Contacts of the strand formed by residues 34 - 39 (chain N) in PDB entry 6NIY
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 MET 34 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4N LEU* 4.9 2.9 - - - -
27N PHE* 3.7 25.6 - - + -
29N PHE* 3.6 43.7 - - + +
32N TYR* 4.2 9.6 + - + +
33N LYS* 1.3 71.5 - - - +
35N ASN* 1.3 72.9 + - - +
50N ASP* 3.2 20.8 - - - +
51N ILE* 3.4 10.7 + - + +
70N ILE* 5.8 0.4 - - - -
72N ARG* 4.2 10.0 - - - +
79N LEU* 3.7 36.6 - - + -
96N CYS* 4.4 9.0 - - - -
97N ALA 3.7 12.6 - - - +
98N ARG* 3.7 22.0 - - + -
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Residues in contact with ASN 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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33N LYS* 3.3 1.8 + - - +
34N MET* 1.3 90.6 + - - +
36N TRP* 1.3 64.5 + - - +
37N VAL* 5.1 0.7 - - + -
47N TRP* 3.1 26.1 + - + +
49N SER 3.3 8.1 - - - +
50N ASP* 3.3 14.4 - - - +
79N LEU* 4.6 2.2 - - - +
96N CYS* 3.5 3.3 - - - -
97N ALA* 2.6 45.2 + - + +
99N CYS* 2.7 38.8 - - - +
107N CYS* 3.9 4.9 - - - +
109N ASP* 3.1 19.8 + - - +
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Residues in contact with TRP 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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6N GLU* 4.4 9.4 - - + -
20N LEU* 3.5 50.5 - - + -
21N SER 4.4 0.4 - - - -
22N CYS* 3.8 30.5 - - + -
35N ASN* 1.3 74.2 - - - +
37N VAL* 1.3 65.8 + - - +
47N TRP* 3.9 1.2 - - - -
48N VAL* 3.0 39.0 + - + +
49N SER* 3.2 10.2 + - - +
70N ILE* 3.6 25.8 - - + +
79N LEU* 3.3 19.8 - - + +
80N TYR 3.1 21.4 + - - -
81N LEU* 3.7 28.0 - - + +
94N TYR* 4.4 10.8 - - + -
95N TYR 3.1 32.3 - - - -
96N CYS* 4.2 4.0 - - + -
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Residues in contact with VAL 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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35N ASN* 5.1 1.6 - - + -
36N TRP* 1.3 81.4 - - - +
38N ARG* 1.3 64.5 + - - +
45N LEU* 4.7 5.8 - - + -
46N GLU 3.3 17.5 - - - +
47N TRP* 3.9 18.6 - - + -
48N VAL* 4.2 1.8 - - - -
94N TYR* 3.6 2.6 - - - -
95N TYR* 2.9 58.1 + - + +
97N ALA* 4.0 19.1 - - + -
109N ASP 3.9 17.7 - - - +
110N VAL* 4.6 6.3 - - - -
118N ARG* 4.4 7.9 - - - +
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Residues in contact with ARG 38 (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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37N VAL* 1.3 78.0 - - - +
39N GLN* 1.3 66.0 + - - +
40N ALA* 4.4 14.9 - - - +
45N LEU* 3.5 9.2 - - - +
46N GLU* 3.2 64.7 + - + +
47N TRP 5.5 0.4 - - - -
48N VAL* 3.7 18.3 - - + +
63N SER* 5.0 6.3 + - - -
64N VAL* 4.4 14.8 - - - +
89N GLU 5.2 1.2 + - - -
90N ASP* 2.7 44.5 + - - +
92N ALA* 4.0 10.0 - - + +
93N VAL 3.4 5.6 - - - -
94N TYR* 3.5 42.6 + - + +
95N TYR* 4.3 0.4 - - - -
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Residues in contact with GLN 39 (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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38N ARG* 1.3 76.3 - - - +
40N ALA* 1.3 69.4 + - - +
41N PRO* 3.7 1.9 - - - +
43N LYS 4.2 6.8 + - - +
44N GLY* 3.7 18.7 - - - +
45N LEU* 4.0 19.0 - - + +
46N GLU 4.9 0.2 - - - +
92N ALA* 3.8 3.0 - - - +
93N VAL* 2.9 38.0 + - + +
95N TYR* 2.6 39.5 + - + -
112N SER* 6.1 0.6 - - - -
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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