Contacts of the strand formed by residues 18 - 23 (chain B) in PDB entry 2A6O
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 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A THR* 2.7 13.2 + - - +
5B VAL* 3.8 28.2 - - - +
16B SER* 3.7 20.6 - - - +
17B CYS* 1.3 73.3 - - - +
19B TYR* 1.3 66.6 + - - +
56B ILE* 4.2 27.2 - - + +
68B LEU* 4.9 3.1 - - + -
69B ALA 3.3 6.1 - - - +
70B ASP* 4.2 10.1 - - - +
115B THR* 3.6 4.7 - - - -
116B VAL* 3.1 53.5 + - + +
117B GLY* 5.5 2.7 - - - -
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Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A CYS* 4.5 4.5 - - - -
19A TYR* 2.4 46.6 + + - -
77A VAL* 4.8 1.4 - - - +
115A THR* 4.1 1.8 - - + -
17B CYS* 3.5 31.8 - - + +
18B LYS* 1.3 75.8 - - - +
20B HIS* 1.3 62.1 + - - +
21B ILE* 3.8 19.4 + - + +
67B ILE 3.5 1.4 - - - +
68B LEU* 3.3 10.0 - - - +
69B ALA* 2.6 44.4 + - - +
71B ILE* 4.4 17.7 - - + -
73B PRO* 5.3 5.0 - - - +
77B VAL* 3.3 33.8 - - + +
113B ILE* 3.8 16.4 - - + -
114B SER 3.5 5.6 - - - +
115B THR* 3.7 18.2 - - + -
116B VAL 4.9 0.2 - - - +
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Residues in contact with HIS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ALA* 4.9 2.9 - - + +
120A PRO* 3.7 30.8 - - + +
124A VAL* 5.7 0.2 - - + -
19B TYR* 1.3 71.7 - - - +
21B ILE* 1.3 62.0 + - - +
22B VAL* 5.7 0.7 - - + -
57B GLU* 5.8 1.6 - - - -
66B HIS* 3.0 32.0 + + + -
67B ILE 3.4 1.8 - - - -
68B LEU* 3.5 26.9 - - + +
112B PHE* 3.5 6.6 - - + +
113B ILE* 3.4 7.6 - - - +
114B SER* 2.9 42.6 + - - +
116B VAL* 3.6 36.1 - - + +
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 4.3 14.8 - - + +
20B HIS* 1.3 80.6 - - - +
22B VAL* 1.3 71.8 + - - +
23B TRP* 3.6 33.2 - - + -
65B ILE 3.6 0.9 - - - +
66B HIS* 3.5 1.3 - - - -
67B ILE* 2.7 46.3 + - + +
69B ALA* 4.6 8.1 - - + -
71B ILE* 4.6 4.0 - - + -
77B VAL* 4.2 12.8 - - + -
80B PHE* 4.1 22.7 - - + -
81B ILE* 3.8 33.9 - - + -
111B CYS* 5.5 0.9 - - + -
112B PHE 3.3 6.5 - - - +
113B ILE* 4.7 2.7 - - + -
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A VAL* 4.0 14.8 - - + -
127A TYR* 4.1 7.9 - - + -
128A ILE* 4.6 12.1 - - + -
20B HIS* 5.2 0.4 - - + -
21B ILE* 1.3 83.3 - - - +
23B TRP* 1.3 71.6 + - - +
64B HIS* 4.0 23.3 - - + -
65B ILE 3.4 11.7 - - - +
66B HIS* 3.8 31.2 - - + +
111B CYS* 3.3 3.3 - - - +
112B PHE* 2.6 54.2 + - + +
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Residues in contact with TRP 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TYR* 4.8 2.5 - - - -
21B ILE* 3.6 32.8 - - + -
22B VAL* 1.3 76.4 - - - +
24B CYS* 1.3 64.4 + - - +
25B PRO* 4.5 0.2 - - - +
44B ILE* 4.2 16.6 - - + -
64B HIS* 3.5 3.1 - - - +
65B ILE* 3.3 46.1 + - + +
67B ILE* 3.7 21.5 - - + -
80B PHE* 5.5 1.6 - + - -
81B ILE* 4.4 12.8 - - + -
84B ALA* 3.6 24.5 - - + -
85B LYS* 3.4 34.5 - - + -
107B TRP* 3.4 47.6 - + - -
110B SER 3.8 18.4 - - - +
111B CYS* 4.0 6.5 - - + +
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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