Contacts of the strand formed by residues 92 - 102 (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 ALA 92 (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* 4.3 5.4 - - + -
40U LEU 3.2 19.7 - - - +
41U PHE* 3.2 34.8 - - + -
42U PRO* 4.2 4.7 - - - -
90U ASP 2.8 6.9 + - - +
91U THR* 1.3 73.9 - - - +
93U THR* 1.3 63.0 + - - +
94U TYR* 3.0 20.3 - - - -
117U THR* 5.1 1.6 - - - -
118U VAL 3.4 15.5 + - - +
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Residues in contact with THR 93 (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* 3.3 1.2 - - - -
40U LEU* 2.8 56.2 + - + +
92U ALA* 1.3 73.9 - - - +
94U TYR* 1.3 62.3 + - - +
95U TYR* 4.0 15.2 + - - -
115U GLY 5.0 3.8 - - - -
116U THR 3.2 12.6 - - - -
117U THR* 3.4 34.3 - - + +
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Residues in contact with TYR 94 (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 6.5 - - - +
18U LEU* 3.9 7.6 - - + +
20U LEU* 3.6 22.9 - - + -
37U TRP* 4.7 5.8 - + + -
38U ILE 3.5 3.6 - - - -
39U ARG* 3.0 49.9 + - + -
49U VAL* 4.6 9.2 - - + -
81U LEU* 3.8 24.5 - - + -
83U LEU* 3.8 8.2 - - + +
90U ASP* 2.8 25.2 + - - +
92U ALA 3.0 30.5 - - - -
93U THR* 1.3 73.0 - - - +
95U TYR* 1.3 61.5 + - - +
115U GLY* 3.2 2.8 - - - -
116U THR 2.6 40.1 + - - +
118U VAL* 3.3 28.7 - - + -
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Residues in contact with TYR 95 (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* 3.6 1.6 - - - -
37U TRP* 3.1 10.3 - - - -
38U ILE* 2.5 52.3 + - + +
40U LEU* 4.2 19.7 - - + +
46U LEU* 4.7 1.1 - - + -
93U THR* 4.0 20.2 + - - -
94U TYR* 1.3 73.9 - - - +
96U CYS* 1.3 59.7 + - - +
112U TRP* 3.8 29.6 - + + -
113U GLY 3.9 9.2 - - - -
114U GLN 3.4 10.1 - - - -
115U GLY* 3.2 31.4 - - - -
38V GLN* 3.7 15.7 + - - +
42V GLY* 2.7 28.1 + - - -
44V ILE* 3.9 23.0 - - + +
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Residues in contact with CYS 96 (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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4U LEU* 3.7 8.5 - - - +
6U GLU* 3.4 25.4 + - - -
22U CYS* 2.0 49.8 - - + -
36U ASN 3.2 11.4 - - - +
37U TRP* 3.4 20.0 - - + -
79U PHE* 3.8 2.5 - - + -
95U TYR* 1.3 74.3 - - - +
97U ALA* 1.3 61.4 + - - +
112U TRP* 4.5 0.3 - - - +
113U GLY* 2.9 25.6 + - - -
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Residues in contact with ALA 97 (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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4U LEU* 3.9 5.4 - - - -
35U TRP* 3.8 2.0 - - - -
36U ASN* 2.8 37.9 + - + +
38U ILE* 5.4 1.2 - - + +
79U PHE* 4.8 0.8 - - - -
96U CYS* 1.3 74.6 - - - +
98U ARG* 1.3 60.9 + - - +
109U MET* 4.1 15.3 - - + -
111U TYR 3.0 14.1 - - - +
112U TRP* 3.5 37.5 - - + -
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Residues in contact with ARG 98 (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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130P ASN* 3.0 26.0 + - - -
2U VAL* 4.8 1.5 - - - +
4U LEU* 4.1 0.8 - - - +
27U TYR* 3.3 24.8 - - - -
33U TYR* 3.5 21.7 - - + -
34U TYR 3.4 14.8 - - - +
35U TRP* 3.4 46.0 - - + -
97U ALA* 1.3 71.0 - - - +
99U SER* 1.3 64.3 + - - +
100U GLU* 2.9 18.0 + - - +
109U MET* 3.2 1.9 - - - -
110U ASP* 2.7 64.8 + - - +
111U TYR* 3.0 35.6 + - + +
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Residues in contact with SER 99 (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* 3.1 21.1 - - - +
34U TYR* 2.8 22.7 + - - +
36U ASN* 3.2 24.0 - - - +
98U ARG* 1.3 74.7 - - - +
100U GLU* 1.3 61.1 + - - +
107U TYR* 3.7 24.6 - - - -
108U ALA 3.2 9.9 - - - -
109U MET* 3.7 15.0 - - - +
96V TRP* 3.8 7.1 - - - -
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Residues in contact with GLU 100 (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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130P ASN* 2.8 37.0 + - - +
33U TYR* 4.1 14.8 - - + -
34U TYR* 5.2 0.2 - - - -
98U ARG* 2.9 21.6 + - - +
99U SER* 1.3 76.6 - - - +
101U TYR* 1.3 61.9 + - - +
102U TYR* 4.0 20.9 - - + -
106U GLY 3.5 2.0 - - - +
107U TYR* 2.8 27.5 - - - +
108U ALA* 2.7 21.1 + - + +
110U ASP* 2.9 29.1 - - - +
49V TYR* 6.0 2.9 - - - -
55V HIS* 5.6 2.6 + - - -
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Residues in contact with TYR 101 (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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144P ALA* 3.3 25.6 - - - +
33U TYR* 4.1 9.3 - - + +
34U TYR* 3.9 29.4 - - + -
100U GLU* 1.3 77.5 - - - +
102U TYR* 1.3 82.0 + - - +
103U SER* 3.7 26.1 + - - -
106U GLY* 3.6 24.2 - - - -
107U TYR* 3.9 29.6 - + + -
32V PHE* 5.7 1.3 - + - -
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Residues in contact with TYR 102 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P ILE* 4.2 2.4 - - + +
130P ASN* 2.8 33.4 + - + +
143P ASP* 2.9 17.0 + - - +
144P ALA* 3.6 30.5 - - + -
147P VAL* 3.5 34.5 - - + -
148P LYS 3.9 4.0 - - - +
150P PRO* 3.6 34.8 - - + -
33U TYR* 5.2 2.9 - + - -
100U GLU* 4.0 25.1 - - + -
101U TYR* 1.3 79.2 - - - +
103U SER* 1.3 62.4 + - - +
104U VAL 2.9 1.8 + - - -
105U THR* 3.1 18.1 + - - +
106U GLY 2.7 35.0 + - - -
49V TYR* 5.5 3.6 - + - -
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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