Contacts of the helix formed by residues 26 - 40 (chain B) in PDB entry 1Y8Q
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 26 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24B GLY 3.6 2.6 - - - -
25B ALA* 1.3 77.1 - - - +
27B GLY* 1.3 70.7 + - - +
28B ILE 3.4 2.2 - - - -
29B GLY 4.0 3.8 - - - +
30B CYS* 3.0 22.3 + - - +
60B GLN* 3.4 20.9 - - - -
115B ALA 5.0 1.0 + - - -
802B ATP 3.5 23.3 + - - -
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Residues in contact with GLY 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY* 1.3 72.6 - - - +
28B ILE* 1.3 61.4 + - - +
30B CYS* 4.2 0.2 - - - +
31B GLU* 3.5 23.0 + - - +
59B ARG* 4.0 13.6 - - - +
60B GLN* 3.5 14.4 - - - +
391B ASN* 3.8 24.6 - - - +
802B ATP 3.0 17.2 + - - -
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Residues in contact with ILE 28 (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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26B GLY 3.4 0.2 - - - -
27B GLY* 1.3 71.8 - - - +
29B GLY* 1.3 56.1 + - - +
31B GLU* 3.2 3.3 + - - +
32B LEU* 2.7 39.1 + - + +
114B ASN 4.8 0.2 - - - +
115B ALA* 3.7 25.4 - - + +
116B LEU 6.0 1.1 - - - +
139B SER* 4.2 15.0 - - - +
140B GLY* 4.2 10.8 - - - +
141B THR* 3.8 23.1 - - + +
391B ASN* 3.2 26.6 + - + +
394B ILE* 4.0 15.7 - - + -
395B ALA* 4.0 5.0 - - + +
398B ILE* 3.7 25.1 - - + -
802B ATP 4.6 2.4 + - - +
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Residues in contact with GLY 29 (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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22B VAL* 4.6 3.8 - - - +
24B GLY 3.4 24.9 - - - -
25B ALA* 4.0 5.6 - - - -
26B GLY 3.3 6.9 + - - +
28B ILE* 1.3 77.1 - - - +
30B CYS* 1.3 62.7 + - - +
32B LEU* 3.0 9.0 + - - +
33B LEU* 2.9 29.4 + - - +
46B LEU* 6.0 0.2 - - - -
115B ALA* 3.8 9.2 - - - +
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Residues in contact with CYS 30 (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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25B ALA* 3.6 17.4 - - - -
26B GLY 3.0 20.3 + - - +
27B GLY 4.2 2.7 - - - +
29B GLY* 1.3 73.5 - - - +
31B GLU* 1.3 64.3 + - - +
33B LEU* 3.4 4.2 + - - +
34B LYS* 3.2 17.7 + - - +
59B ARG 5.0 0.2 - - - +
60B GLN* 3.9 19.3 - - - -
61B PHE* 3.7 15.6 - - + -
62B LEU* 3.8 35.3 - - + +
63B PHE* 3.8 23.6 - - - -
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 2.8 39.1 + - - +
54A ASN* 4.6 0.9 - - - +
57A LEU* 5.1 2.4 - - - +
27B GLY 3.5 13.9 + - - +
28B ILE 3.2 4.1 + - - +
30B CYS* 1.3 76.7 - - - +
32B LEU* 1.3 56.7 + - - +
34B LYS* 2.9 19.6 + - - +
35B ASN* 2.8 36.1 + - - +
59B ARG 4.6 8.1 - - - +
61B PHE* 3.7 19.0 - - + +
388B ALA* 4.6 4.4 - - - +
391B ASN* 4.2 2.7 - - + +
392B ALA* 3.7 28.7 - - - +
395B ALA* 3.4 19.7 - - + -
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Residues in contact with LEU 32 (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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22B VAL* 4.0 21.1 - - + -
28B ILE* 2.7 19.6 + - + +
29B GLY* 3.2 10.3 - - - +
31B GLU* 1.3 74.4 - - - +
33B LEU* 1.3 55.4 + - - +
35B ASN* 3.1 2.4 + - - +
36B LEU* 2.7 57.8 + - + +
113B MET* 3.9 31.2 - - + +
114B ASN 5.4 0.2 - - - +
115B ALA* 5.1 2.2 - - + -
395B ALA* 3.7 8.5 - - + +
398B ILE* 3.9 31.4 - - + -
399B VAL* 3.9 19.3 - - + -
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Residues in contact with LEU 33 (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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22B VAL* 4.9 7.0 - - + -
25B ALA* 5.5 0.9 - - + -
29B GLY 2.9 19.0 + - - +
30B CYS* 3.7 7.6 - - - +
32B LEU* 1.3 72.1 - - - +
34B LYS* 1.3 59.1 + - - +
36B LEU* 3.2 4.9 + - - +
37B VAL* 2.9 37.3 + - + +
44B ILE* 3.8 34.1 - - + -
46B LEU* 3.5 39.9 - - + -
62B LEU* 3.8 10.5 - - + -
76B ALA* 3.8 18.8 - - + +
77B LYS* 5.5 0.9 - - - -
80B VAL* 4.1 18.8 - - + -
89B ILE* 5.2 8.3 - - + -
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Residues in contact with LYS 34 (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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50A GLU* 2.5 37.4 + - - +
53A LYS* 4.3 2.2 - - - +
80A PHE* 4.1 13.0 - - + -
304A ALA* 4.3 1.8 - - - +
30B CYS 3.2 4.2 + - - +
31B GLU* 2.9 33.6 + - - +
33B LEU* 1.3 81.0 - - - +
35B ASN* 1.3 76.4 + - - +
37B VAL* 3.6 1.3 + - - +
38B LEU* 3.0 55.7 + - + +
61B PHE* 3.5 33.9 - - + -
62B LEU* 5.3 1.1 - - + -
80B VAL* 5.0 0.6 - - - +
83B PHE* 4.0 22.9 - - + -
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Residues in contact with ASN 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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50A GLU* 4.0 0.3 - - - +
300A ALA* 3.9 11.6 - - - +
301A PRO* 4.8 4.7 - - + -
304A ALA* 3.7 17.3 - - - +
31B GLU* 2.8 24.9 + - - +
32B LEU 3.8 1.3 - - - +
34B LYS* 1.3 97.5 + - - +
36B LEU* 1.3 62.4 + - - +
38B LEU* 3.9 3.5 - - - +
39B THR* 2.5 35.4 + - - +
395B ALA* 3.4 32.5 - - - +
396B GLY* 3.7 4.4 - - - +
399B VAL* 3.6 19.7 - - + -
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Residues in contact with LEU 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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20B VAL* 4.1 9.6 - - + -
22B VAL* 3.6 19.5 - - + -
32B LEU* 2.7 32.8 + - + +
33B LEU* 3.5 4.9 - - - +
35B ASN* 1.3 72.7 - - - +
37B VAL* 1.3 64.6 + - - +
39B THR* 3.1 8.5 + - - -
40B GLY 3.2 0.5 + - - -
41B PHE* 3.1 56.9 + - + -
44B ILE* 3.9 16.8 - - + -
111B LEU* 5.7 0.2 - - + -
113B MET* 3.6 38.8 - - + -
399B VAL* 4.2 13.2 - - + -
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Residues in contact with VAL 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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33B LEU* 2.9 20.0 + - + +
34B LYS* 3.9 4.5 - - - +
36B LEU* 1.3 76.3 - - - +
38B LEU* 1.3 62.9 + - - +
40B GLY* 3.2 13.5 + - - -
41B PHE 3.8 12.0 + - - +
44B ILE* 3.9 18.2 - - + -
80B VAL* 3.6 24.0 - - + -
83B PHE* 4.2 11.2 - - + -
84B TYR* 3.3 54.9 - - + -
87B ALA* 4.6 8.7 - - + -
89B ILE* 4.7 1.6 - - + -
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Residues in contact with LEU 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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50A GLU* 5.4 1.8 - - - +
77A GLY 3.8 23.6 - - - +
78A ALA* 4.0 28.4 - - - +
79A GLN 4.6 0.4 - - - +
80A PHE* 4.4 13.5 - - + +
300A ALA* 3.7 25.7 - - + +
34B LYS* 3.0 45.6 + - + +
35B ASN 4.2 0.2 - - - +
37B VAL* 1.3 76.9 - - + +
39B THR* 1.3 60.1 + - - +
40B GLY 3.3 0.6 + - - -
83B PHE* 3.9 24.0 - - + -
84B TYR* 5.4 0.7 - - - -
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Residues in contact with THR 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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299A MET* 5.6 2.0 - - + -
300A ALA* 4.0 2.4 - - - +
301A PRO* 3.5 27.3 - - + +
7B LEU* 3.7 28.1 - - + +
15B VAL* 4.5 1.9 - - + +
35B ASN 2.5 23.8 + - - -
36B LEU 3.1 4.5 + - - -
38B LEU* 1.3 77.9 - - - +
40B GLY* 1.3 57.7 + - - +
41B PHE* 4.4 4.9 - - + -
399B VAL* 3.6 19.1 - - + +
403B LEU* 4.2 26.2 - - + -
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Residues in contact with GLY 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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7B LEU* 5.4 1.3 - - - -
15B VAL* 3.2 20.0 - - - +
16B ALA* 4.1 4.3 - - - +
37B VAL 3.2 9.6 + - - -
38B LEU 3.3 0.4 - - - -
39B THR* 1.3 81.5 - - - +
41B PHE* 1.3 65.9 + - - +
42B SER* 3.4 11.6 + - - -
84B TYR* 5.0 8.5 + - - -
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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