Contacts of the strand formed by residues 30 - 37 (chain N) in PDB entry 5HJD
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 HIS 30 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16J PRO* 5.5 4.0 - - + -
17N ALA* 5.3 2.7 - - + -
18N GLN 3.4 13.2 - - - +
19N VAL* 3.5 26.9 - - + +
28N PHE 3.9 4.4 - - - +
29N THR* 1.3 110.2 + - + +
31N ASP* 1.3 69.9 + - - +
32N TRP* 5.4 2.0 - - + -
76N SER* 3.6 4.2 - - - -
77N GLY 3.0 29.3 + - - +
78N TYR 4.7 4.9 + - - -
106N LEU* 3.6 45.5 - - + +
107N HIS 3.3 23.3 + - - -
108N LEU* 5.0 8.2 - - + +
109N GLU* 5.5 1.1 + - - -
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Residues in contact with ASP 31 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N ARG 4.4 0.2 - - - +
17N ALA 3.8 0.2 - - - -
18N GLN* 2.8 38.0 + - - +
19N VAL 4.7 0.9 - - - -
20N ARG* 3.0 55.9 + - - +
21N LYS* 5.5 0.3 + - - -
30N HIS* 1.3 77.4 - - - +
32N TRP* 1.3 61.0 + - - +
75N GLU 5.9 0.2 - - - +
76N SER* 3.1 28.0 - - - +
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Residues in contact with TRP 32 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J KCR 3.7 11.8 - - + +
15N HIS* 5.0 1.3 - - + -
16N ARG 3.8 5.6 - - - +
17N ALA* 3.8 20.9 - - + +
30N HIS* 5.3 1.8 - - + -
31N ASP* 1.3 78.1 - - - +
33N MET* 1.3 70.1 + - - +
34N VAL* 3.4 23.8 - - + -
55N LEU* 3.6 20.4 - - + -
73N VAL* 3.8 4.9 - - + -
74N GLU* 3.7 1.2 - - - +
75N GLU* 3.2 60.0 + - + -
76N SER 4.0 2.6 - - - +
77N GLY* 4.2 20.6 - - - +
79N ALA 4.1 14.1 + - - -
81N PHE* 3.3 24.0 - + - -
104N LEU* 3.4 34.0 - - + +
106N LEU* 4.5 11.2 - - + -
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Residues in contact with MET 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N HIS* 3.1 21.8 - - - -
16N ARG* 3.2 38.1 + - + +
32N TRP* 1.3 79.8 - - - +
34N VAL* 1.3 62.0 + - - +
35N PHE* 3.9 29.2 - - + -
72N LYS* 3.7 26.7 - - + -
73N VAL 3.4 10.8 - - - +
74N GLU* 3.6 27.1 - - + +
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Residues in contact with VAL 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N GLY 3.3 6.5 - - - +
15N HIS* 3.7 9.2 - - + -
32N TRP* 3.4 24.7 - - + -
33N MET* 1.3 73.8 - - - +
35N PHE* 1.3 63.3 + - - +
53N PHE* 3.6 14.0 - - + -
73N VAL* 3.5 28.9 + - + -
83N LEU* 3.5 22.0 - - + -
85N ILE* 4.4 10.8 - - + -
102N TYR* 3.5 35.0 - - + -
104N LEU* 3.9 8.1 - - + -
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Residues in contact with PHE 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N GLU 4.2 4.3 - - - -
13N LEU* 3.4 5.7 - - - +
14N GLY* 2.7 71.9 + - - +
15N HIS* 3.9 5.8 - - - -
16N ARG* 4.7 21.5 - - - -
33N MET* 3.9 25.1 - - + -
34N VAL* 1.3 77.8 - - - +
36N VAL* 1.3 66.8 + - - +
37N ARG* 3.6 51.4 - - + -
53N PHE* 4.4 2.5 - - - -
71N TYR 3.7 11.0 - - - +
72N LYS* 4.4 5.2 - - + -
102N TYR* 5.0 0.2 - - - -
115N ASN* 6.2 0.2 - - - -
116N HIS 5.3 0.4 - - - -
117N LEU* 3.7 18.8 - - + -
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Residues in contact with VAL 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N LEU* 4.7 8.3 - - + -
12N GLU 3.9 3.4 - - - -
13N LEU* 3.7 27.6 - - + -
35N PHE* 1.3 79.7 - - - +
37N ARG* 1.3 67.5 + - - +
44N ILE* 4.5 10.3 - - + -
51N VAL* 4.2 18.4 - - + -
53N PHE* 4.2 2.2 - - + -
71N TYR* 3.2 34.1 + - + +
85N ILE* 3.8 31.0 - - + -
87N VAL* 4.3 19.7 - - + -
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Residues in contact with ARG 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N LEU* 3.7 3.7 - - - +
12N GLU* 2.8 65.1 + - + +
16N ARG* 5.0 10.7 - - - +
35N PHE* 3.6 38.7 - - + -
36N VAL* 1.3 76.5 - - - +
38N GLY* 1.3 72.5 + - - +
41N HIS* 5.6 14.8 + - - +
44N ILE* 3.9 13.9 - - - -
71N TYR* 5.5 0.2 - - - -
117N LEU* 4.5 4.9 - - - +
115Q ASN 4.6 11.1 + - - -
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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