Contacts of the strand formed by residues 35 - 45 (chain Q) in PDB entry 1HNX
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 35 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A C 4.3 9.6 + - - +
597A G 4.6 18.2 - - - +
92H ARG* 4.7 19.0 - - + +
94H TYR* 4.9 9.9 - - + +
26Q GLN* 4.0 23.7 + - + +
27Q PHE* 3.6 27.4 - - - +
28Q PRO* 4.0 5.8 - - + -
33Q GLY 4.0 4.0 - - - +
34Q LYS* 1.3 77.1 - - - +
36Q ILE* 1.3 62.4 + - - +
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Residues in contact with ILE 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L VAL* 3.8 29.8 - - + -
25Q ARG 4.0 0.2 - - - +
26Q GLN* 3.4 6.7 - - - +
27Q PHE* 2.9 70.3 + - + -
29Q HIS* 3.8 12.8 - - + -
34Q LYS* 3.3 25.1 - - + +
35Q VAL* 1.3 76.2 - - - +
37Q LYS* 1.3 60.1 + - - +
38Q ARG* 3.6 32.3 - - - +
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Residues in contact with LYS 37 (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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280A C 4.5 14.1 - - - +
585A G 4.1 30.5 + - - +
24Q GLU* 2.8 43.8 + - + +
25Q ARG 3.4 9.4 - - - +
26Q GLN* 4.1 24.7 - - + +
35Q VAL 4.2 0.2 + - - -
36Q ILE* 1.3 76.6 - - - +
38Q ARG* 1.3 88.8 + - - +
87Q LYS* 5.8 4.8 - - - +
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Residues in contact with ARG 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A G 5.9 0.2 - - - -
280A C 3.5 52.1 + - - +
281A G 5.7 0.4 + - - -
1612A MG 4.7 2.5 - - - -
24Q GLU* 3.4 6.4 - - - +
25Q ARG* 2.7 69.1 + - - +
27Q PHE* 4.0 18.8 - - + -
36Q ILE* 3.6 24.6 - - - +
37Q LYS* 1.3 98.5 + - - +
39Q SER* 1.3 68.9 + - - +
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Residues in contact with SER 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A C 2.7 38.1 + - - -
1612A MG 2.9 22.7 - - - -
22Q LEU* 4.1 15.4 - - - +
23Q VAL 3.5 9.2 - - - -
24Q GLU* 4.6 9.4 - - - -
25Q ARG* 4.8 0.7 - - - +
38Q ARG* 1.3 80.7 - - - +
40Q LYS* 1.3 65.1 + - - +
91Q ARG* 3.6 16.4 + - - -
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Residues in contact with LYS 40 (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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236A G 2.9 25.2 + - - -
237A C 2.6 37.3 + - - +
21Q VAL 3.4 0.9 - - - +
22Q LEU* 3.3 6.8 - - - +
23Q VAL* 2.8 38.6 + - + +
39Q SER* 1.3 78.9 - - - +
41Q LYS* 1.3 67.6 + - - +
42Q TYR* 3.3 38.7 + - + +
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Residues in contact with LYS 41 (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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277A C 3.0 41.2 + - - +
278A G 2.6 34.8 + - - -
11Q VAL* 4.6 0.9 - - + -
20Q THR* 3.6 24.5 - - + -
21Q VAL 3.2 4.5 - - - +
22Q LEU* 3.8 20.9 - - + -
40Q LYS* 1.3 79.0 - - - +
42Q TYR* 1.3 63.5 + - - +
68Q ARG* 4.0 15.4 + - - -
88Q TYR* 3.1 40.0 + - + +
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Residues in contact with TYR 42 (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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236A G 3.3 35.6 + - - -
237A C 3.5 2.3 + - - -
6Q LEU* 3.4 22.9 - - + +
20Q THR* 3.6 0.9 - - - -
21Q VAL* 2.7 40.9 + - + +
23Q VAL* 3.5 26.2 - - + -
40Q LYS* 3.3 47.7 + - + +
41Q LYS* 1.3 75.5 - - - +
43Q LEU* 1.3 65.9 + - - +
44Q ALA 3.4 1.6 + - - -
59Q ILE* 5.0 8.7 - - + -
71Q PHE* 3.3 46.2 - + + -
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Residues in contact with LEU 43 (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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253A U 4.2 14.6 - - - +
254A G 4.4 7.9 - - - -
276A G 4.3 8.3 - - - +
15Q MET* 3.1 26.7 - - + -
18Q THR* 3.9 8.7 - - + -
19Q VAL 3.9 1.1 - - - +
20Q THR* 3.1 35.9 - - + +
41Q LYS 4.2 0.6 + - - -
42Q TYR* 1.3 72.1 - - - +
44Q ALA* 1.3 59.7 + - - +
68Q ARG* 3.7 54.9 - - + +
69Q LYS* 3.5 22.9 - - + +
70Q ARG 4.4 0.3 + - - -
71Q PHE* 4.0 9.3 + - - +
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Residues in contact with ALA 44 (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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18Q THR* 3.1 5.2 - - - -
19Q VAL* 2.7 49.1 + - + +
21Q VAL* 4.1 4.0 - - + -
42Q TYR 3.4 1.5 + - - +
43Q LEU* 1.3 73.8 - - - +
45Q HIS* 1.3 63.3 + - - +
59Q ILE* 3.3 34.8 - - + -
71Q PHE* 3.4 11.4 - - + +
73Q VAL* 3.7 12.6 - - + +
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Residues in contact with HIS 45 (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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255A G 4.5 3.6 - - - -
256A U 5.3 2.9 - - - -
17Q LYS* 2.8 45.5 + - + -
44Q ALA* 1.3 70.9 - - - +
46Q ASP* 1.3 59.7 + - - +
47Q PRO* 3.0 42.1 - - + +
65Q ILE* 3.1 48.2 - - + +
69Q LYS* 3.3 17.2 + - - +
71Q PHE 2.9 9.4 + - - +
72Q ARG* 4.0 11.3 - - + +
73Q VAL* 3.4 22.7 + - - +
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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