Contacts of the strand formed by residues 29 - 35 (chain B) in PDB entry 1KYO
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 SER 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B LYS 4.0 0.2 + - - -
28B ILE* 1.3 72.7 + - - +
30B THR* 1.3 65.2 + - - +
31B LEU 4.1 0.4 - - - -
92B THR* 3.5 2.3 - - - +
93B PHE* 2.8 61.5 + - - -
95B LYS* 3.0 26.2 - - - +
190B GLU 3.8 4.9 - - - -
191B ASN* 2.9 24.1 + - - -
192B VAL* 4.0 6.0 - - - +
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Residues in contact with THR 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 ILE* 4.6 6.1 - - + -
29B SER* 1.3 79.7 - - - +
31B LEU* 1.3 60.1 + - - +
32B ALA* 3.8 3.6 + - - +
90B LYS* 3.6 31.3 - - - +
91B ALA 4.0 3.4 - - - -
92B THR* 3.9 21.3 - - + +
93B PHE* 4.4 0.9 - - - -
188B SER 4.0 0.5 - - - +
189B GLY* 4.9 0.2 - - - -
190B GLU* 3.0 48.0 + - + +
191B ASN* 6.1 0.7 - - + -
192B VAL* 5.2 0.4 - - - -
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Residues in contact with LEU 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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30B THR* 1.3 71.6 - - - +
32B ALA* 1.3 63.1 + - - +
33B VAL* 5.1 1.6 - - + -
89B LEU 3.6 2.8 - - - +
90B LYS* 3.5 1.8 - - - -
91B ALA* 2.8 36.0 + - + +
93B PHE* 3.5 17.1 - - + -
98B LEU* 4.4 8.1 - - + -
101B TYR* 4.0 8.1 - - + -
102B VAL* 3.5 42.4 - - + +
105B LEU* 3.7 20.5 - - + +
187B VAL* 3.9 26.2 - - + -
188B SER 4.2 0.9 - - - -
189B GLY* 4.1 12.1 - - - -
192B VAL* 5.3 2.0 - - + -
197B LEU* 3.9 13.9 - - + -
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Residues in contact with ALA 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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30B THR* 3.8 3.5 + - - +
31B LEU* 1.3 74.5 - - - +
33B VAL* 1.3 66.4 + - - +
34B LYS* 3.9 8.3 - - - +
88B THR* 4.3 17.5 - - + -
89B LEU 3.9 2.9 - - - -
90B LYS* 4.1 14.6 - - + +
186B GLU 4.0 0.3 - - - +
187B VAL* 3.6 3.6 - - - +
188B SER* 2.9 49.5 + - - +
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Residues in contact with VAL 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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31B LEU* 5.1 1.8 - - + -
32B ALA* 1.3 77.8 - - - +
34B LYS* 1.3 63.3 + - - +
35B VAL* 3.6 18.3 + - + +
87B ILE 3.6 5.0 - - - +
89B LEU* 3.1 38.7 + - + +
105B LEU* 3.8 32.5 - - + -
109B LEU* 4.3 20.9 - - + -
185B LEU* 4.8 13.0 - - + -
186B GLU 3.8 4.9 - - - +
187B VAL* 4.5 17.0 - - + -
206B LEU* 5.3 7.6 - - + -
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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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32B ALA* 3.9 7.6 - - + +
33B VAL* 1.3 72.1 - - - +
35B VAL* 1.3 59.6 + - - +
36B HIS* 4.3 0.4 - - - -
86B TYR* 3.8 32.3 - - + -
87B ILE 4.3 2.5 - - - -
88B THR* 3.6 30.3 - - + +
184B ASN 4.2 0.4 - - - +
185B LEU* 3.2 5.2 - - - +
186B GLU* 2.8 58.0 + - + +
188B SER* 5.0 8.7 + - - -
331B SER* 3.5 31.9 + - - +
332B VAL* 3.8 15.8 - - + +
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B VAL* 3.8 11.9 - - + +
34B LYS* 1.3 80.8 - - - +
36B HIS* 1.3 55.0 + - - +
37B GLY* 2.6 16.5 + - - -
86B TYR* 3.5 4.5 - - - -
87B ILE* 3.1 33.2 + - + +
89B LEU* 4.6 2.0 - - + -
109B LEU* 4.1 11.9 - - + -
179B VAL* 3.1 44.9 - - + +
180B TYR* 4.0 24.7 - - + -
184B ASN 3.8 7.9 - - - +
185B LEU* 3.8 13.9 - - + -
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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