Contacts of the strand formed by residues 26 - 37 (chain B) in PDB entry 1KY9
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 VAL 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B VAL* 4.6 9.9 - - + -
23B MSE 2.9 24.1 + - + +
24B PRO 4.6 0.7 - - - +
25B SER* 1.3 80.2 - - - +
27B VAL* 1.3 68.1 + - - +
89B SER* 4.6 6.7 - - - -
90B GLY 3.6 9.0 - - - +
91B VAL* 4.5 14.8 - - + -
118B SER* 4.0 17.0 + - - -
150B ILE* 5.9 1.6 - - + -
167B ILE* 4.0 43.3 - - + +
175B GLU* 3.3 27.3 - - + +
213B ALA* 4.6 4.0 - - + -
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Residues in contact with VAL 27 (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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24B PRO 5.4 0.2 - - - +
25B SER 4.0 0.7 - - - +
26B VAL* 1.3 78.1 - - - +
28B SER* 1.3 72.3 + - - +
29B ILE* 3.9 13.5 - - + -
89B SER* 3.5 1.4 - - - -
90B GLY 3.0 32.6 + - - +
92B ILE* 3.6 36.1 - - + -
100B VAL* 4.1 16.4 - - + -
115B VAL* 3.5 21.8 - - + -
116B GLN 3.7 9.2 - - - +
117B LEU* 3.9 13.9 - - + +
175B GLU* 3.3 13.0 - - - +
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Residues in contact with SER 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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27B VAL* 1.3 77.6 - - - +
29B ILE* 1.3 66.8 + - - +
30B ASN* 5.4 4.7 - - - -
88B GLY 3.8 6.1 - - - -
115B VAL* 3.4 3.6 - - - -
116B GLN* 3.1 45.1 + - - +
117B LEU 5.1 1.2 + - - -
118B SER* 6.1 0.2 - - - -
169B ASN* 5.4 5.2 - - - -
175B GLU* 3.8 25.4 - - - +
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Residues in contact with ILE 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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27B VAL* 3.9 10.8 - - + -
28B SER* 1.3 81.7 - - - +
30B ASN* 1.3 67.7 - - - +
31B VAL* 3.7 18.8 - - + -
87B LEU* 3.1 7.1 - - - +
88B GLY 2.9 39.0 + - - +
89B SER 3.8 8.7 - - - +
90B GLY* 4.0 5.8 - - - -
100B VAL* 4.5 0.9 - - + -
102B THR* 3.6 39.9 - - + +
106B VAL* 4.4 7.6 - - + -
107B VAL* 4.8 2.0 - - + -
113B ILE* 3.6 20.9 - - + -
114B LYS 3.3 3.4 - - - -
115B VAL* 4.2 7.0 - - + -
139B ILE* 3.9 14.1 - - + -
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Residues in contact with ASN 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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28B SER* 5.4 3.5 - - - -
29B ILE* 1.3 79.5 + - - +
31B VAL* 1.3 63.9 + - - +
32B GLU* 5.5 0.2 - - - +
85B MSE 6.0 6.3 - - - +
86B ALA 3.6 5.8 + - - -
87B LEU* 4.1 19.3 - - - +
112B VAL* 3.8 0.9 - - - +
113B ILE* 3.6 0.5 - - - -
114B LYS* 2.7 51.9 + - + +
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Residues in contact with VAL 31 (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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29B ILE* 3.7 20.4 - - + -
30B ASN* 1.3 80.3 + - - +
32B GLU* 1.3 67.1 + - - +
84B PHE* 4.5 9.6 - - + -
85B MSE 3.4 7.3 - - - +
86B ALA* 2.8 35.1 + - + +
106B VAL* 3.5 30.7 - - + +
107B VAL* 4.0 12.6 - - + -
110B ALA* 3.3 34.8 - - + +
112B VAL 3.4 3.4 - - - +
113B ILE* 4.3 7.4 - - + -
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Residues in contact with GLU 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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31B VAL* 1.3 78.1 - - - +
33B GLY* 1.3 61.3 + - - +
83B LYS* 5.2 18.2 + - + +
84B PHE 3.7 8.7 - - - +
85B MSE 4.8 7.2 - - + +
110B ALA* 3.7 1.2 - - - -
111B THR* 2.8 6.2 + - - -
112B VAL* 2.8 59.9 + - + +
114B LYS* 5.9 1.0 + - - +
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Residues in contact with GLY 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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32B GLU* 1.3 79.7 - - - +
34B SER* 1.3 61.5 + - - -
83B LYS* 3.3 6.3 - - - +
84B PHE* 2.8 42.7 + - - -
109B ASN 3.6 11.7 - - - -
111B THR* 3.4 15.3 - - - -
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Residues in contact with SER 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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33B GLY* 1.3 75.1 - - - -
35B THR* 1.3 67.7 + - - +
81B GLN* 3.4 22.9 + - - +
82B GLN 3.0 22.2 - - - -
83B LYS* 4.1 9.0 - - - -
84B PHE* 3.3 7.7 - - - -
109B ASN* 3.7 19.6 + - - +
111B THR* 3.7 8.5 + - - -
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Residues in contact with THR 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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34B SER* 1.3 81.2 + - - +
36B THR* 1.3 76.5 + - - +
37B VAL* 3.7 2.4 + - + -
81B GLN* 3.0 15.0 - - - +
82B GLN* 2.7 40.4 + - + +
84B PHE* 4.0 16.6 - - + -
109B ASN* 4.9 13.0 + - - -
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Residues in contact with THR 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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35B THR* 1.3 83.2 + - - +
37B VAL* 1.3 71.0 + - - +
38B ASN* 5.7 2.2 - - - +
79B GLY* 4.7 6.9 - - - -
80B GLN 3.7 7.8 + - - +
81B GLN* 2.4 21.4 + - - +
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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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35B THR* 3.7 2.4 + - + -
36B THR* 1.3 79.6 - - - +
38B ASN* 1.3 74.0 + - + +
40B PRO* 6.2 0.9 - - + -
79B GLY* 3.6 4.7 - - - -
80B GLN* 3.1 35.8 + - + +
82B GLN* 3.0 46.7 - - + +
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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