Contacts of the helix formed by residues 103 - 118 (chain Q) in PDB entry 5IYB
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 VAL 103 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14Q LEU* 4.9 8.1 - - + -
17Q LEU* 4.0 16.4 - - + -
18Q ALA* 4.6 21.5 - - + +
21Q VAL* 4.5 21.8 - - + -
101Q ASN* 3.7 1.8 - - - +
102Q VAL* 1.3 76.6 - - + +
104Q LYS* 1.3 66.7 + - - +
105Q TYR* 2.4 6.5 + - - +
106Q LYS* 2.3 51.8 + - + +
107Q LEU* 3.1 30.4 + - + -
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Residues in contact with LYS 104 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101Q ASN* 4.6 4.9 - - - +
102Q VAL* 2.2 30.5 + - + +
103Q VAL* 1.3 77.0 - - + +
105Q TYR* 1.3 53.6 + - - +
107Q LEU* 3.7 10.8 - - + -
108Q ASP* 2.7 65.7 + - - +
111Q ARG* 4.3 5.7 - - - +
195Q GLU* 5.5 11.7 + - + +
199Q LEU* 5.3 15.4 - - + +
202Q GLU* 5.5 6.5 - - - +
238R LYS* 4.0 16.8 - - - +
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Residues in contact with TYR 105 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69Q ASP 4.9 0.8 + - - -
70Q LYS* 4.4 23.3 - - + +
99Q LEU* 5.4 4.0 - - + -
101Q ASN* 3.8 33.5 + - + +
102Q VAL 4.4 0.4 + - - -
103Q VAL* 2.4 10.5 + - - +
104Q LYS* 1.3 72.6 - - - +
106Q LYS* 1.3 78.4 + - + +
108Q ASP* 3.8 7.9 - - + +
109Q HIS* 1.9 75.7 + + - -
224R THR* 3.5 7.0 - - + +
225R VAL 4.7 5.5 + - - -
227R SER 5.5 0.9 + - - -
231R GLU* 2.0 65.2 + - + +
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Residues in contact with LYS 106 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Q VAL* 5.6 3.8 - - + -
25Q PHE* 4.6 16.6 - - + -
69Q ASP* 2.8 39.9 + - - -
70Q LYS 3.1 24.2 + - - +
71Q PHE* 3.4 38.6 - - + -
103Q VAL* 2.3 33.6 + - + +
105Q TYR* 1.3 90.7 - - + +
107Q LEU* 1.3 56.6 + - + +
109Q HIS* 3.3 9.1 + - - +
110Q MET* 2.9 32.9 + - - +
224R THR* 4.7 6.6 - - - -
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Residues in contact with LEU 107 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17Q LEU* 4.2 17.0 - - + -
20Q TYR* 5.6 8.1 - - + -
21Q VAL* 4.7 14.6 - - + -
25Q PHE* 5.7 6.5 - - + -
103Q VAL* 3.1 34.9 + - + -
104Q LYS* 3.2 9.8 + - - +
106Q LYS* 1.3 77.5 - - + +
108Q ASP* 1.3 55.3 + - - +
110Q MET* 3.2 9.5 + - + +
111Q ARG* 2.7 53.2 + - - +
188Q TYR* 4.3 21.1 - - + +
195Q GLU* 3.2 20.6 - - + +
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Residues in contact with ASP 108 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Q LYS* 2.7 51.2 + - - +
105Q TYR* 3.8 8.5 + - + +
107Q LEU* 1.3 70.9 - - - +
109Q HIS* 1.3 57.6 + - + +
111Q ARG* 2.2 40.7 + - - +
112Q ARG 3.1 13.0 + - - -
234R GLU* 1.7 36.6 - - + +
238R LYS* 4.4 13.1 + - + +
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Residues in contact with HIS 109 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105Q TYR* 1.9 76.7 + + - -
106Q LYS* 3.4 8.1 - - + +
108Q ASP* 1.3 75.5 - - + +
110Q MET* 1.3 56.6 + - - +
112Q ARG* 3.2 6.8 + - - +
113Q ARG* 3.0 22.2 + - - +
222R SER 3.8 6.4 - - - +
223R VAL 4.9 1.7 - - - +
224R THR* 1.4 102.2 - - + +
231R GLU* 3.0 22.4 - - + -
234R GLU* 2.6 26.9 + - - +
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Residues in contact with MET 110 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q PHE* 3.4 43.3 - - + -
106Q LYS 2.9 17.2 + - - +
107Q LEU* 3.5 13.7 - - + +
109Q HIS* 1.3 71.6 - - - +
111Q ARG* 1.3 60.9 + - - +
113Q ARG* 3.0 9.1 + - - +
114Q ILE* 2.9 36.7 + - + +
210R PHE* 6.0 4.0 - - + -
219R LEU* 3.8 16.2 - - + -
222R SER* 2.7 50.9 + - - +
223R VAL* 4.4 9.0 - - + +
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Residues in contact with ARG 111 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104Q LYS* 3.8 9.7 + - - +
107Q LEU* 2.7 21.9 + - - +
108Q ASP* 2.2 54.7 + - - +
110Q MET* 1.3 71.5 - - - +
112Q ARG* 1.3 51.4 + - - +
114Q ILE* 3.1 15.1 + - + +
115Q GLU* 2.6 39.4 + - - +
188Q TYR* 2.2 46.8 + - + +
195Q GLU* 2.6 30.4 + - - -
238R LYS* 5.6 1.6 - - - +
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Residues in contact with ARG 112 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108Q ASP 3.1 6.3 + - - -
109Q HIS 3.3 9.9 - - - +
111Q ARG* 1.3 75.6 - - - +
113Q ARG* 1.3 54.4 + - - +
115Q GLU* 3.4 34.0 + - - -
116Q THR* 2.7 47.3 + - - +
119Q ARG* 3.8 15.8 - - - +
233R ILE* 5.4 5.5 + - - +
234R GLU* 3.6 32.7 - - + +
237R LEU* 1.5 55.9 - - - +
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Residues in contact with ARG 113 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109Q HIS 3.0 5.4 + - - +
110Q MET* 3.0 17.8 + - - +
112Q ARG* 1.3 76.6 - - - +
114Q ILE* 1.3 75.9 + - - +
116Q THR* 3.5 7.0 + - - -
117Q ASP* 3.2 32.3 + - - +
210R PHE* 6.2 0.8 - - - -
218R LYS* 2.2 63.2 + - - +
221R ARG* 3.1 17.7 - - + +
222R SER* 1.4 94.0 - - - +
223R VAL 5.4 0.7 - - - +
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Residues in contact with ILE 114 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q MET* 2.9 27.3 + - + +
111Q ARG* 3.5 13.2 - - + +
113Q ARG* 1.3 93.4 - - - +
115Q GLU* 1.3 56.2 + - - +
117Q ASP* 3.1 9.4 + - + +
118Q GLU* 3.0 31.5 + - - +
181Q ASN* 3.2 40.8 - - - +
184Q ILE* 5.5 8.3 - - + -
218R LYS* 5.2 3.1 - - - +
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Residues in contact with GLU 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111Q ARG 2.6 20.7 + - - +
112Q ARG* 3.4 38.9 + - - +
114Q ILE* 1.3 69.5 - - - +
116Q THR* 1.3 64.4 + - - +
118Q GLU* 3.6 26.9 - - - +
119Q ARG* 3.3 40.3 + - - +
237R LEU* 5.2 1.2 - - - +
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Residues in contact with THR 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112Q ARG* 2.7 38.6 + - - +
113Q ARG* 3.6 7.6 - - - -
115Q GLU* 1.3 72.9 - - - +
117Q ASP* 1.3 64.8 + - - +
119Q ARG* 3.3 32.0 + - - +
121Q SER* 5.5 0.9 + - - -
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Residues in contact with ASP 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Q ARG* 3.2 23.2 + - - +
114Q ILE* 3.1 15.3 + - + +
116Q THR* 1.3 73.5 - - - +
118Q GLU* 1.3 54.0 + - - +
119Q ARG 2.6 31.6 + - - +
121Q SER* 5.1 0.5 + - - -
174Q ARG* 2.3 44.7 + - - +
177Q LEU* 5.1 7.3 - - - +
178Q ALA* 5.8 0.3 + - - -
218R LYS* 5.4 6.2 - - - +
221R ARG* 5.3 6.2 + - - -
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Residues in contact with GLU 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114Q ILE* 3.0 14.2 + - - +
115Q GLU* 3.6 23.1 + - - +
117Q ASP* 1.3 72.8 + - - +
119Q ARG* 1.3 61.8 + - + +
120Q ASP* 3.7 1.7 + - - -
178Q ALA* 5.8 8.1 - - - +
181Q ASN* 4.2 21.0 + - - +
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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