Contacts of the helix formed by residues 20 - 25 (chain B) in PDB entry 3F5O
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 ASN 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A GLU* 3.3 24.3 + - + +
47A GLU 3.8 0.2 - - - -
49A THR* 3.2 17.9 + - - +
50A ASN 3.3 19.0 + - - -
18B ALA* 3.4 7.2 - - - +
19B ARG* 1.3 81.9 - - - +
21B PHE* 1.3 63.0 + - - +
22B GLU* 3.0 24.2 + - - +
23B ARG* 2.9 26.2 + - - +
1001B P6G 2.8 41.1 + - - -
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Residues in contact with PHE 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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21A PHE* 3.8 22.7 - + - -
24A VAL* 3.8 25.1 - - + -
47A GLU 3.4 20.5 + - - +
48A HIS* 4.0 2.7 - + - -
49A THR 2.8 20.2 + - - +
56A HIS* 3.6 34.9 - + + -
58A GLY 4.5 0.2 - - - -
59A LEU* 3.6 41.7 - - + -
62A THR* 4.7 0.2 - - - -
20B ASN* 1.3 67.9 - - - +
22B GLU* 1.3 57.4 + - - +
23B ARG* 2.9 16.0 + - - +
24B VAL* 3.1 39.3 + - + +
62B THR* 3.6 22.4 - - + -
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Residues in contact with GLU 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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50A ASN* 3.4 11.6 - - - +
51A ALA* 3.2 23.7 + - - +
56A HIS* 3.0 27.7 + - - -
15B MET* 3.4 34.9 - - + +
18B ALA* 4.5 0.4 - - + -
20B ASN* 3.0 23.9 + - - +
21B PHE* 1.3 76.6 - - - +
23B ARG* 1.3 48.9 + - - +
24B VAL* 3.2 1.0 + - - -
25B LEU* 2.7 28.0 + - - +
66B ASN* 3.1 19.7 + - - +
149B UOC 5.0 3.8 - - - +
1001B P6G 3.8 31.6 - - - +
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Residues in contact with ARG 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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23A ARG* 5.1 11.4 - - - +
24A VAL* 4.3 23.6 - - - +
47A GLU* 2.8 50.6 + - - -
15B MET 3.2 13.4 + - - +
16B THR 4.5 6.8 - - - +
18B ALA* 3.3 24.5 - - - +
19B ARG* 3.5 13.8 + - - +
20B ASN 2.9 29.1 + - - +
21B PHE* 2.9 6.3 + - - +
22B GLU* 1.3 74.6 - - - +
24B VAL* 1.3 73.5 + - + +
25B LEU 3.1 14.8 + - - -
26B GLY* 3.2 6.8 + - - -
47B GLU* 4.9 3.5 - - - +
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Residues in contact with VAL 24 (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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21A PHE* 3.8 11.9 - - + -
23A ARG* 4.3 12.3 + - - +
24A VAL* 4.1 16.6 - - + -
21B PHE* 3.1 46.9 + - + +
23B ARG* 1.3 92.4 - - + +
25B LEU* 1.3 59.5 + - + +
26B GLY 3.7 0.8 + - - -
47B GLU* 4.1 6.5 - - - +
48B HIS* 3.8 24.6 + - - -
59B LEU* 3.9 12.7 - - + +
62B THR* 3.8 27.4 - - + -
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Residues in contact with LEU 25 (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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15B MET* 3.8 21.5 - - + +
16B THR 4.1 0.2 + - - -
22B GLU 2.7 23.0 + - - +
23B ARG* 3.2 3.9 - - - +
24B VAL* 1.3 73.4 - - + +
26B GLY* 1.3 60.5 + - - +
27B LYS 4.2 2.9 - - - +
28B ILE* 4.2 20.2 - - + -
42B MET* 5.3 1.3 - - - -
48B HIS* 5.3 2.5 - - - -
59B LEU* 3.7 27.1 - - + -
62B THR* 4.1 13.5 - - + +
63B LEU* 3.7 32.8 - - + -
66B ASN* 3.4 43.1 - - + +
67B ILE* 4.4 9.6 - - + -
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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