Contacts of the strand formed by residues 34 - 41 (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 TYR 34 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33U TYR* 1.3 87.1 - - + +
35U TRP* 1.3 62.2 + - - +
36U ASN* 4.1 0.4 - - - +
51U TYR* 3.8 39.6 + + + -
52U ILE 4.0 1.8 - - - +
53U SER* 3.8 29.2 - - - -
54U ASN* 5.1 3.6 - - - -
98U ARG* 3.4 7.8 - - - +
99U SER* 2.8 43.5 + - - +
101U TYR* 3.9 23.9 - + + -
107U TYR* 3.2 43.4 + + - -
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Residues in contact with TRP 35 (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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2U VAL* 4.9 2.2 - - + -
4U LEU* 4.3 7.0 - - + -
24U VAL* 3.8 35.2 - - + -
27U TYR* 4.1 13.2 - + - -
28U SER 4.0 6.7 - - - -
29U ILE* 3.2 55.7 + - + +
33U TYR 3.6 14.8 + - - +
34U TYR* 1.3 74.0 - - - +
36U ASN* 1.3 63.0 + - - +
37U TRP* 5.5 0.2 - - - -
51U TYR* 3.1 3.3 - - - +
52U ILE* 2.9 52.3 + - + +
53U SER 4.6 0.4 - - - -
54U ASN 4.6 3.1 - - - -
70U ILE* 5.3 0.5 - - - +
79U PHE* 3.7 38.4 - + + -
97U ALA 3.9 2.7 - - - -
98U ARG* 3.4 50.7 - - + -
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Residues in contact with ASN 36 (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 3.7 1.4 + - - -
35U TRP* 1.3 76.4 - - - +
37U TRP* 1.3 62.5 + - - +
38U ILE* 4.5 2.2 - - + -
48U TRP* 3.6 10.1 + - + +
50U GLY 3.3 9.9 - - - +
51U TYR* 3.3 20.6 - - - +
79U PHE* 3.4 10.2 - - - -
96U CYS* 3.2 6.2 - - - -
97U ALA 2.8 41.5 + - - +
98U ARG 4.0 0.2 - - - -
99U SER* 3.2 29.1 - - - +
109U MET* 4.1 11.5 - - - -
96V TRP* 3.3 28.0 - - - -
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Residues in contact with TRP 37 (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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6U GLU* 3.2 26.5 - - - -
20U LEU* 3.8 42.8 - - + -
21U THR 4.2 2.7 - - - -
22U CYS* 3.5 33.0 - - + -
35U TRP 5.5 0.2 - - - -
36U ASN* 1.3 71.7 - - - +
38U ILE* 1.3 63.6 + - - +
48U TRP* 4.0 1.4 - - - -
49U VAL* 3.0 35.2 + - + +
50U GLY 3.0 11.5 + - - +
70U ILE* 3.8 28.5 - - + -
79U PHE* 3.7 17.0 - + - -
80U PHE 3.4 17.2 + - - -
81U LEU* 3.6 29.2 - - + -
94U TYR* 4.7 4.3 - + + -
95U TYR 3.1 28.9 - - - -
96U CYS* 3.4 11.2 - - + -
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Residues in contact with ILE 38 (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* 4.5 3.6 - - + -
37U TRP* 1.3 84.2 - - - +
39U ARG* 1.3 58.0 + - - +
46U LEU* 3.6 25.1 - - + -
47U GLU 3.2 15.7 - - - +
48U TRP* 4.2 8.1 - - + -
49U VAL* 3.8 4.9 - - - -
94U TYR* 3.5 2.6 - - - -
95U TYR* 2.5 49.8 + - + +
97U ALA 5.4 2.0 - - - +
109U MET* 4.3 22.2 - - + -
112U TRP* 3.3 36.6 - - + -
98V PHE* 3.5 24.9 - - + -
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Residues in contact with ARG 39 (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* 1.3 75.2 - - - +
40U LEU* 1.3 58.6 + - - +
41U PHE* 3.5 37.2 - - + -
45U LYS 3.9 1.0 - - - +
46U LEU* 3.5 7.6 - - - +
47U GLU* 2.9 66.5 + - + -
49U VAL* 3.6 18.6 - - - +
64U LEU* 3.6 22.4 - - - +
83U LEU* 3.7 12.0 - - - +
90U ASP* 2.9 31.3 + - - +
92U ALA* 4.3 2.7 - - + -
93U THR 3.3 6.7 - - - +
94U TYR* 3.0 48.6 + - + -
95U TYR* 5.3 0.2 - - - -
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Residues in contact with LEU 40 (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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39U ARG* 1.3 71.3 - - - +
41U PHE* 1.3 75.1 + - - +
42U PRO* 3.6 1.2 - - - +
44U ASN* 4.4 8.3 - - - +
45U LYS 4.0 9.0 - - - +
46U LEU* 3.6 30.1 - - + -
92U ALA* 3.2 3.2 - - - +
93U THR* 2.8 47.2 + - + +
95U TYR* 4.2 13.0 - - + +
38V GLN* 3.3 35.0 - - - +
44V ILE* 6.4 0.2 - - + -
87V PHE* 3.8 19.1 - - + -
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Residues in contact with PHE 41 (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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39U ARG* 3.5 41.0 - - + -
40U LEU* 1.3 78.9 - - - +
42U PRO* 1.3 65.6 - - + +
43U GLY* 3.0 6.3 - - - +
44U ASN* 2.9 24.4 + - - -
45U LYS* 3.2 47.6 + - + +
47U GLU* 3.2 22.9 - - + -
89U GLU* 3.3 30.1 - - + -
90U ASP* 4.6 0.7 - - - -
91U THR 4.3 1.6 - - - -
92U ALA* 3.2 21.3 - - + -
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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