Contacts of the strand formed by residues 16 - 22 (chain B) in PDB entry 2IO1
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 HIS 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B ASP* 1.3 97.4 + - - +
17B ILE* 1.3 59.9 + - - +
18B ASN* 4.5 2.8 - - - +
32B LYS* 3.8 42.0 + - + +
33B ILE* 3.6 14.0 + - - -
34B LYS* 2.9 42.3 + - + -
35B ARG* 5.4 2.0 - - - -
79B ASP* 4.5 3.5 - - - +
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Residues in contact with ILE 17 (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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16B HIS* 1.3 73.0 - - - +
18B ASN* 1.3 69.5 + - - +
19B LEU* 4.1 14.0 + - + -
31B PHE 3.8 0.2 - - - +
32B LYS* 3.3 5.0 - - - -
33B ILE* 2.8 61.8 + - + +
35B ARG* 4.2 26.0 - - + +
72B PRO* 4.4 9.9 - - + -
77B MET* 3.5 18.8 - - + +
78B GLU* 3.0 34.1 - - - +
79B ASP* 3.5 15.5 - - + +
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Residues in contact with ASN 18 (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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16B HIS 4.5 2.3 - - - +
17B ILE* 1.3 79.7 - - - +
19B LEU* 1.3 63.3 + - - +
30B GLN* 5.2 8.4 + - - +
31B PHE 3.2 6.9 + - - +
32B LYS* 3.0 42.3 - - - +
79B ASP* 2.7 19.4 + - - +
80B GLU* 2.8 57.3 + - - +
81B ASP 3.7 1.4 + - - -
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Residues in contact with LEU 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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17B ILE* 4.1 16.1 + - + -
18B ASN* 1.3 76.9 - - - +
20B LYS* 1.3 63.8 + - - +
21B VAL* 5.3 1.6 - - + -
29B VAL 3.8 0.9 - - - +
30B GLN* 3.7 3.1 - - - +
31B PHE* 2.9 33.9 + - + +
33B ILE* 3.2 35.9 - - + -
39B LEU* 3.9 14.8 - - + -
42B LEU* 4.0 11.7 - - + -
72B PRO* 4.4 2.7 - - + -
77B MET* 3.8 36.1 - - + -
81B ASP* 3.6 23.8 - - + +
83B ILE* 4.1 10.3 - - + -
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Residues in contact with LYS 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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19B LEU* 1.3 77.2 - - - +
21B VAL* 1.3 58.2 + - - +
22B ALA* 3.8 1.1 + - + -
28B VAL* 3.8 20.4 - - + -
29B VAL 3.4 4.9 - - - -
30B GLN* 3.4 31.6 - - - +
80B GLU* 3.8 38.7 + - + +
81B ASP 3.0 6.8 + - - +
82B THR* 3.3 17.7 + - - +
83B ILE* 2.7 33.1 + - - +
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Residues in contact with VAL 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 LEU 5.2 0.7 - - - +
20B LYS* 1.3 76.7 - - - +
22B ALA* 1.3 57.8 + - - +
23B GLY 4.0 0.5 + - - -
27B SER 3.7 1.0 - - - +
28B VAL* 3.3 4.8 + - - -
29B VAL 2.8 35.8 + - - +
31B PHE* 4.1 14.1 - - + -
42B LEU* 3.9 29.4 - - + -
46B TYR* 3.4 33.5 - - + -
59B PHE* 4.5 4.5 - - + -
83B ILE* 3.4 18.8 - - + +
85B VAL* 3.4 32.1 - - + -
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Residues in contact with ALA 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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445A LYS* 5.8 1.6 - - - +
20B LYS 3.8 0.6 + - - +
21B VAL* 1.3 73.1 - - - +
23B GLY* 1.3 65.0 + - - +
27B SER 3.3 9.6 - - - +
28B VAL* 4.4 12.8 - - + +
46B TYR* 4.5 0.7 - - - -
82B THR* 4.2 11.7 - - + +
83B ILE 2.9 9.8 + - - +
84B ASP* 3.6 18.7 - - - +
85B VAL* 3.0 24.0 + - - +
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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