Contacts of the strand formed by residues 24 - 29 (chain F) in PDB entry 5DNF
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 24 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19F LEU* 3.6 38.6 - - + -
20F PRO 3.9 7.6 - - - +
21F ARG* 3.1 34.0 + - - +
22F ALA 4.7 2.3 - - - +
23F HIS* 1.3 81.1 + - + +
25F LYS* 1.3 61.6 + - - +
26F GLU 3.7 12.8 - - - +
41F PHE* 3.6 35.7 - - + -
42F VAL 3.8 2.2 - - - +
43F THR* 4.6 7.0 - - + -
44F ARG* 5.0 0.7 - - - +
61F TYR* 4.1 20.4 - - + -
65F LEU* 3.9 16.7 - - + +
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Residues in contact with LYS 25 (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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23F HIS 3.6 0.4 + - - -
24F ILE* 1.3 75.3 - - - +
26F GLU* 1.3 72.9 + - + +
42F VAL* 2.9 25.2 + - - +
43F THR 3.6 12.5 + - - +
44F ARG* 3.9 26.7 + - + +
46F ASN* 2.6 31.6 + - - +
65F LEU* 4.6 9.9 - - - +
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Residues in contact with GLU 26 (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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4C SER 4.1 2.9 + - - -
101C GLA 3.6 23.0 + - - -
47D ARG* 2.8 36.2 + - - +
24F ILE* 3.7 5.8 - - - +
25F LYS* 1.3 91.8 - - + +
27F TYR* 1.3 64.2 + - - +
28F PHE* 5.3 0.4 - - - -
41F PHE* 3.4 3.6 - - - -
42F VAL* 2.6 52.4 + - + +
65F LEU* 4.1 8.5 - - - -
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Residues in contact with TYR 27 (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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23D HIS* 4.4 1.4 + - - -
43D THR* 4.2 4.0 - - - +
45D LYS* 5.4 2.2 - - + -
47D ARG* 2.8 52.7 + - + +
26F GLU* 1.3 75.6 - - - +
28F PHE* 1.3 81.5 + - - +
29F TYR* 3.6 35.1 + + - -
39F VAL* 4.3 2.5 - - + -
40F VAL 3.1 12.3 - - - +
41F PHE* 3.8 13.9 - - + -
42F VAL 4.6 0.2 - - - +
62F ILE* 3.6 35.1 - - + +
65F LEU* 3.7 29.8 - - + +
66F GLU* 2.7 42.7 + - + +
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Residues in contact with PHE 28 (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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4C SER* 3.7 31.4 - - - +
101C GLA 3.6 42.8 - - - -
47D ARG* 4.3 4.7 - - + +
9F PRO* 4.5 15.0 - - + -
26F GLU* 5.3 0.2 - - - -
27F TYR* 1.3 92.4 - - - +
29F TYR* 1.3 78.0 + - - +
30F THR* 4.6 4.3 - - - -
39F VAL* 3.7 3.3 - - - +
40F VAL* 2.9 74.5 + - + -
42F VAL* 4.0 13.9 - - + -
48F GLN* 4.1 11.7 - - - -
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Residues in contact with TYR 29 (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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4C SER 5.6 2.1 + - - +
5C SER 6.0 1.2 - - - -
6C ASP* 5.4 5.2 + - - +
15D ILE* 4.1 22.0 - - + -
17D ARG* 4.2 17.6 + - + -
19D LEU* 4.4 17.0 - - + -
20D PRO* 3.7 23.6 - - - +
23D HIS* 4.9 0.3 + - - -
43D THR* 5.4 0.4 - - + -
47D ARG* 5.1 6.2 - - + +
49D VAL* 3.8 28.5 - - + -
27F TYR* 3.6 26.9 + + - -
28F PHE* 1.3 87.6 - - - +
30F THR* 1.3 69.5 + - - +
31F SER 3.7 0.9 + - - -
38F ALA 3.7 6.1 - - - +
39F VAL* 3.9 27.6 - - + -
53F PRO* 6.1 0.9 - - + -
62F ILE* 3.9 21.3 - - + +
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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