Contacts of the strand formed by residues 23 - 32 (chain A) in PDB entry 1NYE
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 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A MET 6.1 0.2 - - - -
22A THR* 1.3 74.9 + - - +
24A HIS* 1.3 63.1 + - - +
25A LYS* 3.8 25.6 - - + -
259B ARG 3.7 23.6 - - - +
260B PHE* 3.8 36.1 - - + +
261B GLU 5.5 2.5 - - - +
269B GLU* 5.5 2.7 - - + -
304B VAL 3.5 0.3 - - - +
305B SER* 3.2 5.4 - - - -
306B LEU* 2.8 60.1 + - + +
313B PHE* 4.4 7.9 - - + -
621D MET* 5.1 2.9 - - + -
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Residues in contact with HIS 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A THR* 3.5 44.8 + - + +
23A ILE* 1.3 73.4 - - - +
25A LYS* 1.3 75.0 + - - +
26A LYS* 5.3 5.1 - - - -
45A GLU* 3.9 5.0 - - - +
303B ASP* 3.5 29.1 + - - +
304B VAL 3.3 2.4 + - - -
305B SER* 3.4 25.1 + - - -
317B LYS* 6.4 0.9 - - - -
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Residues in contact with LYS 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.8 20.2 - - + -
24A HIS* 1.3 93.8 - - - +
26A LYS* 1.3 63.3 + - - +
45A GLU* 2.8 15.9 - - - +
258B THR 2.7 30.9 + - - -
259B ARG 3.9 9.3 + - - -
262B GLY* 5.7 10.0 - - - -
263B GLU 5.2 2.7 + - - -
265B GLY 4.9 1.2 + - - -
267B ASN* 3.0 29.4 + - - +
269B GLU* 3.7 22.6 - - + +
270B GLU* 3.9 7.6 - - + +
302B ALA 3.7 0.7 - - - +
304B VAL* 2.7 38.9 + - - +
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A HIS* 5.3 4.5 - - - -
25A LYS* 1.3 74.2 - - - +
27A GLY* 1.3 60.1 + - - +
45A GLU* 2.6 50.8 + - + +
270B GLU* 3.6 15.8 - - - +
301B THR* 4.1 22.2 - - + +
302B ALA 3.2 5.2 - - - +
303B ASP* 3.2 37.8 + - + +
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 1.3 75.2 - - - +
28A GLN* 1.3 62.5 + - - +
43A SER 3.7 8.1 - - - -
44A THR* 4.7 1.3 - - - -
45A GLU 5.7 0.2 - - - -
270B GLU 4.1 2.5 - - - -
273B GLY 3.9 3.5 - - - -
274B ALA* 3.6 25.6 - - - -
277B ALA* 4.5 0.4 - - - -
301B THR* 3.4 5.4 - - - +
302B ALA 2.8 33.0 + - - -
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Residues in contact with GLN 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY* 1.3 74.6 - - - +
29A ALA* 1.3 73.7 + - - +
30A HIS* 5.5 1.6 - - - +
42A VAL* 3.5 4.2 - - - +
43A SER* 2.7 54.3 + - - +
44A THR* 5.9 1.1 - - - -
274B ALA* 4.3 3.6 - - - +
277B ALA* 4.0 4.2 - - - +
299B ASP* 4.9 8.4 - - - +
300B THR 3.4 12.6 + - - +
301B THR* 3.4 26.4 + - + +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLN* 1.3 85.8 - - - +
30A HIS* 1.3 61.6 + - - +
41A THR 3.1 12.6 - - - +
42A VAL* 4.2 3.6 - - + -
43A SER* 4.6 1.6 - - - +
54A TYR* 4.3 3.8 - - - +
277B ALA* 3.7 10.1 - - + +
278B ALA* 3.7 33.0 - - - +
281B SER* 4.1 6.2 + - - +
298B ILE 4.0 0.4 - - - +
299B ASP* 3.7 2.6 - - - -
300B THR 3.0 30.8 + - - +
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Residues in contact with HIS 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLN* 5.5 1.8 - - - +
29A ALA* 1.3 75.5 - - - +
31A TRP* 1.3 64.5 + - - +
32A GLU* 2.7 48.3 + - + +
39A LYS 5.2 2.0 - - - -
40A GLY* 3.0 5.7 - - - -
41A THR* 2.7 60.0 + - + +
51A GLN* 5.4 6.1 - - - +
54A TYR* 4.3 2.9 - - - -
281B SER* 5.2 0.7 - - - -
297B SER* 3.6 18.8 - - - -
298B ILE 3.3 5.4 + - - -
299B ASP* 2.7 26.3 + - - +
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Residues in contact with TRP 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A HIS* 1.3 75.2 - - - +
32A GLU* 1.3 67.0 + - - +
33A GLY 2.9 28.5 + - - -
34A ASP 3.3 17.4 + - - -
35A ILE* 3.5 19.3 - - - -
38A GLY 3.9 13.9 - - - -
39A LYS 3.6 7.0 - - - -
40A GLY* 3.6 22.7 - - - -
54A TYR* 3.7 34.3 - + - -
55A GLY* 4.2 3.1 - - - -
56A PHE 4.2 7.9 - - - -
281B SER* 4.2 13.5 - - - -
282B MET* 4.0 32.1 - - + -
285B SER* 3.3 19.9 + - - -
295B PRO* 4.4 0.8 - - + +
297B SER* 3.4 3.5 + - - -
298B ILE* 2.7 60.0 + - + +
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A HIS* 2.7 42.9 + - + +
31A TRP* 1.3 73.4 + - - +
33A GLY* 1.3 61.9 + - - +
38A GLY* 3.2 23.2 - - - -
39A LYS* 3.0 18.4 + - + +
296B THR 3.6 19.3 - - - +
297B SER* 4.9 0.8 - - - -
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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