Contacts of the strand formed by residues 110 - 117 (chain A) 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 ALA 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.6 25.1 - - + -
32A GLU 3.9 4.7 - - - +
107A VAL* 3.2 19.2 + - - +
108A ASP 3.1 1.0 - - - -
109A ASN* 1.3 81.3 - - - +
111A THR* 1.3 61.4 + - - +
112A VAL 4.5 0.7 - - - +
113A ILE* 4.3 22.4 - - + -
127A MSE 4.8 7.6 - - + +
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Residues in contact with THR 111 (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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32A GLU* 2.9 12.1 + - + -
33A GLY* 4.2 3.1 - - - -
34A SER* 4.1 17.4 + - - -
83A LYS* 5.2 10.5 - - - +
109A ASN 3.8 0.9 + - - -
110A ALA* 1.3 76.3 + - - +
112A VAL* 1.3 75.1 + - + +
113A ILE* 5.5 1.6 - - - -
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Residues in contact with VAL 112 (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 ASN 3.9 1.0 - - - +
31A VAL* 3.6 2.8 - - - +
32A GLU* 2.9 53.1 + - + +
111A THR* 1.3 96.4 + - + +
113A ILE* 1.3 67.7 + - - +
114A LYS* 3.8 33.2 - - + -
124A ASP* 5.3 0.7 - - - +
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Residues in contact with ILE 113 (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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29A ILE* 3.1 27.6 - - + -
30A ASN 3.6 3.8 - - - +
31A VAL* 4.3 7.6 - - + +
107A VAL* 4.7 8.7 - - + -
110A ALA* 4.3 16.6 - - + -
111A THR 5.5 0.9 - - - -
112A VAL* 1.3 81.0 - - - +
114A LYS* 1.3 94.8 + - - +
115A VAL* 3.9 8.1 - - + -
124A ASP* 3.9 5.2 - - - +
125A ALA* 3.3 52.9 + - + +
126A LYS* 5.0 0.7 - - - -
127A MSE 4.9 13.5 - - + +
139A ILE* 4.1 11.9 - - + -
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Residues in contact with LYS 114 (chain A).
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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29A ILE* 3.4 1.0 - - - -
30A ASN* 2.9 48.7 + - + +
112A VAL* 3.8 25.4 - - + -
113A ILE* 1.3 80.3 - - - +
115A VAL* 1.3 66.1 + - - +
122A LYS* 5.6 9.2 - - + +
123A PHE 3.5 12.5 + - - +
124A ASP* 2.9 26.5 + - - -
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Residues in contact with VAL 115 (chain A).
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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27A VAL* 3.7 35.2 - - + -
28A SER 3.2 5.6 - - - +
29A ILE* 4.6 1.8 - - + -
30A ASN* 5.2 0.9 - - - -
100A VAL* 5.4 0.2 - - + -
113A ILE* 3.9 7.2 - - + -
114A LYS* 1.3 81.7 - - - +
116A GLN* 1.3 63.2 + - - +
117A LEU* 4.3 9.2 - - + -
121A ARG 3.7 0.3 - - - +
122A LYS* 3.1 6.0 - - - +
123A PHE* 2.8 38.3 + - + +
125A ALA* 3.8 26.9 - - + -
139A ILE* 4.1 9.9 - - + -
141A ILE* 4.3 20.4 - - + -
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Residues in contact with GLN 116 (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 VAL* 3.7 2.1 - - - -
28A SER* 2.9 48.7 + - - +
30A ASN* 4.9 8.2 - - - +
115A VAL* 1.3 75.3 - - - +
117A LEU* 1.3 76.3 + - - +
120A GLY* 3.6 16.8 - - - +
121A ARG 3.2 10.8 - - - +
122A LYS* 3.3 31.6 - - + -
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Residues in contact with LEU 117 (chain A).
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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24A PRO 5.1 7.2 - - - +
26A VAL 4.8 0.2 - - - -
27A VAL* 3.4 30.3 - - + -
92A ILE* 4.3 9.9 - - + -
115A VAL* 4.3 8.3 - - + -
116A GLN* 1.3 83.5 + - - +
118A SER* 1.3 65.5 + - - +
119A ASP* 2.9 16.4 - - - +
120A GLY* 2.8 13.3 + - - -
121A ARG* 3.0 36.2 + - - +
123A PHE* 3.3 34.5 - - + -
141A ILE* 4.9 2.9 - - + -
147A LEU* 3.7 14.1 - - + -
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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