Contacts of the strand formed by residues 109 - 115 (chain B) in PDB entry 1KTZ
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 THR 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B TRP* 3.8 16.2 - - + +
66B ARG* 3.2 6.8 - - - +
67B LYS* 2.9 42.1 + - - +
102B GLU* 3.8 15.5 - - - +
108B GLU* 1.3 74.5 + - - +
110B PHE* 1.3 59.2 + - - +
111B PHE* 3.5 30.1 - - + -
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Residues in contact with PHE 110 (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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64B VAL* 3.5 24.7 - - + -
65B TRP 3.5 3.6 - - - -
66B ARG* 3.5 39.9 - - - +
86B HIS* 3.8 29.8 - + + -
88B PHE* 4.0 9.0 - + - -
102B GLU* 3.4 9.0 + - - +
103B LYS* 2.9 61.4 + - + +
105B LYS* 3.7 39.5 - - + -
108B GLU* 3.9 4.4 + - - +
109B THR* 1.3 76.7 - - - +
111B PHE* 1.3 64.4 + - - +
112B MET* 4.0 12.6 - - + -
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Residues in contact with PHE 111 (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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64B VAL* 3.4 5.5 - - - +
65B TRP* 2.8 57.9 + + + +
100B MET* 3.7 25.5 - - + +
101B LYS* 3.4 12.8 - - - -
102B GLU* 3.4 46.0 - - + -
109B THR* 3.5 23.1 - - + -
110B PHE* 1.3 80.5 - - - +
112B MET* 1.3 63.7 + - - +
126B PHE* 3.8 23.6 - + + -
127B SER 6.0 1.8 - - - -
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Residues in contact with MET 112 (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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62B VAL* 4.3 5.4 - - + -
63B ALA 3.4 12.6 - - - +
64B VAL* 3.8 19.1 - - + -
85B TYR* 4.3 15.7 - - - +
86B HIS* 4.8 0.2 - - - -
88B PHE* 3.6 37.2 - - + -
89B ILE 4.3 7.6 - - - +
90B LEU* 4.0 19.1 - - + -
92B ASP* 4.6 0.5 - - - +
99B ILE 3.9 0.7 - - - +
100B MET* 3.5 4.0 - - - -
101B LYS* 3.0 33.9 + - - +
103B LYS* 3.7 19.7 - - + -
110B PHE* 4.0 12.3 - - + -
111B PHE* 1.3 77.7 - - - +
113B CYS* 1.3 72.3 + - - +
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Residues in contact with CYS 113 (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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62B VAL* 3.5 5.7 - - - +
63B ALA* 3.0 33.0 + - - +
90B LEU* 5.2 0.7 - - - -
92B ASP* 3.5 7.9 - - - +
98B CYS* 2.0 49.8 - - - -
99B ILE 3.2 32.3 - - - +
100B MET* 3.5 26.2 - - - +
112B MET* 1.3 77.6 - - - +
114B SER* 1.3 59.4 + - - +
124B ILE* 4.3 1.3 - - - -
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Residues in contact with SER 114 (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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60B VAL* 4.1 5.8 - - - -
61B CYS 3.0 14.8 - - - -
62B VAL* 4.3 0.7 - - - -
90B LEU* 3.5 34.7 - - - +
92B ASP* 2.6 43.9 + - - +
93B ALA* 3.2 14.3 + - - -
97B LYS 3.9 6.9 - - - +
98B CYS* 4.2 2.1 - - - -
113B CYS* 1.3 74.8 - - - +
115B CYS* 1.3 67.6 + - - +
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Residues in contact with CYS 115 (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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60B VAL* 3.4 2.5 - - - +
61B CYS* 2.9 35.0 + - - -
93B ALA* 3.5 8.2 + - - +
95B SER 3.1 15.3 - - - +
96B PRO 4.0 0.2 - - - -
97B LYS 3.4 17.9 - - - +
98B CYS* 3.9 13.0 - - - +
114B SER* 1.3 79.3 + - - +
116B SER* 1.3 62.1 + - - +
120B CYS* 2.0 60.4 - - + -
121B ASN 3.7 3.1 - - - -
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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