Contacts of the strand formed by residues 4 - 11 (chain B) in PDB entry 1NOY
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 PHE 4 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ASP 4.3 7.2 - - - -
3B GLU* 1.3 83.1 + - - +
5B TYR* 1.3 62.9 + - - +
6B ILE* 3.5 20.6 - - + -
19B TYR* 3.4 1.0 - - - -
20B ILE* 3.0 56.5 + - + +
95B TYR* 3.6 13.2 - - - -
99B ILE* 4.0 23.3 - - + -
100B VAL 3.7 15.0 - - - +
101B TYR* 4.0 21.1 - - + -
102B ASP* 3.6 23.8 - - + -
105B PHE* 4.8 4.9 - + + -
106B VAL* 4.0 11.9 - - + -
346B TYR* 3.2 26.0 - + + -
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Residues in contact with TYR 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 1.3 74.6 - - - +
6B ILE* 1.3 66.6 + - - +
8B ILE* 3.8 28.3 - - + -
17B GLU* 3.6 17.9 - - - +
18B ARG 3.8 5.8 - - - +
19B TYR* 4.2 0.2 - - - -
91B ILE* 3.7 24.0 - - + -
95B TYR* 3.5 20.2 + + - -
99B ILE* 3.6 18.4 - - + -
345B SER 3.3 9.2 + - - -
346B TYR* 2.5 61.3 + + - -
349B LYS* 3.6 2.6 - - - -
350B MET 3.0 41.4 + - - -
351B PRO* 4.6 4.9 - - + -
352B PHE* 4.8 6.7 - + - -
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Residues in contact with ILE 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PHE* 3.5 26.9 - - + -
5B TYR* 1.3 87.8 - - - +
7B SER* 1.3 62.6 + - - +
18B ARG* 2.9 26.0 + - + +
19B TYR* 4.2 2.9 - - - -
20B ILE* 3.6 27.4 - - + -
26B GLU* 5.3 4.7 - - + +
106B VAL* 4.4 14.6 - - + -
208B ALA* 3.2 39.8 - - + +
266B SER* 4.8 2.8 + - - -
346B TYR* 3.9 2.9 - - - +
352B PHE* 3.1 35.8 - - + -
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Residues in contact with SER 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TYR* 4.5 0.6 - - - +
6B ILE* 1.3 83.2 - - - +
8B ILE* 1.3 65.6 + - - +
9B GLU* 3.1 24.5 + - - +
16B VAL 4.5 0.4 + - - -
17B GLU* 3.3 6.6 - - - +
18B ARG* 3.0 46.5 + - - +
264B GLY* 3.1 31.6 + - - -
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Residues in contact with ILE 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TYR* 3.8 31.4 - - + -
7B SER* 1.3 83.4 + - - +
9B GLU* 1.3 65.9 + - - +
15B ILE* 4.2 18.2 - - + -
16B VAL 3.7 2.0 - - - -
17B GLU* 3.5 21.5 - - + +
87B LYS* 3.3 55.4 + - + +
90B TYR* 3.9 18.6 - - + -
91B ILE* 4.1 13.7 - - + -
95B TYR* 5.3 0.2 - - + -
351B PRO* 5.1 8.8 - - + +
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Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B SER* 3.1 20.0 + - - +
8B ILE* 1.3 80.5 + - - +
10B THR* 1.3 62.6 + - - +
11B VAL* 4.1 0.9 - - + -
15B ILE* 3.3 7.7 - - - +
16B VAL* 2.7 44.9 + - + +
87B LYS* 3.5 16.9 + - - +
242B ILE* 4.1 30.2 - - + +
263B ASP* 4.2 13.5 - - - +
264B GLY* 2.9 33.9 + - - +
265B VAL 5.8 0.2 - - - -
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Residues in contact with THR 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLU* 1.3 72.9 + - - +
11B VAL* 1.3 60.7 + - - +
12B GLY 4.1 5.1 + - - +
14B ASN 3.2 7.9 - - - +
15B ILE* 3.3 31.2 - - + -
83B MET* 3.3 29.2 - - - +
86B PHE* 4.0 23.3 - - + -
87B LYS* 3.7 22.0 - - + +
242B ILE* 6.0 1.8 - - - +
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Residues in contact with VAL 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLU* 5.4 1.1 - - + -
10B THR* 1.3 72.1 - - - +
12B GLY* 1.3 59.0 + - - +
14B ASN* 2.7 40.6 + - + +
16B VAL* 3.2 34.3 - - + -
242B ILE* 5.5 16.4 - - + +
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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