Contacts of the strand formed by residues 18 - 23 (chain D) in PDB entry 5NX1
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 ILE 18 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLN* 3.9 12.3 - - - +
16D ALA* 4.1 21.3 - - + -
17D MET* 1.3 77.2 - - - +
19D SER* 1.3 64.3 - - - +
20D ARG* 3.2 42.7 + - - +
34D PHE* 3.6 4.3 - - - -
35D TYR* 2.8 42.5 + - + +
37D GLY* 4.1 21.3 - - - -
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Residues in contact with SER 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 5.5 2.5 - - - -
119A GLN* 3.0 21.9 + - - +
120A PRO* 4.1 33.0 + - - +
122A PRO* 5.2 1.7 - - - +
18D ILE* 1.3 71.0 - - - +
20D ARG* 1.3 78.8 + - - +
21D TRP* 5.1 6.1 + - - -
32D PRO* 4.3 13.3 - - - +
33D PHE 3.7 6.6 + - - -
34D PHE* 3.8 6.9 - - - -
46D ASP 4.9 4.2 - - - +
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Residues in contact with ARG 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D ILE* 3.2 38.7 + - - +
19D SER* 1.3 81.9 + - - +
21D TRP* 1.3 69.5 + - - +
32D PRO* 3.2 8.5 - - - +
33D PHE* 2.9 43.5 + - + +
35D TYR* 3.7 28.4 - - + -
44D ASN* 3.2 26.8 + - - +
45D PHE 3.5 17.9 - - - -
46D ASP* 3.9 19.9 + - - +
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Residues in contact with TRP 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D SER* 5.1 5.9 + - - -
20D ARG* 1.3 84.0 + - - +
22D TYR* 1.3 60.8 + - - +
30D CYS* 4.0 5.2 - - + -
31D ALA* 3.4 29.2 - - - -
32D PRO* 3.7 32.3 - - + -
33D PHE* 3.7 3.7 - - - -
44D ASN* 3.4 7.8 - - - -
45D PHE* 2.8 40.9 + - - +
46D ASP 3.9 5.1 + - - -
47D THR* 3.5 31.4 + - - +
48D GLU* 3.6 55.8 - - + +
51D CYS* 4.1 9.2 - - + -
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Residues in contact with TYR 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ARG* 3.8 9.4 + - - -
208A HIS* 5.8 2.0 + + - -
7B GLU 4.8 1.3 - - - -
8B GLN* 5.8 0.2 - - - -
9B ALA* 3.8 30.1 - - + -
21D TRP* 1.3 72.9 - - - +
23D PHE* 1.3 81.7 + - - +
24D ASP* 3.4 33.2 + - + -
30D CYS* 3.1 1.4 - - - -
31D ALA* 2.8 54.2 + - + -
32D PRO 4.2 9.0 - - - -
33D PHE* 3.6 21.3 - + + -
43D ASN* 3.3 34.1 - - - +
51D CYS* 3.6 8.5 - - - -
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Residues in contact with PHE 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B CYS* 3.3 33.3 - - + +
7B GLU 4.7 0.7 - - - +
22D TYR* 1.3 76.0 - - - +
24D ASP* 1.3 59.0 + - - +
25D VAL* 3.7 27.1 + - + +
28D GLY* 3.4 38.4 - - - -
29D LYS* 3.6 12.8 - - - -
30D CYS* 4.0 5.6 - - - -
43D ASN* 2.9 28.1 + - - +
51D CYS* 3.6 2.4 - - - -
52D MET* 3.8 12.6 - - + -
55D CYS* 3.5 45.1 - - + -
56D GLY* 4.5 1.6 - - - -
57D SER* 5.7 2.0 - - - -
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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