Contacts of the helix formed by residues 99 - 108 (chain B) in PDB entry 4BLU
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 GLY 99 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B HIS* 4.0 1.8 - - - -
43B ALA 5.6 0.2 - - - -
46B GLY* 2.8 22.2 + - - -
47B ARG* 4.1 0.6 - - - +
48B TYR* 4.1 17.4 - - - -
97B TYR 3.7 2.4 + - - -
98B PRO* 1.3 77.7 - - - +
100B SER* 1.3 65.4 + - - -
101B PRO* 3.2 7.4 - - - -
102B LEU 3.0 12.9 + - - -
103B ILE* 3.2 8.7 + - - +
1282B GOL 5.3 2.9 - - - -
1286B EDO 4.1 6.1 - - - -
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Residues in contact with SER 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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18B LYS* 3.6 14.9 + - - +
19B HIS* 2.8 27.7 + - - -
22B GLN* 3.0 30.6 + - - -
38B TYR* 3.4 19.1 + - - -
40B ASP* 3.7 4.9 - - - -
99B GLY* 1.3 70.3 - - - -
101B PRO* 1.4 70.3 - - - +
103B ILE* 3.3 2.0 + - - -
104B ALA* 3.1 8.8 + - - +
162B LEU* 4.1 12.2 - - - +
164B ASP* 5.0 0.9 + - - -
1282B GOL 5.5 1.4 + - - -
1286B EDO 5.2 0.2 + - - -
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Residues in contact with PRO 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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38B TYR* 4.3 10.1 - - + -
40B ASP* 3.5 17.3 - - - +
43B ALA* 3.3 39.3 - - + +
46B GLY* 5.0 4.0 - - - -
99B GLY* 3.4 7.0 - - - -
100B SER* 1.4 90.5 - - - +
102B LEU* 1.3 56.5 + - - +
104B ALA* 3.5 2.9 + - - +
105B ARG* 2.8 26.3 + - - +
114B LEU* 4.2 0.3 - - - +
116B LEU* 3.9 22.9 - - + -
127B LEU* 4.0 8.1 - - + -
131B PHE* 3.5 16.2 - - + -
1282B GOL 5.7 0.7 - - - +
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Residues in contact with LEU 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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46B GLY* 3.3 26.5 - - - +
47B ARG* 3.8 19.3 - - + -
84B VAL* 4.2 3.9 - - - +
88B PHE* 3.7 29.1 - - + -
98B PRO* 4.0 10.8 - - + -
99B GLY 3.0 9.2 + - - +
101B PRO* 1.3 76.0 - - - +
103B ILE* 1.3 65.9 + - - +
104B ALA 3.2 0.7 - - - -
105B ARG* 3.8 27.5 - - + +
106B LEU* 3.2 26.9 + - + +
130B GLU* 4.0 35.7 - - + +
131B PHE* 4.2 4.0 - - + -
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Residues in contact with ILE 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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19B HIS* 4.0 17.9 - - + +
22B GLN* 3.7 26.2 - - + +
23B SER* 4.5 10.8 - - - +
26B ILE* 4.8 0.7 - - + -
81B TYR* 3.9 28.3 - - + -
84B VAL* 4.2 15.7 - - + -
98B PRO* 4.1 20.8 - - + +
99B GLY 3.2 14.2 + - - +
100B SER 3.6 5.6 - - - +
102B LEU* 1.3 77.2 - - - +
104B ALA* 1.3 64.2 + - - +
106B LEU* 3.4 0.9 + - - +
107B LEU* 3.1 51.3 + - + +
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Residues in contact with ALA 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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22B GLN* 3.8 2.9 - - - +
26B ILE* 4.1 11.2 - - + -
38B TYR* 3.5 43.7 - - + -
100B SER 3.1 8.0 + - - +
101B PRO 3.6 8.1 - - - +
103B ILE* 1.3 77.8 - - - +
105B ARG* 1.3 63.0 + - - +
108B LEU* 2.9 35.0 + - + +
114B LEU* 3.8 7.6 - - + -
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Residues in contact with ARG 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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87A HIS* 4.3 12.3 + - - -
88A PHE* 6.0 1.0 - - - +
90A ARG* 3.8 34.6 + - - +
101B PRO 2.8 18.0 + - - +
102B LEU* 3.8 17.2 - - + +
103B ILE 3.3 0.4 - - - -
104B ALA* 1.3 76.8 - - - +
106B LEU* 1.3 71.8 + - + +
107B LEU 3.8 0.2 + - - -
108B LEU 4.4 0.2 - - - +
114B LEU* 4.1 5.4 - - - +
130B GLU 3.8 17.0 + - - -
131B PHE* 3.4 33.7 - - + +
132B GLN 5.9 0.6 + - - -
134B ASP* 3.3 23.8 + - - +
136B ARG* 3.1 36.0 + - - +
1295B SO4 4.1 21.4 + - - -
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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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87A HIS* 4.8 0.9 - - + -
90A ARG* 3.2 43.5 + - - +
84B VAL* 4.0 21.8 - - + -
87B HIS* 3.5 38.6 - - + +
88B PHE* 4.0 21.3 - - + -
102B LEU* 3.2 19.0 + - - +
105B ARG* 1.3 105.8 - - + +
107B LEU* 1.3 63.2 + - - +
108B LEU 3.7 0.6 - - - +
1293B EDO 3.3 17.8 + - - +
1294B EDO 5.2 1.6 - - - +
1295B SO4 4.8 3.4 - - - +
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Residues in contact with LEU 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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23B SER* 3.7 37.2 - - - +
26B ILE* 3.8 18.2 - - + -
27B GLU* 4.0 18.2 - - - +
30B LYS* 2.8 32.4 + - - +
80B ALA* 4.2 18.8 - - + +
81B TYR 5.1 0.2 - - - +
84B VAL* 4.0 21.3 - - + -
103B ILE* 3.1 31.3 + - + +
104B ALA 4.3 0.4 - - - +
106B LEU* 1.3 81.0 - - - +
108B LEU* 1.3 67.8 + - - +
1293B EDO 5.5 2.6 - - - +
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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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90A ARG* 5.0 2.6 + - - +
26B ILE* 3.8 24.5 - - + -
30B LYS* 4.9 1.6 - - - -
36B PHE* 3.8 25.8 - - + -
38B TYR* 3.9 9.9 - - + -
104B ALA* 2.9 22.5 + - + +
105B ARG 4.3 1.8 + - - +
106B LEU 3.7 4.5 - - - +
107B LEU* 1.3 81.4 + - - +
109B ARG* 1.3 59.0 + - - +
112B ASP* 3.7 21.8 - - + -
113B SER 3.5 24.9 - - - +
114B LEU* 3.7 22.2 - - + -
136B ARG* 3.4 21.6 + - - +
1293B EDO 5.0 6.4 + - - -
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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