Contacts of the helix formed by residues 102 - 120 (chain B) in PDB entry 4BHT
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 ASN 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLU* 4.9 4.6 + - - -
80B TRP* 3.8 14.1 - - + -
100B SER 4.1 9.5 + - - +
101B VAL* 1.3 77.6 - - - +
103B LEU* 1.3 67.7 + - - +
104B SER* 3.3 10.8 + - - -
105B ILE* 2.7 45.0 + - - +
106B LEU* 2.9 25.5 + - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B GLN* 3.7 22.4 - - - +
60B VAL* 3.8 32.5 - - + -
62B GLN* 5.8 3.6 - - - +
80B TRP* 3.9 27.3 - - + +
82B VAL* 3.8 10.8 - - + -
102B ASN* 1.3 75.1 - - - +
104B SER* 1.3 57.3 + - - +
106B LEU* 3.2 2.1 + - - -
107B LYS* 2.8 48.7 + - + +
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Residues in contact with SER 104 (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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20B ASN 5.0 0.9 - - - -
21B GLN* 3.3 41.6 - - - +
23B GLU* 2.7 25.0 + - - -
24B PHE* 3.2 18.8 + - - -
102B ASN* 3.2 10.6 + - - -
103B LEU* 1.3 78.0 - - - +
105B ILE* 1.3 63.0 + - - +
107B LYS* 3.9 2.1 - - - +
108B PHE* 3.1 23.4 + - - +
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Residues in contact with ILE 105 (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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23B GLU* 3.6 31.0 - - + +
96B ARG* 4.4 14.8 - - - +
100B SER* 3.5 34.8 - - - +
101B VAL* 5.0 4.3 - - - -
102B ASN* 2.7 29.5 + - - +
104B SER* 1.3 72.7 - - - +
106B LEU* 1.3 65.4 + - + +
108B PHE* 3.3 13.0 + - + -
109B LEU* 3.1 40.5 + - + +
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Residues in contact with LEU 106 (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 TRP* 3.5 49.4 - - + -
82B VAL* 3.9 16.6 - - + +
96B ARG* 4.8 8.5 - - + -
101B VAL* 3.8 18.2 - - + -
102B ASN 2.9 14.6 + - - +
103B LEU* 3.8 3.8 - - - +
105B ILE* 1.3 79.6 - - + +
107B LYS* 1.3 56.8 + - - +
109B LEU* 3.4 7.7 + - + -
110B GLY* 2.9 25.1 + - - -
128B LYS* 3.6 21.7 - - + +
129B GLY* 3.4 25.4 - - - +
130B GLY 3.8 9.2 - - - +
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Residues in contact with LYS 107 (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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18B ASP* 2.9 32.3 + - - -
21B GLN* 2.9 28.8 + - - +
24B PHE* 3.6 32.5 - - + -
55B VAL 5.2 0.2 + - - -
56B GLU* 5.5 2.0 + - - -
57B PRO* 4.3 25.5 - - + +
60B VAL* 5.2 1.1 - - + -
82B VAL* 4.4 13.7 - - + -
84B PHE* 3.6 9.0 - - + -
103B LEU* 2.8 40.0 + - + +
104B SER 3.9 2.5 - - - +
106B LEU* 1.3 69.6 - - - +
108B PHE* 1.3 61.8 + - - +
111B PHE* 2.9 32.4 + - - +
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Residues in contact with PHE 108 (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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23B GLU* 3.7 35.9 - - + +
24B PHE* 3.9 9.3 - - - -
27B ALA* 3.5 21.9 - - + +
96B ARG* 6.0 0.7 - - - -
104B SER 3.1 16.1 + - - +
105B ILE* 3.4 21.3 - - + -
107B LYS* 1.3 78.1 - - - +
109B LEU* 1.3 88.0 + - + +
111B PHE* 3.4 3.0 + - - +
112B GLU* 3.1 45.8 + - - +
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Residues in contact with LEU 109 (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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96B ARG* 3.5 44.4 - - - +
105B ILE* 3.1 26.9 + - + +
106B LEU* 3.9 3.1 - - + +
107B LYS 3.3 0.2 - - - -
108B PHE* 1.3 106.1 - - + +
110B GLY* 1.3 51.1 + - - +
112B GLU* 3.4 6.4 + - - +
113B GLN* 2.8 40.5 + - - +
128B LYS* 3.7 34.1 - - + +
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Residues in contact with GLY 110 (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 VAL* 5.2 0.7 - - - -
84B PHE* 3.9 13.7 - - - +
106B LEU 2.9 16.0 + - - -
107B LYS 3.9 0.4 - - - -
109B LEU* 1.3 73.1 - - - +
111B PHE* 1.3 64.4 + - - +
113B GLN* 3.5 6.6 - - - +
114B THR* 3.0 26.7 + - - -
126B GLY 4.4 1.6 - - - -
127B GLY* 3.9 7.9 - - - -
128B LYS* 3.7 15.8 - - - +
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Residues in contact with PHE 111 (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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24B PHE* 4.3 7.0 - + + -
27B ALA* 3.9 24.0 - - + -
28B VAL* 3.9 13.7 - - + -
31B VAL* 3.6 33.4 - - + -
32B MET* 4.4 7.4 - - + -
54B LEU* 4.0 17.3 - - + -
55B VAL* 4.2 21.5 - - + -
84B PHE* 3.6 33.4 - + + -
107B LYS 2.9 19.0 + - - +
108B PHE* 3.5 3.8 - - - +
110B GLY* 1.3 73.4 - - - +
112B GLU* 1.3 67.0 + - + +
114B THR* 3.1 19.9 + - - -
115B PHE* 3.3 36.9 - + - -
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Residues in contact with GLU 112 (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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27B ALA* 4.6 11.2 - - + +
30B GLU* 5.7 5.4 - - - +
31B VAL* 5.2 9.8 - - + +
108B PHE* 3.1 40.5 + - + +
109B LEU* 3.8 7.3 - - - +
111B PHE* 1.3 89.7 - - + +
113B GLN* 1.3 63.9 + - - +
115B PHE* 3.1 18.9 + - + +
116B LYS* 3.1 14.8 + - - +
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Residues in contact with GLN 113 (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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92B LYS 3.7 14.1 - - - +
93B GLY* 4.1 8.3 - - - -
94B GLY 5.6 0.2 - - - +
109B LEU* 2.8 20.9 + - - +
110B GLY* 3.5 11.9 - - - +
111B PHE 3.2 0.2 - - - -
112B GLU* 1.3 76.7 - - - +
114B THR* 1.3 57.4 + - - +
116B LYS* 3.3 28.0 + - - +
117B ASN* 2.8 54.0 + - - +
126B GLY* 4.6 0.2 - - - -
127B GLY 3.7 17.7 - - - +
128B LYS* 3.7 20.1 + - + +
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Residues in contact with THR 114 (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 LEU* 5.3 6.1 - - + -
84B PHE* 3.8 10.3 - - + +
85B SER* 3.5 31.6 - - - +
88B ILE* 5.6 2.4 - - + +
110B GLY 3.0 16.0 + - - -
111B PHE* 3.3 11.7 - - - -
113B GLN* 1.3 76.6 - - - +
115B PHE* 1.3 72.5 + - + +
117B ASN* 3.9 1.9 - - - +
118B ALA* 3.1 26.2 + - + +
124B MET 5.0 1.6 - - - +
125B GLY* 4.7 2.7 - - - +
126B GLY* 3.4 23.0 - - - +
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Residues in contact with PHE 115 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B VAL* 4.5 19.5 - - + -
35B LEU* 5.9 3.6 - - + -
54B LEU* 3.8 39.3 - - + -
111B PHE* 3.3 57.0 - + - -
112B GLU* 3.1 9.6 + - + +
114B THR* 1.3 83.8 - - + +
116B LYS* 1.3 64.3 + - - +
118B ALA* 3.2 9.8 + - + +
119B LEU* 3.0 27.4 + - - +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112B GLU 3.1 15.0 + - - +
113B GLN* 3.8 27.2 + - - +
115B PHE* 1.3 75.8 - - - +
117B ASN* 1.3 64.5 + - - +
119B LEU* 3.2 26.7 + - + +
120B THR* 3.4 15.0 + - + +
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Residues in contact with ASN 117 (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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92B LYS* 3.0 31.8 + - - +
113B GLN* 2.8 36.3 + - - +
114B THR 3.9 1.3 - - - +
116B LYS* 1.3 78.9 - - - +
118B ALA* 1.3 59.7 + - - +
120B THR* 2.9 29.3 + - - +
122B LEU 3.8 7.4 - - - +
124B MET* 3.7 28.3 - - + +
125B GLY 2.7 29.7 + - - +
126B GLY* 4.2 0.2 - - - -
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Residues in contact with ALA 118 (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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88B ILE* 3.7 30.5 - - + +
114B THR* 3.1 19.5 + - + +
115B PHE* 3.2 12.3 + - + +
117B ASN* 1.3 75.9 - - - +
119B LEU* 1.3 63.1 + - - +
121B THR* 3.3 15.4 + - - -
122B LEU 4.8 2.7 - - - +
124B MET 4.4 2.4 + - - -
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Residues in contact with LEU 119 (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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115B PHE 3.0 14.3 + - - +
116B LYS* 3.2 18.2 - - + +
117B ASN 3.1 0.2 - - - -
118B ALA* 1.3 78.3 - - - +
120B THR* 1.3 60.9 + - - +
121B THR* 3.0 10.4 + - - +
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Residues in contact with THR 120 (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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116B LYS* 3.4 17.9 - - + +
117B ASN* 2.9 19.4 + - - +
119B LEU* 1.3 75.9 - - - +
121B THR* 1.3 71.2 + - - +
122B LEU* 2.9 39.8 + - + +
124B MET* 3.7 12.2 - - + +
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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