Contacts of the strand formed by residues 33 - 38 (chain V) 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 LEU 33 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4V LEU* 3.8 29.6 - - + -
23V CYS* 4.2 7.9 - - + -
29V ILE* 3.8 11.4 - - + -
31V ASN 2.7 11.4 + - - +
32V PHE* 1.3 75.6 - - - +
34V ASN* 1.3 68.4 + - - +
35V TRP* 3.2 36.3 - - + +
48V ILE 4.3 0.3 - - - +
49V TYR* 4.0 0.9 - - - -
50V TYR* 3.7 0.4 + - - +
51V THR* 2.9 31.2 + - - +
71V TYR* 3.5 47.1 - - + -
88V CYS* 4.4 2.2 - - - -
89V GLN 3.4 8.7 - - - +
91V HIS* 3.7 1.6 - - - -
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Residues in contact with ASN 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107U TYR 3.2 10.1 + - - +
108U ALA* 3.9 2.8 - - - -
33V LEU* 1.3 74.5 - - - +
35V TRP* 1.3 65.8 + - - +
36V TYR* 3.7 23.3 + - + -
46V LEU* 4.3 2.9 - - + -
48V ILE 3.0 9.2 - - - +
49V TYR* 3.0 29.7 - - - +
50V TYR 3.1 11.1 - - - +
88V CYS* 3.2 9.7 - - - +
89V GLN* 2.9 40.6 + - - +
91V HIS* 2.9 32.3 + - - -
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Residues in contact with TRP 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6V GLN* 4.2 12.6 - - - -
21V ILE* 4.3 7.2 - - + -
22V SER* 4.0 15.0 - - - -
23V CYS* 3.6 29.2 - - + -
33V LEU* 3.2 27.3 - - + +
34V ASN* 1.3 71.8 - - - +
36V TYR* 1.3 63.9 + - - +
46V LEU* 4.7 0.7 - - - -
47V LEU* 3.0 34.3 + - + +
48V ILE* 2.7 32.7 + - + +
51V THR 4.8 4.7 + - - -
64V GLY* 5.7 0.4 - - - -
65V SER 5.4 0.2 + - - -
71V TYR* 4.0 8.9 - - - +
72V SER 2.9 31.4 + - - -
73V LEU* 3.5 41.1 - - + -
86V TYR* 5.0 6.7 - + + -
87V PHE 3.1 25.8 - - - -
88V CYS* 3.8 9.2 - - + -
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Residues in contact with TYR 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46U LEU* 5.7 0.2 - - + -
108U ALA* 4.2 0.2 - - - -
109U MET* 3.3 43.0 + - + +
112U TRP* 3.6 24.0 - + - -
34V ASN* 3.7 11.0 + - + -
35V TRP* 1.3 75.8 - - - +
37V GLN* 1.3 60.8 + - - +
44V ILE* 4.6 12.3 - - + -
45V LYS 3.4 16.2 - - - +
46V LEU* 3.5 17.0 - - + -
47V LEU* 4.5 1.1 - - - -
85V THR 4.1 0.3 - - - +
86V TYR* 3.5 5.0 - - - +
87V PHE* 2.8 42.5 + - + +
88V CYS* 4.9 1.8 - - - -
89V GLN* 2.7 57.1 + - + +
98V PHE* 4.1 16.4 - + + -
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Residues in contact with GLN 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35V TRP 4.1 0.6 + - - -
36V TYR* 1.3 73.2 - - - +
38V GLN* 1.3 63.1 + - - +
39V LYS* 4.0 22.1 + - - +
43V THR 3.9 0.7 - - - +
44V ILE* 3.3 4.3 - - - +
45V LYS* 2.7 56.5 + - + +
47V LEU* 3.6 27.0 - - + +
62V PHE* 3.8 14.1 - - - -
81V GLU 4.8 2.3 + - - -
82V ASP* 4.6 9.1 + - - +
84V ALA* 4.2 13.5 - - + -
85V THR 3.9 2.2 - - - -
86V TYR* 3.1 38.0 + - + -
87V PHE* 5.6 0.2 - - - -
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Residues in contact with GLN 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40U LEU* 3.3 30.9 - - - +
44U ASN* 4.5 4.0 - - - +
95U TYR* 3.7 13.7 + - - +
37V GLN* 1.3 74.8 - - - +
39V LYS* 1.3 70.4 + - - +
40V PRO 5.7 0.4 + - - -
42V GLY* 4.3 10.4 - - - +
43V THR 3.5 7.4 - - - +
44V ILE* 4.4 17.9 - - + -
84V ALA* 3.0 18.8 - - - +
85V THR* 2.8 36.9 + - - +
87V PHE* 3.7 24.1 - - + -
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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