Contacts of the strand formed by residues 15 - 22 (chain F) in PDB entry 3CHB
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 THR 15 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F CYS* 2.8 32.5 + - - -
12F TYR* 3.2 26.2 + - + +
13F HIS 3.1 0.4 - - - +
14F ASN* 1.3 79.7 + - - +
16F GLN* 1.3 63.7 + - - +
86F CYS* 4.0 9.0 - - - -
87F VAL 3.1 9.2 - - - +
88F TRP* 3.4 38.8 - - + +
89F ASN* 3.7 7.5 + - - +
97F ALA* 5.0 0.4 - - + -
109F UNX 3.4 8.8 - - - -
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Residues in contact with GLN 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F CYS* 3.8 6.3 - - - -
15F THR* 1.3 76.8 - - - +
17F ILE* 1.3 61.9 + - - +
18F HIS* 3.7 19.0 + - + -
85F LEU 3.8 0.2 - - - +
86F CYS* 3.5 1.6 - - - -
87F VAL* 2.8 39.1 + - + +
89F ASN* 3.5 22.7 - - + +
94F ARG* 3.0 36.0 + - - +
109F UNX 3.8 6.3 - - - -
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Residues in contact with ILE 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 3.9 37.9 - - + +
6F THR* 4.0 24.9 - - + +
9F CYS* 3.9 20.9 - - + -
16F GLN* 1.3 77.3 - - - +
18F HIS* 1.3 75.8 + - - +
19F THR* 3.9 12.4 + - - +
84F LYS* 4.1 16.2 - - + +
85F LEU 3.4 10.5 - - - +
86F CYS* 4.1 0.2 - - + -
109F UNX 4.4 0.8 - - - -
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Residues in contact with HIS 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F GLN* 3.7 10.9 + - + +
17F ILE* 1.3 79.0 - - - +
19F THR* 1.3 61.7 + - - +
20F LEU* 3.5 19.6 - - + +
48F PHE* 3.9 22.9 - + + -
84F LYS* 3.2 5.2 - - - +
85F LEU* 2.8 38.4 + - + +
87F VAL* 3.6 30.5 - - + +
94F ARG* 3.4 37.9 + - - -
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Residues in contact with THR 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F ILE* 3.9 6.3 + - - +
18F HIS* 1.3 75.6 - - - +
20F LEU* 1.3 64.8 + - - +
21F ASN* 3.6 26.2 - - - +
83F GLU* 3.7 7.4 - - + +
84F LYS* 3.6 32.1 + - + +
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F HIS* 3.5 28.5 - - + +
19F THR* 1.3 77.9 - - - +
21F ASN* 1.3 72.8 + - - +
22F ASP* 3.1 12.5 + - + +
42F PHE* 3.8 42.6 - - + -
44F ASN* 4.1 22.0 - - - +
46F ALA* 4.8 2.0 - - + -
48F PHE* 4.6 7.6 - - + -
82F VAL* 3.9 10.3 - - + +
83F GLU 2.9 6.7 + - - +
85F LEU* 4.0 31.4 - - + +
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Residues in contact with ASN 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F THR* 3.6 22.8 - - - +
20F LEU* 1.3 76.3 - - - +
22F ASP* 1.3 57.5 + - - +
81F LYS* 3.2 32.1 + - - -
82F VAL 2.9 14.8 + - - -
83F GLU* 3.1 29.4 + - - +
102F ALA 5.1 2.1 - - - +
103F ASN* 4.9 7.1 - - - +
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Residues in contact with ASP 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU* 3.2 10.9 - - + +
21F ASN* 1.3 79.8 - - - +
23F LYS* 1.3 88.7 + - - +
42F PHE* 3.6 12.2 - - + +
43F LYS* 3.4 46.2 + - - +
81F LYS* 3.6 6.7 - - - +
82F VAL* 2.9 31.0 + - - +
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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