Contacts of the helix formed by residues 95 - 110 (chain B) 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 PRO 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B LYS 4.2 19.3 - - - +
83B PHE* 4.5 17.7 - - - -
96B ARG* 1.3 75.4 + - + +
97B ARG* 3.2 9.5 - - - +
98B ARG* 4.0 17.8 - - + +
99B ASP* 3.7 19.8 + - - +
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Residues in contact with ARG 96 (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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95B PRO* 1.3 85.2 - - + +
97B ARG* 1.3 60.8 + - - +
99B ASP* 4.0 4.4 + - - +
100B HIS* 3.6 19.6 + - - +
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Residues in contact with ARG 97 (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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35B GLU* 2.6 51.0 + - - +
36B ASN 4.9 0.8 + - - -
37B ILE* 4.0 5.3 - - - +
41B GLU* 2.5 31.7 + - - -
45B LEU* 5.4 0.6 - - - +
95B PRO 4.8 5.3 - - - -
96B ARG* 1.3 78.6 - - - +
98B ARG* 1.3 75.8 + - - +
99B ASP 3.3 0.4 - - - -
100B HIS* 3.1 6.0 + - - +
101B ILE* 2.9 56.0 + - + +
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Residues in contact with ARG 98 (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* 3.5 34.1 - - + +
48B ASP* 3.7 22.2 + - - -
81B LEU 2.5 29.1 + - - -
82B LYS* 2.7 41.3 + - - +
83B PHE* 3.5 23.1 - - + -
95B PRO* 3.9 16.2 + - + +
96B ARG 3.6 0.4 - - - -
97B ARG* 1.3 96.3 - - - +
99B ASP* 1.3 57.6 + - - +
101B ILE* 4.0 0.4 - - - -
102B SER* 2.8 35.3 + - - -
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Residues in contact with ASP 99 (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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29B TYR* 2.4 29.9 + - - -
49B ARG* 2.9 31.6 + - - +
52B LEU* 4.9 0.2 - - - +
83B PHE* 3.9 14.9 - - + -
95B PRO 3.7 14.2 + - - +
96B ARG* 4.3 4.7 - - - +
97B ARG 3.3 0.6 - - - -
98B ARG* 1.3 79.5 - - - +
100B HIS* 1.3 61.7 + - - +
102B SER* 3.2 7.6 + - - -
103B HIS* 3.3 10.6 - - - +
131B ARG* 2.4 42.5 + - - +
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Residues in contact with HIS 100 (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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29B TYR* 3.9 22.6 - + + -
30B LEU 5.2 0.4 + - - -
31B GLN* 3.1 29.8 + - + -
32B PRO 4.4 0.2 - - - -
33B PRO* 3.6 29.1 - - + +
96B ARG 3.6 13.0 + - - +
97B ARG* 3.1 10.2 + - - +
99B ASP* 1.3 81.4 + - - +
101B ILE* 1.3 66.8 + - + +
103B HIS* 3.5 1.0 + - - +
104B PHE* 3.3 44.4 + + - -
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Residues in contact with ILE 101 (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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11B LEU* 4.8 5.4 - - + -
33B PRO* 4.1 23.1 - - + -
35B GLU* 4.2 11.9 - - + +
37B ILE* 3.6 28.3 - - + -
45B LEU* 3.6 16.2 - - + -
97B ARG* 2.9 56.9 + - + +
100B HIS* 1.3 74.6 - - + +
102B SER* 1.3 60.8 + - - +
104B PHE* 3.0 4.0 + - - +
105B ILE* 2.9 48.1 + - + +
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Residues in contact with SER 102 (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* 3.8 24.4 - - - +
49B ARG* 2.6 51.8 + - - +
83B PHE* 4.0 4.9 - - - -
98B ARG 2.8 23.1 + - - -
99B ASP* 3.2 1.0 + - - -
101B ILE* 1.3 77.4 - - - +
103B HIS* 1.3 55.8 + - - +
105B ILE* 3.3 7.5 + - - +
106B LEU* 2.9 34.7 + - - +
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Residues in contact with HIS 103 (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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29B TYR* 3.7 36.6 - + + +
49B ARG* 3.6 9.9 - - - +
99B ASP 3.3 17.0 + - - +
100B HIS 3.6 4.5 - - - +
101B ILE 3.1 0.2 - - - -
102B SER* 1.3 83.7 + - - +
104B PHE* 1.3 68.1 + + - +
106B LEU* 3.5 0.4 + - - -
107B ARG* 3.2 55.2 + - - +
120B PHE* 3.8 19.0 - + - -
124B GLU* 2.7 45.4 + - + +
222B PHE* 5.1 0.7 - + - -
226B LEU* 4.0 9.3 - - + +
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Residues in contact with PHE 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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11B LEU* 3.7 24.6 - - + +
29B TYR* 4.1 8.1 - - + -
30B LEU 4.1 6.1 - - - -
31B GLN 3.3 17.9 - - - -
32B PRO* 3.8 28.9 - - + -
33B PRO* 3.6 12.3 - - + -
100B HIS* 3.3 43.6 + + - -
101B ILE 3.0 4.7 + - - +
103B HIS* 1.3 91.7 - + - +
105B ILE* 1.3 65.3 + - - +
107B ARG* 3.1 55.8 - - - +
108B LEU* 3.9 10.4 - - - +
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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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11B LEU* 3.9 13.2 - - + -
37B ILE* 4.1 2.9 - - + -
42B PHE* 3.4 65.1 - - + +
45B LEU* 4.4 8.7 - - + -
46B ALA* 3.7 23.1 - - + +
101B ILE* 2.9 37.8 + - + +
102B SER* 3.7 5.6 - - - +
104B PHE* 1.3 77.9 - - - +
106B LEU* 1.3 63.2 + - - +
108B LEU* 3.1 24.5 + - - +
109B ALA 3.7 1.9 + - - -
246B LEU* 5.1 0.2 - - + -
249B LEU* 4.2 8.3 - - + +
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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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46B ALA* 3.7 24.9 - - + +
49B ARG* 3.6 31.6 - - + -
50B VAL* 3.6 33.4 - - + +
53B LEU* 3.8 20.6 - - + -
102B SER 2.9 19.1 + - - +
103B HIS 3.5 1.3 + - - +
105B ILE* 1.3 74.7 - - - +
107B ARG* 1.3 64.7 + - - +
108B LEU 3.2 0.2 - - - -
109B ALA* 3.2 2.7 + - - +
110B TYR* 3.0 40.4 + - + +
120B PHE* 3.6 15.9 - - + -
249B LEU* 4.1 8.5 - - + -
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Residues in contact with ARG 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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29B TYR* 3.1 26.3 + - - +
30B LEU 4.9 4.4 + - - -
103B HIS* 3.2 40.4 + - - +
104B PHE* 3.1 45.5 - - - +
105B ILE 3.1 0.8 - - - -
106B LEU* 1.3 77.6 - - - +
108B LEU* 1.3 63.1 + - + +
111B CYS* 3.3 28.9 + - - +
120B PHE* 4.0 13.7 - - + -
222B PHE* 5.3 0.8 - - - -
226B LEU* 3.6 19.8 - - - +
229B ALA* 4.8 16.4 - - - +
230B LEU* 3.4 26.9 - - + +
233B THR* 4.9 9.0 + - + +
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Residues in contact with LEU 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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10B LYS* 5.9 2.9 - - - +
11B LEU* 4.3 18.8 - - + +
42B PHE* 4.9 2.7 - - + -
104B PHE 3.9 9.0 - - - +
105B ILE* 3.1 15.7 + - - +
107B ARG* 1.3 79.6 - - + +
109B ALA* 1.3 61.6 + - - +
111B CYS* 3.5 11.1 - - - -
112B GLN* 4.3 3.3 - - - +
233B THR* 5.6 9.9 - - + -
237B LEU* 4.9 8.5 - - + -
240B VAL* 3.5 40.1 - - + +
246B LEU* 4.2 20.0 - - + +
96C LEU* 3.3 44.0 - - + +
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Residues in contact with ALA 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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105B ILE 3.7 0.8 + - - -
106B LEU* 3.2 9.5 + - - +
108B LEU* 1.3 78.4 - - - +
110B TYR* 1.3 64.1 + - + +
111B CYS 3.4 0.7 - - - -
112B GLN* 3.0 33.7 - - - +
116B LEU* 4.1 5.2 - - - +
246B LEU* 5.1 2.5 - - + -
249B LEU* 3.8 28.7 - - + -
250B LEU* 4.3 8.7 - - + -
253B LEU* 4.0 24.4 - - + +
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Residues in contact with TYR 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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50B VAL* 3.9 15.0 - - + +
106B LEU* 3.0 51.7 + - + +
107B ARG 4.0 1.8 - - - +
109B ALA* 1.3 78.3 - - + +
111B CYS* 1.3 59.4 + - - +
112B GLN 3.4 2.2 - - - -
116B LEU* 3.4 39.2 - - + +
117B ARG* 3.2 28.6 + - - +
119B TRP* 3.8 30.4 - + - -
120B PHE* 3.6 33.9 - + + -
230B LEU* 4.4 3.2 - - - +
253B LEU* 3.5 49.2 + - + +
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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