Contacts of the strand formed by residues 34 - 40 (chain F) in PDB entry 4DHZ
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 TYR 34 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27F PRO* 3.4 4.9 - - - +
28F ASP* 2.7 56.5 + - + +
31F ASN* 3.3 24.9 + - + +
33F ARG* 1.3 79.5 - - - +
35F PHE* 1.3 61.7 + - - +
36F HIS* 3.4 18.4 - + - -
55F GLU* 2.6 35.2 + - + +
56F LEU 3.9 9.4 - - - -
57F PHE* 4.3 17.7 - + + -
70F ARG* 5.5 2.4 + - - -
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Residues in contact with PHE 35 (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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8F ILE* 5.5 0.9 - - + -
11F GLU 6.1 0.2 - - - -
12F THR* 3.8 22.7 - - + -
15F LEU* 4.4 23.8 - - + -
16F LEU* 5.4 0.7 - - + -
25F ALA* 5.0 2.5 - - + -
26F GLU* 3.9 7.4 - - - -
27F PRO* 3.7 32.1 - - + -
32F ALA 3.3 24.2 - - - -
33F ARG 3.7 8.3 - - - -
34F TYR* 1.3 79.8 - - - +
36F HIS* 1.3 63.5 + - - +
37F VAL* 3.8 7.8 + - + +
54F LEU 3.8 0.2 - - - +
55F GLU* 3.6 6.1 - - - +
56F LEU* 2.9 59.5 + - + +
58F LEU* 3.8 20.9 - - + -
101F ILE* 4.4 12.3 - - + -
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Residues in contact with HIS 36 (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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24F LYS* 4.1 4.7 - - - +
25F ALA* 3.6 1.6 - - - -
26F GLU* 3.0 34.2 + - + +
27F PRO 4.6 0.9 - - - -
28F ASP* 2.6 47.2 + - + +
34F TYR* 3.4 28.0 - + - -
35F PHE* 1.3 70.2 - - - +
37F VAL* 1.3 60.0 + - - +
38F VAL* 4.4 1.5 + - - -
54F LEU 3.8 3.4 - - - -
55F GLU* 3.2 24.5 + - - +
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Residues in contact with VAL 37 (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 ILE* 3.9 18.2 - - + -
24F LYS 3.3 14.4 - - - +
25F ALA* 4.0 13.7 - - + -
35F PHE* 4.0 18.2 - - + +
36F HIS* 1.3 80.1 - - - +
38F VAL* 1.3 62.2 + - - +
39F ILE* 4.1 15.5 - - + -
52F PHE 3.7 0.7 - - - +
53F LYS* 3.2 4.3 - - - +
54F LEU* 2.5 53.0 + - + +
56F LEU* 4.6 10.1 - - + -
101F ILE* 6.2 0.9 - - + -
105F LEU* 4.0 22.0 - - + -
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Residues in contact with VAL 38 (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 ILE* 3.5 3.1 - - - -
24F LYS* 2.9 61.7 + - + +
36F HIS 5.7 0.4 - - - -
37F VAL* 1.3 77.6 - - - +
39F ILE* 1.3 65.9 + - - +
40F ALA* 4.0 2.4 + - + +
51F THR* 3.5 33.0 - - - +
52F PHE 3.5 8.5 - - - +
53F LYS* 4.7 8.3 - - + +
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Residues in contact with ILE 39 (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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22F GLY 3.9 3.6 - - - +
23F ILE* 3.8 26.2 - - + -
37F VAL* 4.1 13.0 - - + -
38F VAL* 1.3 74.5 - - - +
40F ALA* 1.3 72.6 + - - +
42F PRO* 5.9 0.2 - - + -
52F PHE* 2.8 41.8 + - + +
54F LEU* 3.7 30.5 - - + -
71F PHE* 5.1 1.6 - - + -
105F LEU* 5.0 5.8 - - + +
108F ILE* 3.9 26.2 - - + -
109F GLN* 4.5 17.0 - - + +
112F LEU* 4.4 20.0 - - + -
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Residues in contact with ALA 40 (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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22F GLY* 3.1 24.7 + - - +
38F VAL* 4.0 3.9 + - + +
39F ILE* 1.3 78.2 - - - +
41F GLY* 1.3 68.7 + - - +
42F PRO* 3.4 5.4 - - - +
50F GLY 3.7 6.7 - - - +
51F THR* 4.2 13.5 - - + +
109F GLN* 5.3 2.8 - - - +
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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