Contacts of the helix formed by residues 81 - 96 (chain Q) in PDB entry 1HNW
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 ARG 81 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A U 5.8 0.2 + - - -
647A C 4.3 24.4 + - - -
9Q VAL* 4.9 1.9 - - + +
54Q GLY* 3.1 23.1 + - - +
56Q VAL* 3.8 25.4 - - + +
78Q GLU* 3.3 31.8 + - - +
79Q SER 4.6 1.8 - - - +
80Q GLY* 1.3 76.2 - - - +
82Q MET* 1.3 62.2 + - - +
83Q ASP* 2.8 45.6 + - - +
84Q LEU* 3.1 41.0 + - + +
85Q VAL* 3.9 2.4 + - - +
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Residues in contact with MET 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Q LEU* 3.4 49.4 - - + +
54Q GLY* 3.7 9.2 - - - -
80Q GLY* 5.4 1.8 - - - -
81Q ARG* 1.3 71.8 - - - +
83Q ASP* 1.3 66.8 + - - +
84Q LEU 2.9 3.1 - - - -
85Q VAL* 3.4 20.4 - - + -
86Q GLU* 2.7 36.4 + - + +
89Q LEU* 6.1 0.4 - - + -
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Residues in contact with ASP 83 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81Q ARG* 2.8 57.1 + - - +
82Q MET* 1.3 81.3 - - - +
84Q LEU* 1.3 61.3 + - - +
86Q GLU* 3.2 22.9 - - - +
87Q LYS* 3.6 14.5 + - - +
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Residues in contact with LEU 84 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q VAL* 3.5 36.1 - - + -
11Q VAL* 5.6 1.1 - - - +
22Q LEU* 5.6 2.1 - - - +
24Q GLU* 5.8 4.0 - - - +
56Q VAL* 5.1 2.7 - - + -
81Q ARG* 3.3 47.3 - - - +
82Q MET 2.9 0.4 - - - -
83Q ASP* 1.3 81.9 + - - +
85Q VAL* 1.3 64.7 + - - +
86Q GLU 3.1 1.7 + - - -
87Q LYS* 3.5 37.9 + - + +
88Q TYR* 3.5 16.5 + - - +
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Residues in contact with VAL 85 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9Q VAL* 4.4 7.6 - - + -
10Q VAL 4.0 7.9 - - - +
11Q VAL* 4.6 12.8 - - + +
53Q LEU* 3.4 35.4 - - + -
54Q GLY* 4.1 8.1 - - - -
81Q ARG 4.4 0.2 - - - +
82Q MET* 2.8 32.2 + - + +
84Q LEU* 1.3 78.0 - - - +
86Q GLU* 1.3 53.2 + - - +
88Q TYR* 3.1 7.1 + - - +
89Q LEU* 2.6 60.9 + - + +
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Residues in contact with GLU 86 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82Q MET* 2.7 28.6 + - + +
83Q ASP* 3.2 14.1 - - - +
85Q VAL* 1.3 76.1 - - - +
87Q LYS* 1.3 69.5 + - - +
88Q TYR 2.8 1.9 + - - -
89Q LEU* 3.0 20.1 + - - +
90Q ILE* 2.8 51.2 + - + +
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Residues in contact with LYS 87 (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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583A A 4.8 7.7 - - - +
584A G 4.2 27.3 + - - +
24Q GLU* 5.9 3.3 + - - +
83Q ASP* 3.6 11.3 + - - +
84Q LEU* 3.5 35.3 + - + +
86Q GLU* 1.3 78.2 - - + +
88Q TYR* 1.3 63.8 + - - +
90Q ILE* 4.4 5.6 - - - +
91Q ARG* 3.3 29.3 + - - +
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Residues in contact with TYR 88 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A C 4.7 1.0 + - - -
11Q VAL* 3.5 34.1 - - + +
22Q LEU* 3.7 25.6 - - + -
41Q LYS* 3.1 49.3 + - + +
84Q LEU 3.5 6.1 + - - +
85Q VAL 3.1 11.1 + - - +
86Q GLU 2.8 1.0 + - - -
87Q LYS* 1.3 79.8 - - - +
89Q LEU* 1.3 77.0 + - + +
91Q ARG* 3.0 33.2 + - + +
92Q ARG* 3.0 51.3 + - + +
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Residues in contact with LEU 89 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q VAL 5.2 4.5 - - - +
53Q LEU* 6.2 2.7 - - + -
82Q MET* 6.1 0.7 - - + -
85Q VAL* 2.6 41.4 + - + +
86Q GLU* 3.0 20.0 + - - +
88Q TYR* 1.3 83.9 - - + +
90Q ILE* 1.3 62.8 + - + +
92Q ARG* 3.0 38.1 + - - +
93Q GLN* 2.8 25.3 + - - +
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Residues in contact with ILE 90 (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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582A U 3.9 24.2 - - - +
583A A 3.9 26.5 - - - +
86Q GLU* 2.8 44.6 + - + +
87Q LYS* 4.4 3.6 - - - +
89Q LEU* 1.3 73.1 - - + +
91Q ARG* 1.3 64.7 + - - +
93Q GLN* 2.8 31.1 + - + +
94Q ASN* 2.9 14.6 + - - +
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Residues in contact with ARG 91 (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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279A A 5.7 3.3 + - - -
280A C 3.3 47.1 + - - +
583A A 4.0 20.8 + - - +
584A G 4.8 11.9 + - - -
22Q LEU* 4.7 14.5 - - - +
39Q SER* 3.8 10.3 + - - -
87Q LYS* 3.3 20.9 + - - +
88Q TYR* 3.0 26.4 + - + +
90Q ILE* 1.3 77.6 - - - +
92Q ARG* 1.3 63.4 + - - +
94Q ASN* 3.2 17.5 + - - +
95Q TYR* 3.0 47.0 + - + -
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Residues in contact with ARG 92 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A G 5.9 1.4 + - - -
277A C 5.7 1.6 + - - -
278A G 4.6 13.9 + - - +
11Q VAL* 5.2 2.4 + - - +
12Q SER* 5.7 4.9 - - - -
14Q LYS* 5.4 8.9 - - - +
41Q LYS* 5.4 0.2 - - - +
88Q TYR* 3.0 51.8 + - + +
89Q LEU* 3.0 30.5 + - - +
91Q ARG* 1.3 78.3 - - - +
93Q GLN* 1.3 55.1 + - - +
95Q TYR* 2.7 42.6 + - - +
96Q GLN* 3.5 3.3 + - - +
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Residues in contact with GLN 93 (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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89Q LEU* 2.8 14.3 + - - +
90Q ILE* 3.1 25.6 - - + +
92Q ARG* 1.3 77.4 - - - +
94Q ASN* 1.3 59.6 + - - +
96Q GLN* 3.2 29.4 - - + +
97Q SER* 5.2 1.0 - - - -
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Residues in contact with ASN 94 (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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582A U 3.3 27.7 + - - -
583A A 3.5 24.2 + - - -
759A A 4.5 3.6 - - - +
760A G 2.7 30.9 + - - +
90Q ILE* 2.9 18.8 + - - +
91Q ARG* 3.4 12.6 - - + +
92Q ARG 2.8 0.6 + - - -
93Q GLN* 1.3 72.9 - - - +
95Q TYR* 1.3 68.9 + - + +
96Q GLN 3.0 2.2 - - - -
97Q SER* 2.6 29.5 + - - -
98Q LEU* 3.7 9.7 - - + +
104Q LYS 5.8 0.5 - - - -
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Residues in contact with TYR 95 (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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278A G 3.5 70.9 + + + +
279A A 2.4 71.8 + + + -
91Q ARG* 3.0 41.4 - - + -
92Q ARG* 2.7 20.3 + - - +
94Q ASN* 1.3 71.0 - - + +
96Q GLN* 1.3 53.2 + - - +
97Q SER 2.5 28.1 + - - +
98Q LEU* 4.0 16.4 - - + +
99Q SER* 5.4 0.7 - - - -
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Residues in contact with GLN 96 (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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278A G 6.0 0.4 - - - +
92Q ARG 3.5 2.5 + - - +
93Q GLN* 3.2 25.5 + - + +
94Q ASN 3.0 0.2 - - - -
95Q TYR* 1.3 75.9 - - - +
97Q SER* 1.3 59.3 + - - +
99Q SER* 5.6 0.2 - - - -
102Q GLY 5.3 0.2 - - - +
103Q GLY* 5.8 1.7 - - - -
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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