - - +
104B VAL* 3.8 9.8 - - + +
108B ALA* 3.9 24.0 - - + -
112B LEU* 5.0 1.3 - - + -
133B LEU* 4.4 13.5 - - + -
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Residues in contact with ALA 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 SER 3.8 6.3 + - - +
83B VAL 3.1 8.3 + - - +
85B PRO* 1.3 76.8 - - - +
87B ALA* 1.3 63.4 + - - +
89B PHE* 3.3 4.3 + - - +
90B LEU* 3.1 23.7 + - - +
133B LEU* 3.9 27.5 - - + +
136B LEU* 3.8 28.9 - - + -
137B GLU* 4.1 6.2 - - - +
140B ILE* 3.9 10.7 - - + +
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LEU* 4.7 2.9 - - + -
62B ALA* 4.1 20.9 - - - +
65B TYR* 4.1 14.0 - - + -
66B MET* 4.8 5.6 - - + +
83B VAL* 2.8 22.6 + - + +
84B ALA* 3.4 11.7 - - - +
86B ALA* 1.3 72.8 - - - +
88B LEU* 1.3 56.2 + - - +
90B LEU* 3.3 6.1 + - - +
91B ALA* 2.9 29.5 + - - +
140B ILE* 3.6 14.9 - - + +
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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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45B LEU* 3.6 11.0 - - + +
48B MET* 3.7 37.9 - - + -
49B GLY* 3.9 9.4 - - - +
52B LEU* 3.8 22.2 - - + -
54B VAL* 4.6 6.1 - - + -
58B THR* 4.5 11.7 - - + -
59B ILE* 4.5 21.5 - - + -
62B ALA* 3.9 21.3 - - + -
84B ALA 2.8 18.8 + - - +
85B PRO 3.6 4.7 - - - +
87B ALA* 1.3 72.9 - - - +
89B PHE* 1.3 57.4 + - - +
92B ALA* 3.0 31.4 + - + +
104B VAL* 5.4 2.9 - - + -
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 3.3 31.0 - - - -
58A GLY* 4.5 1.3 - - - -
85B PRO 3.0 17.1 + - - +
86B ALA* 3.5 7.0 - - - +
88B LEU* 1.3 77.5 - - - +
90B LEU* 1.3 60.3 + - - +
92B ALA* 3.8 4.9 + - - +
93B LYS* 3.4 34.8 + - + +
99B LYS* 3.4 26.0 - - + +
101B LEU* 3.7 34.5 - - + -
104B VAL* 3.9 24.0 - - + +
133B LEU* 3.7 19.7 - - + -
134B VAL* 5.4 0.9 - - + -
137B GLU* 3.5 31.9 - - + -
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Residues in contact with LEU 90 (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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64A LEU* 4.0 20.4 - - + -
65B TYR* 4.0 20.4 - - + -
86B ALA 3.1 12.5 + - - +
87B ALA 3.5 7.2 - - - +
89B PHE* 1.3 74.9 - - - +
91B ALA* 1.3 60.8 + - - +
93B LYS* 3.1 4.5 + - - +
94B VAL* 2.9 30.6 + - + +
137B GLU* 3.8 28.3 - - + +
140B ILE* 4.1 24.7 - - + -
141B LEU* 3.7 37.2 - - + -
148B LEU* 4.3 4.3 - - + -
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Residues in contact with ALA 91 (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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58B THR* 3.6 25.6 - - + +
61B THR* 3.9 4.9 - - + -
62B ALA* 3.7 17.9 - - + +
65B TYR* 3.8 15.7 - - + -
87B ALA 2.9 17.2 + - - +
88B LEU 3.4 3.8 + - - +
90B LEU* 1.3 76.4 - - - +
92B ALA* 1.3 52.3 + - - +
94B VAL* 3.7 2.6 - - - -
95B GLU* 2.7 40.2 + - - +
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Residues in contact with ALA 92 (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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54B VAL* 4.8 4.0 - - + -
58B THR* 3.5 18.1 - - + +
88B LEU* 3.0 19.0 + - + +
89B PHE* 4.0 5.6 - - - +
91B ALA* 1.3 76.0 - - - +
93B LYS* 1.3 61.8 + - - +
96B GLY 3.3 2.4 + - - -
97B GLN 2.8 51.1 + - - +
98B PRO* 3.3 0.4 - - - -
99B LYS* 4.2 18.8 - - + +
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Residues in contact with LYS 93 (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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57A GLU* 2.7 29.0 + - + +
59A PHE 2.6 30.8 + - - +
61A ILE* 3.8 39.9 - - + +
64A LEU* 4.1 16.2 - - + +
89B PHE* 3.4 27.8 + - + +
90B LEU* 3.1 7.4 + - - +
92B ALA* 1.3 76.3 - - - +
94B VAL* 1.3 65.2 + - - +
95B GLU 3.3 0.3 + - - -
96B GLY* 3.5 6.6 + - - -
98B PRO* 4.4 17.0 - - + -
99B LYS 5.2 2.0 - - - +
137B GLU* 2.9 28.0 + - - -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 4.0 17.7 - - + -
68A LYS* 5.6 8.1 - - + +
65B TYR* 3.5 23.6 - - - +
90B LEU* 2.9 22.1 + - + +
91B ALA 3.8 3.6 - - - +
93B LYS* 1.3 77.5 - - - +
95B GLU* 1.3 73.7 + - + +
96B GLY 3.5 0.3 + - - -
148B LEU* 3.6 43.7 - - + +
149B THR* 5.5 1.1 - - - -
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LEU* 3.5 27.0 - - + +
58B THR* 3.8 24.7 - - + +
61B THR* 3.0 38.6 + - + +
91B ALA 2.7 23.4 + - - +
92B ALA 4.6 0.4 - - - +
93B LYS 3.2 0.2 - - - -
94B VAL* 1.3 81.9 - - + +
96B GLY* 1.3 59.7 + - - +
97B GLN* 3.5 7.6 + - - +
148B LEU 5.2 0.3 - - - +
150B ILE 4.9 10.9 + - - +
152B HIS* 5.0 0.7 + - - -
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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