Contacts of the helix formed by residues 94 - 111 (chain D) in PDB entry 4BPU
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 94 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D PRO* 1.3 76.0 - - + +
96D ARG* 3.1 10.2 - - - +
97D ARG* 3.2 26.2 + - + +
98D ARG* 3.1 30.3 + - - +
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Residues in contact with PRO 95 (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 LYS* 3.7 16.2 - - + +
83D PHE* 4.1 4.3 - - - -
84D SER* 3.5 41.2 + - - +
94D GLU* 1.3 92.3 - - + +
96D ARG* 1.3 61.2 + - + +
97D ARG 3.2 0.2 - - - -
98D ARG* 3.8 7.1 - - + +
99D ASP* 2.9 28.4 + - - +
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Residues in contact with ARG 96 (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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26D LEU 5.4 13.0 - - - +
27D GLN* 5.5 0.5 - - - +
84D SER* 6.1 3.4 - - - -
94D GLU 3.1 6.2 - - - +
95D PRO* 1.3 79.3 - - + +
97D ARG* 1.3 55.9 + - - +
99D ASP* 3.6 6.7 - - - +
100D HIS* 2.7 36.0 + - - +
131D ARG* 6.2 1.6 - - - +
139D LYS* 4.8 17.4 - - - +
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Residues in contact with ARG 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLU* 2.4 53.7 + - - +
36D ASN 5.0 0.2 + - - -
37D ILE* 4.1 2.4 - - - +
41D GLU* 2.5 33.7 + - - -
45D LEU* 5.3 0.6 - - - +
94D GLU* 3.2 28.9 + - - +
95D PRO 3.2 0.4 - - - -
96D ARG* 1.3 77.4 - - - +
98D ARG* 1.3 74.5 + - - +
100D HIS* 3.1 5.3 + - + +
101D ILE* 2.9 55.1 + - + +
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Residues in contact with ARG 98 (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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44D ASN* 6.1 1.2 - - - +
45D LEU* 3.5 31.9 - - + +
48D ASP* 3.4 24.7 + - - +
81D LEU 2.7 28.9 + - - -
82D LYS* 3.2 42.2 + - - +
83D PHE* 3.6 20.9 - - + -
94D GLU 3.1 13.2 + - - +
95D PRO* 3.8 7.2 - - - +
96D ARG 3.3 0.2 - - - -
97D ARG* 1.3 95.1 - - - +
99D ASP* 1.3 55.9 + - - +
102D SER* 2.8 34.8 + - - -
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Residues in contact with ASP 99 (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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26D LEU 5.4 1.0 + - - -
27D GLN* 5.2 2.4 - - - +
29D TYR* 2.7 30.5 + - - -
49D ARG* 2.8 24.3 + - - +
83D PHE* 3.8 11.3 - - + -
95D PRO 2.9 19.4 + - - +
96D ARG* 3.7 7.5 - - - +
98D ARG* 1.3 76.5 - - - +
100D HIS* 1.3 62.8 + - - +
102D SER* 3.1 14.6 + - - -
103D HIS* 3.4 8.3 + - - +
131D ARG* 2.4 43.3 + - - +
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Residues in contact with HIS 100 (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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27D GLN* 3.1 37.3 + - - +
29D TYR* 4.3 5.2 - + - -
31D GLN* 3.2 25.4 + - + -
32D PRO 4.3 0.7 - - - -
33D PRO* 3.4 35.0 - - + +
96D ARG 2.7 22.8 + - - +
97D ARG* 3.5 6.7 - - - +
99D ASP* 1.3 79.6 - - - +
101D ILE* 1.3 62.9 + - + +
103D HIS* 3.5 4.7 + - - +
104D PHE* 3.4 36.7 - + - -
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Residues in contact with ILE 101 (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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33D PRO* 4.2 23.6 - - + -
35D GLU* 4.2 11.4 - - + +
37D ILE* 3.7 28.7 - - + -
45D LEU* 3.6 15.3 - - + -
97D ARG* 2.9 56.7 + - + +
100D HIS* 1.3 73.1 - - + +
102D SER* 1.3 61.2 + - - +
104D PHE* 3.0 4.6 + - + +
105D ILE* 2.9 49.3 + - + +
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Residues in contact with SER 102 (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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45D LEU* 3.8 24.6 - - - +
49D ARG* 2.7 51.7 + - - +
83D PHE* 4.0 4.8 - - - -
98D ARG 2.8 22.9 + - - -
99D ASP* 3.1 1.0 + - - -
101D ILE* 1.3 76.8 - - - +
103D HIS* 1.3 55.2 + - - +
105D ILE* 3.3 7.7 + - - +
106D LEU* 2.9 34.7 + - - +
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Residues in contact with HIS 103 (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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29D TYR* 3.2 38.0 - + + +
49D ARG* 3.7 16.6 - - - +
99D ASP 3.4 14.3 + - - +
100D HIS 3.8 4.7 - - - +
101D ILE 3.2 0.6 - - - -
102D SER* 1.3 81.0 + - - +
104D PHE* 1.3 62.7 + + - +
106D LEU* 3.4 1.7 + - - -
107D ARG* 3.2 56.6 + - - +
120D PHE* 3.5 25.9 - + - -
124D GLU* 2.6 38.7 + - + -
226D LEU* 3.5 12.7 - - + +
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Residues in contact with PHE 104 (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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29D TYR* 3.9 10.8 - - + -
30D LEU 3.9 2.9 - - - -
31D GLN 3.4 25.6 - - - -
32D PRO* 3.9 21.3 - - + -
33D PRO* 3.9 21.1 - - + -
100D HIS* 3.4 30.7 + + - +
101D ILE* 3.0 7.6 + - + +
103D HIS* 1.3 86.6 - + - +
105D ILE* 1.3 67.0 + - + +
107D ARG* 3.0 61.7 - - - +
108D LEU* 4.1 8.7 + - - +
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Residues in contact with ILE 105 (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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37D ILE* 4.1 2.7 - - + -
42D PHE* 3.4 68.4 - - + +
45D LEU* 4.3 10.8 - - + -
46D ALA* 3.7 23.3 - - + -
101D ILE* 2.9 37.8 + - + +
102D SER* 3.6 6.5 - - - +
104D PHE* 1.3 78.7 - - - +
106D LEU* 1.3 63.1 + - - +
108D LEU* 3.1 24.8 + - - +
249D LEU* 3.7 9.1 - - + +
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Residues in contact with LEU 106 (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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46D ALA* 3.7 24.9 - - + +
49D ARG* 3.8 20.6 - - + -
50D VAL* 3.6 35.7 - - + +
53D LEU* 3.7 29.2 - - + -
102D SER 2.9 18.5 + - - +
103D HIS 3.4 2.0 + - - +
105D ILE* 1.3 72.5 - - - +
107D ARG* 1.3 59.6 + - - +
108D LEU 3.1 0.2 - - - -
109D ALA* 3.0 4.5 + - - +
110D TYR* 2.8 42.8 + - + +
120D PHE* 3.6 14.8 - - + -
249D LEU* 4.2 9.9 - - + -
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Residues in contact with ARG 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D TYR* 2.6 30.5 + - - +
30D LEU 4.7 3.6 + - - -
103D HIS* 3.2 39.6 + - - +
104D PHE* 3.0 48.9 - - - +
105D ILE 3.1 1.0 - - - -
106D LEU* 1.3 77.2 - - - +
108D LEU* 1.3 64.1 + - + +
111D CYS* 3.3 28.9 + - - +
120D PHE* 4.3 8.3 - - + -
226D LEU* 4.0 12.8 - - - +
229D ALA* 3.4 29.3 + - - +
230D LEU* 3.8 24.9 - - + +
233D THR* 4.1 23.5 + - + +
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Residues in contact with LEU 108 (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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96A LEU* 5.4 6.3 - - + -
42D PHE* 4.5 12.8 - - + -
104D PHE 4.3 8.3 - - - +
105D ILE* 3.1 14.1 + - - +
106D LEU 3.1 0.6 - - - -
107D ARG* 1.3 80.6 - - - +
109D ALA* 1.3 61.5 + - - +
111D CYS* 3.6 7.1 - - - -
112D GLN* 4.0 0.7 - - - +
233D THR* 5.1 16.2 - - + +
236D SER* 6.4 0.4 - - - -
237D LEU* 3.5 33.2 - - + +
240D VAL* 5.1 4.9 - - + -
246D LEU* 4.3 28.5 - - + -
249D LEU* 4.5 2.9 - - + -
250D LEU* 3.5 22.4 - - + +
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Residues in contact with ALA 109 (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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105D ILE 3.9 0.6 + - - -
106D LEU* 3.0 9.6 + - - +
108D LEU* 1.3 80.6 - - - +
110D TYR* 1.3 75.2 + - + +
111D CYS 3.5 1.0 + - - -
112D GLN* 2.5 30.6 + - - +
116D LEU* 3.9 5.9 - - - +
249D LEU* 3.5 39.9 - - + +
250D LEU* 4.2 5.6 - - - +
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Residues in contact with TYR 110 (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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50D VAL* 4.1 22.7 - - + +
54D LYS* 5.0 4.0 - - - -
106D LEU* 2.8 49.3 + - + +
107D ARG* 4.0 1.3 - - - -
108D LEU 3.5 0.2 - - - -
109D ALA* 1.3 85.8 - - + +
111D CYS* 1.3 58.5 + - - +
112D GLN 3.4 1.8 - - - -
116D LEU* 3.3 40.5 - - + +
117D ARG* 3.1 29.1 + - - +
119D TRP* 3.4 39.2 - + - -
120D PHE* 3.5 33.2 - + + -
230D LEU* 4.6 3.3 - - - +
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Residues in contact with CYS 111 (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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107D ARG 3.3 19.1 + - - +
108D LEU* 3.6 13.9 - - - -
110D TYR* 1.3 77.4 - - - +
112D GLN* 1.3 66.4 + - - +
113D SER 3.2 2.9 - - - -
117D ARG* 3.0 30.6 + - - -
230D LEU* 3.5 26.5 - - + +
233D THR* 3.7 7.4 - - - +
234D ALA* 3.7 27.9 - - - +
237D LEU* 3.7 18.2 - - - -
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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
------------------------------------------------------------
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