Contacts of the strand formed by residues 83 - 92 (chain A) 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 LEU 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A PRO* 3.8 23.8 - - + -
81A GLN 3.7 5.8 + - - +
82A ASP* 1.3 73.7 - - - +
84A GLU* 1.3 69.3 + - - +
85A PRO* 4.8 0.3 - - - +
103A ASN* 3.5 51.3 - - + +
104A MET 5.8 0.9 - - - -
105A VAL 3.3 3.6 - - - +
106A VAL* 3.8 33.4 - - + +
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Residues in contact with GLU 84 (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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82A ASP* 4.1 15.8 - - - +
83A LEU* 1.3 85.4 - - - +
85A PRO* 1.3 77.8 - - + +
103A ASN* 3.4 3.9 - - - -
104A MET 2.7 26.0 + - - -
105A VAL* 2.7 29.8 + - + +
107A LYS* 3.9 30.8 - - + +
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Residues in contact with PRO 85 (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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83A LEU 4.8 0.9 - - - +
84A GLU* 1.3 104.8 - - + +
86A LEU* 1.3 58.9 + - - +
87A THR* 5.8 0.2 - - - -
100A GLN* 4.3 28.5 - - - +
101A LEU 3.0 18.8 - - - +
102A SER* 3.7 13.5 - - - -
103A ASN 3.9 2.0 - - - +
104A MET* 4.3 0.7 - - - +
105A VAL* 4.2 6.7 - - - +
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Residues in contact with LEU 86 (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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24A PHE* 3.5 32.1 - - + -
36A PRO* 4.9 6.7 - - + -
39A TYR* 3.7 40.4 - - + -
85A PRO* 1.3 74.7 - - - +
87A THR* 1.3 73.9 + - - +
88A ILE* 3.8 14.0 + - + +
100A GLN* 3.1 4.1 - - - -
101A LEU* 2.7 38.1 + - - +
104A MET* 3.6 25.1 - - + +
105A VAL* 4.6 7.4 - - + -
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Residues in contact with THR 87 (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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36A PRO* 3.8 12.3 - - - +
85A PRO 5.8 0.2 - - - -
86A LEU* 1.3 80.6 - - - +
88A ILE* 1.3 65.9 + - - +
98A VAL* 3.9 22.2 - - + -
99A GLU 3.4 13.0 - - - +
100A GLN* 3.6 20.1 + - + -
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Residues in contact with ILE 88 (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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24A PHE* 4.2 11.0 - - + -
32A TRP* 3.7 29.6 - - + -
33A VAL* 4.2 10.1 - - + -
35A GLU 3.5 8.7 - - - +
36A PRO* 4.3 4.3 - - + -
86A LEU* 3.8 25.1 - - + +
87A THR* 1.3 80.9 - - - +
89A LEU* 1.3 60.4 + - - +
90A TYR* 4.0 15.5 - - + -
97A LYS 3.9 0.2 - - - +
98A VAL* 3.4 5.6 - - - +
99A GLU* 2.8 40.3 + - + +
101A LEU* 3.7 38.4 - - + -
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Residues in contact with LEU 89 (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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33A VAL* 3.9 1.4 - - - +
34A HIS* 2.8 51.6 + - + +
35A GLU* 2.8 27.7 + - + +
88A ILE* 1.3 76.4 - - - +
90A TYR* 1.3 63.7 + - - +
91A TYR* 5.0 4.3 - - + +
96A PRO* 4.0 14.6 - - + -
97A LYS 3.3 26.9 - - - +
98A VAL* 3.6 22.2 - - + -
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Residues in contact with TYR 90 (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 TRP* 3.3 35.9 - + + +
33A VAL* 4.4 0.4 - - - -
34A HIS* 4.1 5.8 - - - +
88A ILE* 4.0 17.0 - - + -
89A LEU* 1.3 77.6 - - - +
91A TYR* 1.3 66.9 + - - +
92A VAL* 3.7 21.6 - - + +
96A PRO* 3.5 1.3 - - - +
97A LYS* 2.7 71.4 + - + +
99A GLU* 2.8 41.2 + - + -
53B ILE* 3.9 24.9 - - + -
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Residues in contact with TYR 91 (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 TRP 4.5 3.3 + - - +
34A HIS* 3.8 38.8 + + + +
89A LEU* 5.0 4.1 - - + +
90A TYR* 1.3 81.9 - - - +
92A VAL* 1.3 64.9 + - - +
93A GLY 3.7 7.9 - - - +
94A ARG* 3.7 23.3 - - - -
95A THR 3.5 6.1 - - - -
96A PRO* 3.7 35.5 - - + +
50B ILE* 3.6 45.5 - - + +
51B THR 4.3 4.1 + - - +
52B SER* 3.8 14.2 - - - -
53B ILE* 3.1 27.4 + - - +
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Residues in contact with VAL 92 (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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90A TYR* 3.7 25.5 + - + -
91A TYR* 1.3 76.3 - - - +
93A GLY* 1.3 66.9 + - - +
94A ARG 3.4 0.2 + - - -
95A THR* 3.0 25.0 + - - +
97A LYS* 3.9 27.4 - - + -
53B ILE* 3.3 17.9 - - + +
54B CYS 4.9 0.4 - - - +
55B GLU* 3.7 26.9 - - + +
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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