Contacts of the helix formed by residues 38 - 44 (chain B) in PDB entry 4F0Z
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 SER 38 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B SER 3.8 1.0 + - - -
37B LEU* 1.3 75.8 - - - +
39B VAL* 1.3 63.6 + - - +
40B GLU* 3.4 17.7 + - - +
41B GLU* 3.0 42.9 + - - +
42B PHE* 3.2 15.4 + - - -
58B ILE* 5.8 0.2 - - - -
68B GLU* 4.0 26.4 + - - +
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Residues in contact with VAL 39 (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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38B SER* 1.3 72.3 - - - +
40B GLU* 1.3 74.1 + - - +
42B PHE* 3.2 4.5 + - - +
43B MET* 3.0 46.0 + - + +
55B GLN* 3.6 37.9 - - - +
58B ILE* 4.1 27.5 - - + +
67B GLY 4.4 11.2 + - - +
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Residues in contact with GLU 40 (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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31B LEU* 5.9 0.2 - - - -
38B SER* 3.1 18.3 + - - +
39B VAL* 1.3 85.0 + - - +
41B GLU* 1.3 62.5 + - + +
43B MET* 3.2 10.0 + - - +
44B SER* 3.0 26.7 + - - -
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Residues in contact with GLU 41 (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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29B LEU* 3.5 26.6 - - - +
30B ASP* 3.8 0.7 - - - +
31B LEU* 3.1 35.6 + - + +
32B ASP* 3.1 14.0 + - - +
36B SER 3.0 4.2 - - - +
37B LEU* 3.2 8.5 - - + +
38B SER* 3.0 37.9 + - - +
40B GLU* 1.3 76.1 - - + +
42B PHE* 1.3 65.6 + - - +
44B SER* 3.3 19.5 + - - -
45B LEU* 4.3 5.4 + - - +
202B CA 2.5 31.2 - - - -
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Residues in contact with PHE 42 (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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364A MET* 4.1 13.9 - - + -
365A LEU* 6.3 0.2 - - + -
368A VAL* 4.0 36.6 - - + -
29B LEU* 5.3 4.5 - - + -
37B LEU* 3.6 40.8 - - + -
38B SER 3.2 22.0 + - - -
39B VAL 3.2 7.2 + - - +
41B GLU* 1.3 74.9 - - - +
43B MET* 1.3 62.9 + - - +
45B LEU* 3.1 27.5 + - + +
48B LEU* 3.5 20.6 - - + +
54B VAL* 4.6 3.4 - - + -
58B ILE* 3.7 34.1 - - + -
61B PHE* 5.3 6.7 - + - -
69B VAL* 4.1 18.4 - - + -
74B PHE* 4.7 7.2 - + - -
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Residues in contact with MET 43 (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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39B VAL* 3.0 37.1 + - + +
40B GLU* 3.6 9.4 - - + +
41B GLU 3.2 0.8 - - - -
42B PHE* 1.3 72.2 - - - +
44B SER* 1.3 60.0 + - - +
45B LEU 3.0 11.3 + - - +
48B LEU* 4.4 16.6 - - - +
49B GLN* 3.5 26.1 - - - +
51B ASN 5.6 1.3 - - - +
54B VAL* 3.7 34.8 - - + -
55B GLN* 5.1 6.3 - - + +
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Residues in contact with SER 44 (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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31B LEU* 3.8 24.4 - - - +
40B GLU 3.0 14.3 + - - -
41B GLU 3.5 10.5 - - - -
42B PHE 3.1 1.2 - - - -
43B MET* 1.3 77.6 - - - +
45B LEU* 1.3 63.2 + - - +
46B PRO* 3.4 9.5 - - - +
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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