Contacts of the strand formed by residues 34 - 41 (chain B) in PDB entry 1NYU
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 GLY 34 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.5 19.4 - - - -
18B VAL 3.0 17.3 - - - -
20B PHE* 3.4 17.3 - - - -
32B PRO* 3.2 17.2 - - - +
33B SER* 1.3 79.9 - - - +
35B TYR* 1.3 61.1 + - - -
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Residues in contact with TYR 35 (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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17B PHE* 3.6 8.8 - - - -
18B VAL* 2.8 61.1 + - + +
20B PHE* 3.4 29.4 - + - -
23B ILE* 5.6 5.1 - - + +
34B GLY* 1.3 72.3 - - - -
36B HIS* 1.3 76.0 + - - +
37B ALA* 4.3 8.8 - - + +
89B MET* 3.3 30.7 - - + -
108B MET* 3.9 32.1 - - + +
109B ILE* 4.1 9.2 - - + -
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Residues in contact with HIS 36 (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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82A PHE* 4.3 26.7 - + + -
15B GLN* 4.9 8.5 - - + -
16B PHE 3.3 16.2 - - - -
17B PHE* 3.4 34.7 - + + +
35B TYR* 1.3 86.4 - - - +
37B ALA* 1.3 61.9 + - - +
38B ASN* 3.5 26.3 + - - +
87B ARG* 5.7 5.8 + - - +
108B MET 4.3 3.8 - - - +
109B ILE* 3.6 27.3 - - + +
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Residues in contact with ALA 37 (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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16B PHE* 2.5 57.2 + - + +
18B VAL* 4.5 11.9 - - + -
35B TYR* 3.7 13.9 + - + +
36B HIS* 1.3 69.8 - - - +
38B ASN* 1.3 65.9 + - - +
39B TYR* 4.0 4.7 + - + -
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Residues in contact with ASN 38 (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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13B LYS* 3.9 20.1 - - + +
14B LYS 3.0 6.3 - - - +
15B GLN* 3.1 24.6 - - - +
16B PHE 3.1 5.0 + - - +
36B HIS* 3.5 17.5 + - - +
37B ALA* 1.3 93.1 - - - +
39B TYR* 1.3 60.3 + - - +
87B ARG* 4.8 3.8 - - - +
109B ILE* 3.9 15.6 - - - +
110B VAL* 3.1 59.3 + - + +
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Residues in contact with TYR 39 (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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14B LYS* 2.7 68.2 + - + +
16B PHE* 4.0 24.7 - + + -
37B ALA* 4.5 4.5 - - + -
38B ASN* 1.3 77.2 - - - +
40B CYS* 1.3 63.3 + - - +
41B GLU* 4.5 16.4 - - + -
110B VAL* 5.5 0.2 - - - -
113B CYS* 4.4 0.9 - - - -
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Residues in contact with CYS 40 (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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12B CYS 3.5 0.2 - - - -
39B TYR* 1.3 74.9 - - - +
41B GLU* 1.3 59.8 + - - +
81B CYS* 3.8 28.5 - - - +
82B VAL* 3.5 1.3 - - - -
83B PRO* 3.2 38.5 - - + +
110B VAL* 4.1 4.0 - - - -
113B CYS* 2.0 51.8 - - + -
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Residues in contact with GLU 41 (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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10B ILE 3.6 0.7 - - - +
12B CYS* 3.0 39.5 + - - +
14B LYS* 5.3 2.5 - - + -
39B TYR* 3.6 22.6 + - + +
40B CYS* 1.3 74.2 - - - +
42B GLY* 1.3 59.1 + - - +
81B CYS* 4.0 1.3 - - - -
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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