Contacts of the helix formed by residues 39 - 45 (chain D) in PDB entry 3OX4
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 ASP 39 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D SER* 1.3 83.0 + - - +
40D ALA* 1.3 63.3 + - - +
41D PHE* 3.0 8.0 + - + +
42D MET* 3.5 18.4 - - - +
43D ASN* 3.4 13.5 + - - +
66D ASP* 3.4 9.9 - - - +
67D GLY 3.3 4.3 - - - +
68D VAL 2.9 26.1 - - - +
69D MET* 5.1 0.5 - - - -
70D PRO* 5.8 0.2 - - - +
96D GLY* 4.0 6.1 - - - -
97D GLY 4.3 1.6 + - - -
99D SER* 4.9 1.6 - - - -
100D PRO* 3.4 26.2 - - - +
1385D NAD 3.1 41.6 + - - +
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASP* 1.3 74.8 - - - +
41D PHE* 1.3 58.7 + - - +
43D ASN* 3.8 2.3 - - - +
44D LYS* 3.1 33.6 + - + +
66D ASP* 4.2 8.5 - - - +
67D GLY* 3.1 30.9 + - - +
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Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASP* 3.6 0.6 - - + +
40D ALA* 1.3 76.0 - - - +
42D MET* 1.3 70.2 + - - +
43D ASN 2.9 4.5 + - - -
44D LYS* 2.9 33.5 + - - +
45D SER* 2.7 57.3 + - - -
47D VAL* 5.9 0.2 - - + -
182D GLY* 5.4 1.8 - - - -
184D PRO* 6.1 1.8 - - + -
1385D NAD 3.3 66.9 - + - +
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Residues in contact with MET 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D SER* 2.9 28.3 - - - +
39D ASP* 3.5 20.7 + - - +
41D PHE* 1.3 96.8 - - + +
43D ASN* 1.3 56.4 + - - +
45D SER* 3.3 5.1 + - - -
47D VAL* 3.0 65.8 + - + -
48D VAL* 3.0 9.7 + - + -
95D LEU* 4.0 10.8 - - + +
96D GLY* 4.2 1.1 - - - -
138D THR* 3.3 39.0 - - + -
179D LEU* 5.3 2.2 - - + +
1385D NAD 4.4 11.0 - - - +
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Residues in contact with ASN 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASP 3.4 11.7 + - - +
40D ALA 3.8 4.5 - - - +
41D PHE 2.9 0.8 - - - -
42D MET* 1.3 80.2 - - - +
44D LYS* 1.3 62.4 + - - +
46D GLY* 3.4 11.3 + - - -
48D VAL* 3.4 30.5 - - + +
49D LYS* 5.0 4.9 + - - +
64D VAL* 4.5 5.3 - - - +
66D ASP* 2.6 33.5 - - + +
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Residues in contact with LYS 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ALA* 3.1 15.0 + - + +
41D PHE* 2.9 57.3 + - + +
43D ASN* 1.3 74.7 - - - +
45D SER* 1.3 61.7 + - - +
46D GLY* 3.0 6.6 + - - -
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PHE* 2.7 46.7 + - - -
42D MET* 3.3 6.6 + - - -
44D LYS* 1.3 74.3 - - - +
46D GLY* 1.3 57.2 + - - +
47D VAL* 3.3 25.2 - - - +
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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