Contacts of the helix formed by residues 34 - 44 (chain D) in PDB entry 5W97
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 34 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D ASN 4.2 0.2 + - - -
33D LEU* 1.3 77.3 - - - +
35D ALA* 1.3 60.3 + - - +
36D SER* 3.5 10.9 + - - -
37D GLN* 2.9 41.2 + - - +
38D LYS* 3.0 27.2 + - - +
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Residues in contact with ALA 35 (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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34D SER* 1.3 74.1 - - - +
36D SER* 1.3 62.9 + - - +
38D LYS* 3.5 11.9 + - - +
39D ALA* 3.1 21.3 + - - +
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Residues in contact with SER 36 (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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34D SER* 3.3 10.3 + - - -
35D ALA* 1.3 77.9 - - - +
37D GLN* 1.3 58.6 + - - +
39D ALA* 3.1 9.0 + - - +
40D LEU* 2.9 28.5 + - - +
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Residues in contact with GLN 37 (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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30D VAL* 4.9 2.4 - - - +
32D ASN 3.7 7.3 + - - -
33D LEU* 3.4 23.5 - - + +
34D SER* 2.9 38.1 + - - +
36D SER* 1.3 75.7 - - - +
38D LYS* 1.3 60.3 + - - +
40D LEU* 3.3 9.0 + - - +
41D LYS* 2.9 34.3 + - - +
58D GLU* 3.9 23.4 - - - +
62D LEU* 3.7 27.5 - - + +
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Residues in contact with LYS 38 (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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33D LEU* 3.7 35.5 + - + +
34D SER 3.0 22.9 + - - +
35D ALA* 3.7 9.0 - - - +
37D GLN* 1.3 76.6 - - - +
39D ALA* 1.3 60.5 + - - +
41D LYS* 3.3 10.2 + - - +
42D GLU* 3.2 26.7 + - - +
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Residues in contact with ALA 39 (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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35D ALA 3.1 14.1 + - - +
36D SER* 3.1 11.2 + - - +
38D LYS* 1.3 75.9 - - - +
40D LEU* 1.3 57.8 + - - +
42D GLU* 3.3 9.6 + - - +
43D LYS* 3.1 27.5 + - - +
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Residues in contact with LEU 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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36D SER 2.9 12.7 + - - +
37D GLN* 3.5 9.6 - - - +
39D ALA* 1.3 74.3 - - - +
41D LYS* 1.3 64.4 + - - +
43D LYS* 3.4 8.6 + - + +
44D GLU* 3.0 21.8 + - - +
51D LEU* 4.2 8.7 - - + -
55D GLU* 3.6 44.2 - - + +
58D GLU* 3.5 44.2 - - + +
59D LEU* 3.7 24.6 - - + +
62D LEU* 4.4 7.0 - - + -
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Residues in contact with LYS 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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33D LEU* 3.4 26.7 - - + -
37D GLN 2.9 19.3 + - - +
38D LYS* 3.3 9.5 + - - +
40D LEU* 1.3 76.5 - - - +
42D GLU* 1.3 61.9 + - - +
44D GLU* 3.1 45.1 + - - +
45D LYS* 3.7 13.9 - - - +
59D LEU* 3.9 18.7 + - + +
62D LEU* 4.3 15.7 - - + +
63D LYS* 5.6 10.1 - - - +
60E ASP* 5.9 0.6 + - - -
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Residues in contact with GLU 42 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D LYS* 3.2 17.9 + - + +
39D ALA* 3.5 9.9 - - - +
40D LEU 3.2 0.2 - - - -
41D LYS* 1.3 74.2 - - - +
43D LYS* 1.3 60.7 + - - +
44D GLU 3.1 1.6 - - - -
45D LYS* 2.9 58.4 + - - +
46D ALA* 3.9 3.1 + - - +
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Residues in contact with LYS 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 ALA 3.1 11.1 + - - +
40D LEU* 3.6 12.1 - - + +
42D GLU* 1.3 78.7 - - - +
44D GLU* 1.3 60.0 + - - +
46D ALA* 3.3 24.5 + - + +
47D SER 4.6 2.9 - - - +
50D SER* 3.9 28.4 + - - +
51D LEU* 4.1 19.2 - - + +
55D GLU* 2.8 42.6 + - - +
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Residues in contact with GLU 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 LEU 3.0 13.4 + - - +
41D LYS* 3.1 43.0 + - - +
42D GLU 3.1 0.8 - - - -
43D LYS* 1.3 75.2 - - - +
45D LYS* 1.3 58.4 + - - +
46D ALA 3.3 0.4 - - - -
48D TRP* 2.9 25.8 + - + +
51D LEU* 4.7 3.8 - - - +
59D LEU* 3.8 26.7 - - + +
56E ARG* 2.8 21.7 + - - -
59E ASN* 3.0 24.2 - - - +
60E ASP* 3.5 3.9 - - - +
61E PHE* 2.7 31.0 + - + +
62E ALA* 4.0 4.2 + - - +
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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