Contacts of the helix formed by residues 102 - 119 (chain Q) in PDB entry 5IY6
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 102 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69Q ASP 5.5 6.1 - - - +
100Q VAL* 4.3 10.5 - - + -
101Q ASN* 1.3 86.7 + - - +
103Q VAL* 1.3 78.4 - - - +
104Q LYS* 1.9 6.6 + - - -
105Q TYR* 2.3 62.4 + - + +
106Q LYS* 3.2 9.8 + - + +
231R GLU* 5.0 14.4 - - + -
234R GLU* 5.2 3.4 - - + -
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Residues in contact with VAL 103 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14Q LEU* 4.8 9.4 - - + -
17Q LEU* 4.3 21.1 - - + -
21Q VAL* 5.1 11.7 - - + -
100Q VAL* 3.4 35.3 - - + +
101Q ASN 2.8 4.2 + - - +
102Q VAL* 1.3 83.5 - - - +
104Q LYS* 1.3 55.5 + - - +
106Q LYS* 3.5 20.2 - - - +
107Q LEU 3.6 3.8 + - - -
188Q TYR* 3.6 17.0 + - + +
195Q GLU* 3.1 28.0 - - + +
218R LYS* 4.5 1.0 + - - -
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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 3.8 7.4 - - - +
102Q VAL* 1.9 12.1 + - - -
103Q VAL* 1.3 64.8 - - - +
105Q TYR* 1.3 65.4 + - - +
106Q LYS 3.2 0.9 - - - -
107Q LEU* 3.0 25.6 + - + +
108Q ASP* 3.1 29.5 + - - +
195Q GLU* 2.7 26.8 + - + +
199Q LEU* 4.9 14.1 - - + -
238R LYS* 2.8 55.9 - - + +
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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
----------------------------------------------------------
102Q VAL* 2.3 54.1 + - + +
104Q LYS* 1.3 70.9 - - - +
106Q LYS* 1.3 61.7 + - - -
108Q ASP* 3.1 21.4 + - + +
109Q HIS* 1.5 59.7 + + - -
221R ARG 3.5 3.3 + - - -
222R SER* 2.9 38.2 - - - -
223R VAL 3.5 1.2 + - - -
224R THR* 3.2 18.5 + - - -
225R VAL 5.4 1.6 - - - -
234R GLU* 2.2 55.3 + - + -
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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
----------------------------------------------------------
25Q PHE* 5.0 21.8 - - + -
26Q TYR* 4.9 3.4 + - - -
69Q ASP* 3.9 13.2 + - - -
102Q VAL* 3.2 8.0 + - + +
103Q VAL* 3.5 13.2 - - - +
105Q TYR* 1.3 80.5 - - + +
107Q LEU* 1.3 54.1 + - - +
109Q HIS* 3.3 2.6 + - - +
110Q MET 2.8 13.7 + - - -
218R LYS* 2.6 55.9 - - + +
219R LEU* 2.8 40.2 - - + +
222R SER* 3.0 33.4 - - - +
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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
----------------------------------------------------------
103Q VAL 3.6 1.2 + - - -
104Q LYS* 3.0 21.4 + - + +
106Q LYS* 1.3 77.1 - - - +
108Q ASP* 1.3 64.2 + - - +
111Q ARG* 2.9 69.4 + - + +
188Q TYR* 3.4 39.9 - - + +
192Q ARG* 3.9 23.3 - - + -
195Q GLU* 5.6 0.9 - - - +
213R ASP* 4.4 2.0 - - - +
218R LYS* 2.5 28.2 - - - +
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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* 3.1 34.0 + - - +
105Q TYR* 3.1 16.7 + - + +
107Q LEU* 1.3 80.9 - - - +
109Q HIS* 1.3 62.2 + - + +
111Q ARG* 4.4 2.2 - - - +
112Q ARG* 3.2 26.9 + - - +
234R GLU* 4.8 7.6 - - + +
237R LEU* 4.8 17.0 - - + -
238R LYS* 4.4 16.4 - - - +
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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* 1.5 74.8 + + - -
106Q LYS 3.7 3.8 - - - +
108Q ASP* 1.3 75.0 - - + +
110Q MET* 1.3 51.8 - - - +
112Q ARG* 4.5 0.4 - - - -
113Q ARG 2.7 0.3 + - - -
221R ARG* 1.6 87.1 + - + +
222R SER* 3.7 3.1 - - - -
233R ILE* 5.8 6.5 - - + -
234R GLU* 4.4 4.9 - - + -
237R LEU* 4.3 22.9 - - + +
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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
----------------------------------------------------------
106Q LYS 2.8 8.8 + - - +
107Q LEU* 5.1 2.2 - - - -
109Q HIS* 1.3 71.1 - - - +
111Q ARG* 1.3 61.3 + - - +
113Q ARG* 3.1 3.6 - - + +
114Q ILE* 2.8 48.2 + - + +
184Q ILE* 5.1 0.4 - - + -
212R VAL 4.6 0.2 - - - +
213R ASP* 1.5 83.5 - - + +
214R GLU* 3.2 12.8 - - + +
215R GLU 3.6 6.1 - - - +
217R GLN* 5.0 2.7 - - + -
218R LYS* 2.0 69.5 - - + +
221R ARG* 2.9 3.7 + - - +
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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
----------------------------------------------------------
107Q LEU* 2.9 45.8 + - + +
108Q ASP* 4.4 2.5 - - - +
110Q MET* 1.3 72.3 - - + +
112Q ARG* 1.3 52.7 + - - +
114Q ILE* 2.9 10.0 + - - +
115Q GLU* 2.6 44.8 + - + +
181Q ASN* 4.9 9.0 + - - -
184Q ILE* 3.5 23.5 + - - +
185Q GLU* 2.6 50.8 + - - +
188Q TYR* 3.6 32.5 - - - +
192Q ARG* 5.2 2.8 - - - +
213R ASP* 4.7 3.6 + - - -
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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
----------------------------------------------------------
108Q ASP 3.2 16.7 + - - +
109Q HIS* 5.9 0.2 - - - +
111Q ARG* 1.3 77.7 - - - +
113Q ARG* 1.3 52.6 + - - +
115Q GLU* 3.5 8.9 - - + +
116Q THR* 2.8 43.3 + - - +
221R ARG* 2.8 21.8 - - - +
237R LEU* 4.5 33.2 - - - +
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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
----------------------------------------------------------
110Q MET* 3.1 7.6 - - - +
112Q ARG* 1.3 70.0 - - - +
114Q ILE* 1.3 60.4 + - + +
116Q THR* 3.5 12.0 + - - -
117Q ASP* 3.5 11.3 + - - +
216R PHE* 6.2 1.0 - - - -
217R GLN* 2.1 72.9 + - + +
218R LYS* 4.0 1.1 - - - +
220R TRP* 3.5 37.5 - - - -
221R ARG* 1.4 114.9 - - - +
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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
----------------------------------------------------------
110Q MET* 2.8 42.4 + - + +
111Q ARG* 3.3 10.5 - - - +
113Q ARG* 1.3 74.8 - - + +
115Q GLU* 1.3 62.9 + - - +
117Q ASP* 3.3 9.5 + - - +
118Q GLU* 3.2 20.0 + - + +
180Q PHE* 5.1 9.0 - - + -
181Q ASN* 3.7 27.6 - - + +
184Q ILE* 3.6 47.1 - - + -
214R GLU* 6.1 2.0 - - + -
217R GLN* 5.7 7.6 - - + +
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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 28.0 + - + +
112Q ARG* 3.5 11.7 - - + +
114Q ILE* 1.3 71.8 - - - +
116Q THR* 1.3 65.1 + - - +
118Q GLU* 3.3 12.4 + - - +
119Q ARG* 3.1 46.3 + - - +
181Q ASN* 2.6 32.0 + - - +
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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* 2.8 33.8 + - - +
113Q ARG* 3.7 8.7 - - - -
114Q ILE 3.4 0.2 - - - -
115Q GLU* 1.3 73.4 - - - +
117Q ASP* 1.3 62.9 + - - +
119Q ARG* 3.8 14.0 + - - +
221R ARG* 5.0 0.5 + - - -
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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
----------------------------------------------------------
113Q ARG 3.5 7.6 + - - +
114Q ILE* 3.3 12.2 + - - +
115Q GLU 3.2 0.6 - - - -
116Q THR* 1.3 81.8 - - - +
118Q GLU* 1.3 60.9 + - - +
119Q ARG 3.5 3.6 + - - +
169Q PRO* 4.5 6.6 - - - +
177Q LEU* 3.8 21.3 - - - +
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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* 3.2 11.0 + - + +
115Q GLU* 3.3 22.1 + - - +
117Q ASP* 1.3 79.2 + - - +
119Q ARG* 1.3 79.7 + - - +
120Q ASP* 3.2 9.6 + - - +
169Q PRO* 4.8 1.4 - - - +
174Q ARG* 4.2 16.4 + - - +
177Q LEU* 3.6 46.9 - - + +
178Q ALA* 3.1 27.6 + - - +
181Q ASN* 4.2 13.1 + - + +
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Residues in contact with ARG 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115Q GLU* 3.1 33.6 + - - +
116Q THR* 4.1 11.1 - - - +
117Q ASP 3.4 6.1 - - - +
118Q GLU* 1.3 88.5 + - - +
120Q ASP* 1.3 72.7 + - - +
169Q PRO* 5.8 0.2 - - - +
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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
------------------------------------------------------------
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