Contacts of the strand formed by residues 45 - 53 (chain U) 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 LYS 45 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39U ARG 3.9 1.0 - - - +
40U LEU* 4.1 2.1 - - - +
41U PHE* 3.2 52.3 + - + +
43U GLY* 3.3 25.0 + - - -
44U ASN* 1.3 76.5 - - - +
46U LEU* 1.3 67.6 + - - +
47U GLU* 6.3 0.2 - - + -
87V PHE* 4.7 0.4 - - - -
99V GLY 4.4 11.9 - - - +
100V ALA* 5.3 1.1 - - - +
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Residues in contact with LEU 46 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38U ILE* 3.6 20.2 - - + -
39U ARG 3.5 15.0 - - - +
40U LEU* 3.6 30.1 - - + -
45U LYS* 1.3 75.2 - - - +
47U GLU* 1.3 61.6 + - - +
95U TYR* 4.7 8.3 - - + -
36V TYR* 5.7 1.1 - - + -
44V ILE* 4.3 13.7 - - + -
87V PHE* 3.5 39.3 - - + -
97V THR* 5.6 2.3 - - - +
98V PHE* 3.5 52.8 + - + +
99V GLY 4.7 3.3 + - - +
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Residues in contact with GLU 47 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38U ILE* 3.2 6.2 - - - +
39U ARG* 2.9 64.3 + - + +
41U PHE* 3.2 29.0 - - + -
45U LYS* 5.0 0.7 - - + +
46U LEU* 1.3 76.8 - - - +
48U TRP* 1.3 69.1 + - - +
49U VAL* 3.5 1.3 + - - +
61U ASN* 4.3 9.6 - - - +
63U SER* 4.0 13.4 + - - -
64U LEU* 3.7 14.9 - - - +
98V PHE* 4.2 5.4 - - - -
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Residues in contact with TRP 48 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36U ASN* 3.6 17.9 + - + -
37U TRP 4.0 5.8 - - - -
38U ILE* 4.2 10.1 - - + -
47U GLU* 1.3 76.0 - - - +
49U VAL* 1.3 60.5 + - - +
50U GLY* 3.4 24.6 + - - -
51U TYR* 3.8 14.8 - + - -
59U ASN* 3.3 43.3 - - - -
60U TYR 3.9 9.0 - - - -
61U ASN* 2.9 44.4 + - + +
109U MET* 5.4 1.1 - - + -
94V PHE* 4.1 10.1 - + + -
95V PRO* 3.4 40.6 - - + -
96V TRP* 3.6 48.8 + + + +
98V PHE* 4.0 11.7 - - + -
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Residues in contact with VAL 49 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37U TRP* 3.0 22.3 + - + +
38U ILE* 3.8 11.2 - - - -
39U ARG* 3.6 33.9 - - + +
48U TRP* 1.3 73.2 - - - +
50U GLY* 1.3 61.3 + - - +
61U ASN* 3.2 24.2 + - - +
64U LEU* 4.0 15.2 - - + +
68U LEU* 3.2 34.4 - - + +
70U ILE* 5.2 0.2 - - + -
81U LEU* 4.2 18.2 - - + -
83U LEU* 5.7 3.6 - - + -
94U TYR* 4.6 8.7 - - + -
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Residues in contact with GLY 50 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36U ASN* 3.3 2.6 - - - -
37U TRP 3.0 26.0 + - - -
48U TRP* 3.4 16.4 + - - +
49U VAL* 1.3 81.7 - - - +
51U TYR* 1.3 60.8 + - - -
59U ASN 3.2 13.0 - - - -
60U TYR* 4.2 1.8 - - - -
70U ILE* 3.5 17.2 - - - +
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Residues in contact with TYR 51 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34U TYR* 3.8 45.2 + + + -
35U TRP 3.1 17.0 - - - +
36U ASN* 3.3 26.7 - - - +
48U TRP* 4.0 12.3 - + - -
50U GLY* 1.3 72.3 - - - +
52U ILE* 1.3 69.6 + - - +
53U SER* 5.0 0.9 - - - -
57U ASP* 4.4 9.2 - - + -
58U ASN* 3.4 9.4 + - - +
59U ASN* 2.8 63.4 + - + +
70U ILE* 3.7 8.8 - - - +
107U TYR* 4.7 1.8 + + - -
94V PHE* 3.8 30.9 - + - -
96V TRP* 4.1 8.5 - + - -
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Residues in contact with ILE 52 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U ILE* 5.4 0.7 - - + -
35U TRP* 2.9 47.2 + - + +
51U TYR* 1.3 77.8 - - - +
53U SER* 1.3 71.4 + - - +
56U GLY* 4.2 13.7 - - - +
57U ASP 3.3 7.6 - - - +
58U ASN* 3.5 21.1 - - - +
70U ILE* 4.2 9.0 - - + +
71U THR* 4.0 18.4 - - - -
72U ARG* 3.8 32.3 - - + -
79U PHE* 4.1 18.4 - - + -
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Residues in contact with SER 53 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U TYR 4.1 0.9 - - - -
34U TYR* 3.8 27.1 - - - -
35U TRP* 4.6 3.1 - - - -
51U TYR* 4.3 1.9 - - - -
52U ILE* 1.3 82.2 - - - +
54U ASN* 1.3 67.5 - - - +
55U VAL* 2.9 17.0 + - - +
56U GLY 3.3 8.8 + - - -
57U ASP* 2.7 46.2 + - - +
72U ARG* 3.2 12.0 + - - -
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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