Contacts of the strand formed by residues 20 - 26 (chain U) in PDB entry 5OA3
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 ILE 20 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17U ILE* 4.7 4.5 - - + -
18U HIS 4.2 5.4 - - - +
19U ARG* 1.3 74.2 - - - +
21U ARG* 1.3 67.8 + - - +
22U ILE* 4.2 1.6 + - + -
90U ASP* 3.8 1.9 - - - +
91U LEU* 2.9 41.1 + - + +
93U SER* 3.5 25.4 - - - +
94U PRO 3.8 6.1 - - - +
95U SER* 3.8 17.3 - - - +
98U VAL* 3.8 42.2 - - + -
114U VAL* 4.8 3.4 - - + -
115U THR 3.9 3.1 - - - +
116U ILE* 3.7 36.6 - - + +
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Residues in contact with ARG 21 (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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14032 C 3.3 13.7 + - - -
14042 U 2.5 59.5 + - - -
15812 C 5.2 1.0 + - - -
19U ARG* 4.0 6.0 + - + +
20U ILE* 1.3 74.4 - - - +
22U ILE* 1.3 65.1 + - - +
23U THR* 5.4 2.9 - - - +
88U LEU* 5.2 11.2 - - + +
89U ILE 4.0 1.3 - - - -
90U ASP* 3.2 33.0 + - + +
114U VAL* 3.8 3.6 - - - +
115U THR* 2.7 60.7 + - - +
116U ILE* 4.5 0.4 - - - +
117U ALA 6.1 0.4 - - - +
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Residues in contact with ILE 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U ILE* 5.1 2.0 - - + -
21U ARG* 1.3 79.1 - - - +
23U THR* 1.3 64.2 + - - +
24U LEU* 4.1 6.4 + - + -
39U LEU* 4.4 22.0 - - + -
88U LEU* 3.5 4.0 - - - +
89U ILE* 2.9 57.9 + - + +
91U LEU* 3.9 29.4 - - + -
98U VAL* 4.1 12.6 - - + -
102U THR* 4.0 18.6 - - - +
112U VAL* 4.0 25.1 - - + -
113U GLU 3.8 3.4 - - - +
114U VAL* 5.3 6.3 - - + -
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Residues in contact with THR 23 (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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14042 U 5.2 1.2 + - - -
7D LYS* 5.7 0.4 - - - -
21U ARG* 4.2 3.2 + - - +
22U ILE* 1.3 70.7 + - - +
24U LEU* 1.3 66.5 + - - +
25U THR* 4.1 7.4 + - + -
86U LYS* 4.0 20.4 - - + -
87U ARG 3.7 4.3 - - - +
88U LEU* 3.3 27.4 - - + +
111U GLU 4.1 0.2 - - - +
112U VAL* 3.7 1.7 - - - -
113U GLU* 2.9 63.3 + - - +
115U THR* 4.5 10.9 + - - +
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Residues in contact with LEU 24 (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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22U ILE* 4.1 10.5 + - + +
23U THR* 1.3 74.5 - - - +
25U THR* 1.3 62.5 + - - +
32U LEU* 3.7 29.1 - - + +
35U VAL* 4.5 12.6 - - + -
36U CYS* 4.2 23.1 - - - +
39U LEU* 4.5 19.5 - - + -
85U HIS 3.8 1.1 - - - +
86U LYS* 3.4 3.8 - - - +
87U ARG* 2.9 44.5 + - + +
88U LEU 6.5 0.2 - - - -
89U ILE* 5.2 4.7 - - + -
110U VAL* 4.1 9.9 - - + -
111U GLU 3.8 0.7 - - - -
112U VAL* 3.6 42.0 - - + -
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Residues in contact with THR 25 (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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7D LYS* 3.4 44.3 + - + +
11D PHE* 3.8 18.4 - - - -
23U THR* 4.1 8.8 + - + +
24U LEU* 1.3 77.5 - - - +
26U SER* 1.3 61.8 + - - +
84U ILE* 5.1 3.4 - - + -
85U HIS 3.5 4.3 - - - +
86U LYS* 4.1 21.3 - - + -
110U VAL* 3.9 1.0 - - - +
111U GLU* 2.9 47.2 + - - +
113U GLU* 6.1 0.6 - - + +
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Residues in contact with SER 26 (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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11D PHE* 3.8 12.1 - - - -
25U THR* 1.3 76.0 - - - +
27U ARG* 1.3 62.1 + - - +
28U ASN* 4.2 5.8 - - - -
32U LEU* 3.1 42.3 - - - +
84U ILE* 3.8 2.1 - - - -
85U HIS* 2.9 33.4 + - - +
109U GLY 3.9 8.1 - - - -
110U VAL* 3.8 24.9 - - - -
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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