Contacts of the strand formed by residues 32 - 39 (chain D) in PDB entry 6X34
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 GLN 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D ASN* 4.4 18.2 - - - +
26D ALA 4.6 3.1 - - - -
27D THR* 5.1 3.4 - - - +
28D VAL 4.9 1.3 - - - +
31D GLU* 1.3 78.2 - - - +
33D LEU* 1.3 58.2 + - - +
53D SER* 4.9 6.1 + - - -
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Residues in contact with LEU 33 (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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25D ASN* 3.2 3.2 + - - +
26D ALA* 2.8 49.7 + - + +
28D VAL* 4.3 15.0 - - + -
31D GLU 3.4 0.8 + - - +
32D GLN* 1.3 74.8 - - - +
34D LYS* 1.3 55.3 + - - +
35D LEU 4.1 0.8 + - - -
51D PRO* 6.0 5.8 - - + -
53D SER* 4.3 4.5 - - - -
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Residues in contact with LYS 34 (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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23D GLN* 3.4 24.0 - - + +
24D CYS 3.3 13.5 - - - +
25D ASN* 4.2 11.2 - - + +
32D GLN 4.3 0.4 - - - -
33D LEU* 1.3 73.6 - - - +
35D LEU* 1.3 60.0 + - - +
51D PRO* 3.7 4.2 - - - +
52D THR* 3.3 18.4 + - - +
53D SER* 3.2 23.6 + - - +
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Residues in contact with LEU 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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23D GLN* 3.4 22.6 - - - +
24D CYS* 3.2 16.3 + - + +
26D ALA* 5.4 4.6 - - + +
33D LEU 4.1 1.8 + - - -
34D LYS* 1.3 73.2 - - - +
36D CYS* 1.3 60.2 + - - +
49D LEU* 3.8 36.1 - - + -
50D GLU 3.2 13.2 - - - +
51D PRO* 3.7 7.6 - - + -
52D THR* 4.7 0.9 - - - -
182D LEU* 5.8 1.1 - - + -
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Residues in contact with CYS 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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21D VAL* 3.7 21.1 - - - -
22D LEU 3.2 24.2 - - - -
23D GLN* 5.0 4.0 - - + +
35D LEU* 1.3 76.6 - - - +
37D LEU* 1.3 72.4 + - - +
38D ALA* 6.1 0.2 - - + -
49D LEU* 3.3 3.4 - - - -
50D GLU* 2.5 51.6 + - + +
52D THR* 4.6 15.3 - - + -
65D CYS* 4.4 13.2 - - - -
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Residues in contact with LEU 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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22D LEU* 4.2 20.6 + - + +
23D GLN* 5.7 0.2 - - - +
36D CYS* 1.3 77.0 - - - +
38D ALA* 1.3 64.0 + - - +
39D ALA* 4.7 1.8 - - + +
47D CYS* 3.8 34.1 - - + -
48D PHE 3.5 9.6 - - - +
49D LEU* 4.5 3.3 - - + +
65D CYS* 3.4 19.8 - - - +
67D PHE* 3.9 31.3 - - + -
109D LEU* 6.3 2.9 - - + -
135D VAL* 5.0 5.6 - - + -
191D VAL* 4.3 30.3 - - + -
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Residues in contact with ALA 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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36D CYS* 3.6 5.6 + - + +
37D LEU* 1.3 78.0 - - - +
39D ALA* 1.3 60.9 + - - +
40D GLU 4.3 0.2 + - - -
47D CYS* 3.3 3.7 - - - +
48D PHE* 3.0 50.8 + - + +
50D GLU* 4.9 8.5 - - + -
61D ASP 5.6 0.4 - - - +
64D ILE* 4.5 21.8 - - + -
65D CYS* 4.1 18.2 - - + +
67D PHE* 5.0 0.7 - - - -
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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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37D LEU* 4.7 3.3 - - + +
38D ALA* 1.3 73.8 - - - +
40D GLU* 1.3 65.0 + - - +
41D GLY 4.4 4.7 - - - +
44D ASN 5.4 0.4 - - - +
45D ARG 5.2 3.4 - - - +
46D LEU 4.6 2.9 - - - +
47D CYS* 3.7 21.3 - - + +
48D PHE* 5.7 0.7 - - - -
64D ILE* 4.1 13.0 + - - +
67D PHE* 5.1 7.1 - - + -
111D HIS* 3.1 30.0 + - + +
137D LEU* 4.9 16.4 - - + +
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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