Contacts of the helix formed by residues 99 - 110 (chain B) in PDB entry 4U7B
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 SER 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ALA* 3.1 7.8 - - - +
98B VAL* 1.3 87.7 - - - +
100B GLN* 1.3 67.0 + - - +
101B GLN* 3.5 17.9 + - - +
102B ALA* 3.5 9.4 + - - +
103B VAL* 3.5 1.9 - - - +
45F T 2.7 36.3 + - - +
46F T 3.7 22.7 - - - +
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Residues in contact with GLN 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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89B GLN* 2.8 39.5 + - + +
90B LYS* 4.1 22.2 - - + +
93B ALA* 3.7 11.0 - - + +
99B SER* 1.3 75.1 - - - +
101B GLN* 1.3 69.7 + - - +
103B VAL* 2.7 28.3 + - - +
104B SER 3.2 8.0 + - - -
8E T 3.2 26.8 - - + +
9E A 2.8 49.4 + - - -
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Residues in contact with GLN 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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99B SER* 3.5 5.4 + - - +
100B GLN* 1.3 98.3 + - - +
102B ALA* 1.3 65.7 + - - +
104B SER* 3.2 5.9 + - - -
105B ASN* 2.8 33.1 + - - +
9E A 3.3 20.8 - - + +
10E C 3.6 17.0 - - + +
11E A 5.1 1.1 - - - +
45F T 4.4 5.2 - - + -
46F T 3.4 38.3 + - + +
47F G 2.4 34.1 + - - -
48F T 4.2 1.0 + - - -
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.5 10.7 + - - +
98B VAL* 3.8 10.3 - - + -
99B SER* 3.5 12.9 + - - +
101B GLN* 1.3 79.2 - - - +
103B VAL* 1.3 60.7 + - - +
105B ASN* 3.3 11.7 + - - +
106B ARG* 3.1 19.9 + - - +
44F C 4.2 18.8 + - - +
45F T 3.5 32.8 - - + +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.8 9.2 - - - +
77B LEU* 4.6 10.5 - - + -
89B GLN* 4.2 9.9 - - + +
92B LEU* 4.1 24.0 - - + -
93B ALA* 3.6 27.1 - - + +
96B LEU* 4.9 4.9 - - + -
98B VAL* 3.8 9.6 - - + -
99B SER 3.5 16.2 - - - +
100B GLN 2.7 14.2 + - - +
102B ALA* 1.3 69.0 - - - +
104B SER* 1.3 65.8 + - - +
106B ARG* 4.0 1.1 - - - +
107B LEU* 3.1 45.9 + - + +
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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
----------------------------------------------------------
89B GLN* 3.5 29.4 + - - +
100B GLN 3.2 5.3 + - - -
101B GLN* 3.3 15.9 - - - -
103B VAL* 1.3 78.2 - - - +
105B ASN* 1.3 68.2 + - - +
107B LEU* 3.1 10.5 + - - +
108B ARG* 3.1 17.6 + - - +
9E A 3.1 40.1 + - - +
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Residues in contact with ASN 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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101B GLN* 2.8 26.7 + - - +
102B ALA* 3.5 9.6 - - - +
103B VAL 3.3 0.2 - - - -
104B SER* 1.3 78.6 + - - +
106B ARG* 1.3 53.3 + - + +
107B LEU 3.0 0.2 + - - -
108B ARG* 3.1 19.1 + - + +
109B GLU* 2.7 37.4 + - - +
10E C 5.9 2.6 - - - -
44F C 5.4 5.3 - - - -
45F T 4.6 12.3 + - - +
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Residues in contact with ARG 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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70B LYS* 3.6 24.7 - - - +
72B TYR* 2.4 67.9 + - + +
73B GLU* 3.6 2.2 - - - +
74B ASP* 2.6 37.9 + - - +
77B LEU* 3.9 17.7 - - + +
102B ALA 3.1 6.5 + - - +
103B VAL 4.0 2.0 - - - +
104B SER 3.4 0.2 - - - -
105B ASN* 1.3 78.6 - - + +
107B LEU* 1.3 56.8 + - - +
109B GLU* 3.5 21.2 + - - +
110B MET* 2.8 38.0 + - - +
43F A 5.2 1.2 - - - -
44F C 2.7 36.0 + - - +
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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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171A TYR* 4.3 26.5 - - + -
77B LEU* 4.1 19.3 - - + -
81B LEU* 4.3 15.3 - - + -
89B GLN* 4.1 21.5 - - + +
92B LEU* 4.7 3.4 - - + -
103B VAL* 3.1 41.5 + - + +
104B SER* 3.1 4.6 + - - +
105B ASN 3.1 0.6 - - - -
106B ARG* 1.3 74.9 - - - +
108B ARG* 1.3 55.6 + - - +
110B MET* 2.7 28.0 - - - +
112B LYS* 3.2 45.9 + - + +
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Residues in contact with ARG 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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104B SER* 3.1 15.7 + - - +
105B ASN* 3.1 26.2 + - - +
107B LEU* 1.3 75.0 - - - +
109B GLU* 1.3 60.4 + - - +
110B MET 2.9 9.6 - - - +
112B LYS 4.5 6.3 - - - -
9E A 5.0 1.4 - - - +
10E C 2.8 32.8 + - - -
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Residues in contact with GLU 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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70B LYS* 4.8 8.3 + - - -
74B ASP* 3.3 25.2 - - - +
105B ASN 2.7 17.4 + - - +
106B ARG* 3.5 28.7 + - - +
108B ARG* 1.3 77.2 - - + +
110B MET* 1.3 65.4 + - - +
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Residues in contact with MET 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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74B ASP* 3.4 56.1 - - + +
77B LEU* 3.9 23.8 - - + -
78B GLN* 3.4 31.0 - - + +
81B LEU* 5.7 0.4 - - + -
106B ARG* 2.8 27.0 + - - +
107B LEU* 2.7 18.1 - - + +
108B ARG* 2.9 14.6 - - - +
109B GLU* 1.3 73.0 - - - +
111B GLY* 1.3 60.7 + - - +
112B LYS* 3.1 21.7 + - + -
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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