Contacts of the helix formed by residues 103 - 111 (chain B) in PDB entry 1SVU
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 ASP 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B LEU* 6.2 0.4 - - - -
18B PHE* 4.8 1.8 - - + -
61B ILE* 3.1 17.3 - - + +
62B THR* 3.0 21.7 + - - +
99B THR 2.5 30.7 - - - +
100B LEU* 2.8 30.6 - - + +
102B PHE* 1.3 80.6 - - - +
104B ILE* 1.3 64.3 + - - +
106B ARG* 3.1 28.9 + - - +
107B ILE* 2.9 32.1 + - - +
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Residues in contact with ILE 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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17B LEU* 5.4 8.1 - - + -
18B PHE* 4.4 9.4 - - + -
75B LEU* 4.2 9.6 - - + -
77B ALA* 4.0 22.9 - - + -
79B PHE* 3.7 34.8 - - + -
100B LEU 4.4 7.6 - - - +
101B PHE* 2.4 30.6 + - + +
103B ASP* 1.3 70.3 - - - +
105B ALA* 1.3 56.8 + - - +
107B ILE* 2.8 10.1 + - - +
108B VAL* 2.6 53.1 + - + +
116B VAL* 4.8 0.7 - - + -
118B MET* 3.8 23.1 - - - -
140B MET* 5.3 2.0 - - - -
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Residues in contact with ALA 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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97B ARG* 5.2 0.4 - - + -
101B PHE* 2.8 20.9 + - + +
102B PHE* 4.1 9.6 - - + -
104B ILE* 1.3 73.8 - - - +
106B ARG* 1.3 53.4 + - - +
107B ILE 2.6 8.0 + - - -
108B VAL* 2.6 10.1 + - - -
109B ARG* 2.6 34.5 + - - -
139B THR* 4.3 23.3 - - + +
140B MET* 5.6 3.1 - - - -
143B LEU* 4.2 11.2 - - + -
407B UNX 4.6 10.3 - - - -
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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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61B ILE* 2.9 48.0 + - - +
62B THR* 3.9 5.1 + - - +
64B VAL 2.4 29.1 + - - +
65B ASN* 4.3 0.4 - - - +
66B GLU* 2.8 38.7 + - + +
102B PHE 3.3 18.6 + - - +
103B ASP* 3.1 25.8 + - - +
104B ILE 3.4 0.2 - - - -
105B ALA* 1.3 78.3 - - - +
107B ILE* 1.3 64.2 + - - +
109B ARG* 4.2 4.2 - - - +
110B GLU* 3.1 26.0 + - - +
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Residues in contact with ILE 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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17B LEU* 3.8 22.0 - - + -
61B ILE* 5.1 7.2 - - + -
66B GLU* 3.9 14.4 - - + +
69B ILE* 3.4 48.2 - - + -
72B HIS* 4.6 4.7 - - - +
75B LEU* 3.7 22.2 - - + -
103B ASP 2.9 20.2 - - - +
104B ILE* 2.8 8.4 + - - +
105B ALA 2.6 5.3 + - - -
106B ARG* 1.3 84.9 - - + +
108B VAL* 1.3 59.8 + - - +
109B ARG 3.0 0.7 - - - -
110B GLU 2.7 22.5 + - - -
111B LYS* 2.8 17.5 + - + +
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Residues in contact with VAL 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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75B LEU* 4.0 13.7 - - + -
104B ILE* 2.6 43.3 + - + +
105B ALA* 2.6 3.6 + - - +
107B ILE* 1.3 74.4 - - - +
109B ARG* 1.3 55.3 + - - +
112B LYS* 3.2 14.4 - - - +
113B PRO* 3.2 23.1 - - + +
116B VAL* 3.4 34.8 - - + -
140B MET* 3.8 6.7 - - + -
143B LEU* 3.1 21.3 - - + -
145B TYR* 3.7 16.2 - - + +
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Residues in contact with ARG 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 ALA* 2.6 17.4 + - + +
106B ARG* 4.7 3.6 - - - +
108B VAL* 1.3 71.5 - - - +
110B GLU* 1.3 62.2 + - - +
112B LYS* 3.3 25.4 - - - +
143B LEU* 3.1 32.4 - - + +
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Residues in contact with GLU 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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66B GLU* 3.4 31.7 - - + +
67B LYS* 2.9 36.0 - - + +
106B ARG 3.1 20.0 + - - +
107B ILE 2.7 9.5 + - - +
109B ARG* 1.3 76.8 - - - +
111B LYS* 1.3 60.4 + - + +
112B LYS* 3.2 5.7 + - - +
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Residues in contact with LYS 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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66B GLU 3.8 13.2 - - - +
67B LYS* 3.9 12.8 + - - +
69B ILE* 2.6 36.1 + - + +
70B PRO* 3.1 16.1 - - - +
71B ASP* 3.2 46.1 + - - +
72B HIS* 4.3 17.9 + - + +
107B ILE* 2.8 13.3 + - + +
110B GLU* 1.3 77.5 - - + +
112B LYS* 1.3 69.3 + - - +
113B PRO* 3.1 7.6 - - + +
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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