Contacts of the helix formed by residues 34 - 50 (chain D) in PDB entry 6F0X
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 LYS 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 THR 5.0 2.0 - - - +
33D ALA* 1.3 78.0 - - - +
35D LYS* 1.3 66.7 + - - +
36D GLU* 3.5 10.0 + - - +
37D ASP* 3.7 20.0 + - - +
38D ILE* 3.2 16.0 + - - +
219P ARG* 3.7 31.9 - - + +
230P LEU* 4.6 15.0 - - + -
258P GLU 3.9 6.9 + - - -
259P ASP* 3.1 30.1 + - - +
260P TYR 4.7 0.2 + - - -
261P ILE* 3.6 25.8 - - + +
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Residues in contact with LYS 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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27D GLN* 4.9 3.8 - - - +
34D LYS* 1.3 75.9 - - - +
36D GLU* 1.3 71.2 + - + +
38D ILE* 2.6 32.9 + - - +
39D ASN 2.9 9.5 + - - -
99D ILE* 3.6 42.9 - - + +
205D ARG* 6.2 0.6 - - - +
230P LEU* 5.3 13.9 + - + -
231P ASN* 4.4 18.0 + - - +
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Residues in contact with GLU 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 LYS* 4.2 8.3 - - - +
35D LYS* 1.3 94.2 + - + +
37D ASP* 1.3 65.1 + - - +
39D ASN* 3.2 13.5 + - - +
40D LEU* 2.9 31.1 + - + +
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Residues in contact with ASP 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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33D ALA* 5.5 2.9 - - + +
34D LYS* 3.7 19.1 + - - +
35D LYS 3.2 0.4 - - - -
36D GLU* 1.3 79.2 - - - +
38D ILE* 1.3 58.3 + - - +
40D LEU* 3.3 16.8 + - - +
41D SER* 2.9 33.2 + - - -
65D PHE* 3.8 22.7 - - + -
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Residues in contact with ILE 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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25D VAL* 4.3 16.4 - - + -
26D HIS 6.0 0.2 - - - +
27D GLN* 3.5 45.8 - - + +
31D SER* 4.6 3.4 - - - +
33D ALA* 3.7 8.1 - - + +
34D LYS 3.2 23.3 - - - +
35D LYS* 2.6 16.2 + - - +
37D ASP* 1.3 71.0 - - + +
39D ASN* 1.3 63.3 + - - +
41D SER* 3.2 5.9 + - - +
42D VAL* 2.9 43.2 + - + +
65D PHE* 4.6 9.0 - - + -
66D LEU* 4.5 9.2 - - + -
69D ASN* 5.1 5.4 - - + -
70D VAL* 4.8 8.5 - - + -
99D ILE* 4.3 6.3 - - + -
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Residues in contact with ASN 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 LYS 2.9 8.5 + - - +
36D GLU* 3.2 19.0 + - - +
38D ILE* 1.3 76.2 - - - +
40D LEU* 1.3 66.5 + - - +
43D ARG* 2.9 53.8 + - - +
97D LEU* 3.1 20.4 - - + +
99D ILE* 4.1 11.7 - - + +
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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 GLU* 2.9 22.4 + - + +
37D ASP* 3.3 19.3 + - - +
39D ASN* 1.3 79.8 - - - +
41D SER* 1.3 59.8 + - - +
43D ARG* 3.3 7.4 + - - +
44D LYS* 2.9 52.4 + - - +
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Residues in contact with SER 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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37D ASP 2.9 17.9 + - - -
38D ILE 3.8 1.1 - - - -
40D LEU* 1.3 77.8 - - - +
42D VAL* 1.3 56.5 + - - +
44D LYS* 3.2 12.3 + - - +
45D LEU 2.9 22.9 + - - -
63D GLU* 4.4 11.2 + - - +
65D PHE* 3.2 18.7 - - - -
66D LEU* 3.5 40.4 - - - +
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Residues in contact with VAL 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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23D VAL* 4.8 5.2 - - + -
25D VAL* 4.4 18.2 - - + -
38D ILE* 2.9 34.8 + - + +
39D ASN* 3.9 2.5 - - - +
41D SER* 1.3 75.7 - - - +
43D ARG* 1.3 66.7 + - - +
45D LEU* 3.1 13.5 + - + +
46D LEU* 2.9 27.5 + - + +
66D LEU* 4.3 12.6 - - + -
70D VAL* 5.2 4.3 - - + -
73D VAL* 5.0 19.7 - - + -
97D LEU* 3.9 27.4 - - + -
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Residues in contact with ARG 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 ASN* 2.9 45.1 + - - +
40D LEU* 3.8 7.2 - - - +
42D VAL* 1.3 75.6 - - - +
44D LYS* 1.3 58.3 + - + +
46D LEU* 3.2 17.0 + - + +
47D ASN* 2.9 34.2 + - - +
95D VAL* 3.3 34.8 + - - +
96D ALA* 4.7 2.0 - - - +
97D LEU* 3.8 22.9 - - + +
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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 LEU* 2.9 42.0 + - - +
41D SER* 3.5 10.5 - - - +
42D VAL 3.1 0.2 - - - -
43D ARG* 1.3 76.4 - - + +
45D LEU* 1.3 64.4 + - - +
47D ASN* 3.2 18.9 + - + +
48D ARG* 2.9 22.4 + - - +
63D GLU* 5.9 3.8 - - - +
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Residues in contact with LEU 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 SER 2.9 13.2 + - - +
42D VAL* 3.2 17.0 - - + +
44D LYS* 1.3 75.7 - - - +
46D LEU* 1.3 69.4 + - + +
48D ARG* 3.1 22.3 + - - +
49D HIS* 3.0 51.7 + - + +
58D TRP* 4.5 18.4 - - + -
61D PHE* 4.5 21.8 - - + -
66D LEU* 4.6 11.7 - - + -
73D VAL* 4.3 26.2 - - + -
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Residues in contact with LEU 46 (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 VAL* 5.0 3.1 - - + -
42D VAL* 2.9 23.0 + - + +
43D ARG* 3.3 17.3 - - + +
44D LYS 3.2 0.2 - - - -
45D LEU* 1.3 80.1 - - + +
47D ASN* 1.3 61.7 + - - +
49D HIS* 4.5 2.9 - - + +
50D ASN* 2.6 37.0 + - - +
51D ILE 6.5 0.4 - - - -
58D TRP* 6.1 5.8 - - + -
75D ILE* 5.1 14.1 - - + -
91D SER* 4.8 17.4 - - - +
95D VAL* 3.6 40.4 - - + -
97D LEU* 4.7 6.5 - - + -
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Residues in contact with ASN 47 (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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43D ARG* 2.9 25.7 + - - +
44D LYS* 3.3 24.9 - - - +
46D LEU* 1.3 77.0 - - - +
48D ARG* 1.3 65.2 + - - +
50D ASN* 4.1 9.4 + - - +
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Residues in contact with ARG 48 (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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44D LYS 2.9 13.3 + - - +
45D LEU* 3.2 22.0 - - - +
47D ASN* 1.3 81.4 - - - +
49D HIS* 1.3 86.7 + - + +
50D ASN* 4.5 1.4 - - - +
62D ASP* 2.9 50.1 + - - +
63D GLU* 4.4 9.1 - - - +
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Residues in contact with HIS 49 (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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45D LEU* 3.0 45.8 + - + +
46D LEU* 5.2 3.1 - - + -
48D ARG* 1.3 94.2 + - + +
50D ASN* 1.3 63.2 + - - +
51D ILE* 2.8 32.9 + - + +
58D TRP* 4.1 29.7 + + + +
60D GLU 5.9 1.0 + - - -
61D PHE* 6.2 0.4 - - - -
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Residues in contact with ASN 50 (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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46D LEU* 2.6 25.9 + - - +
47D ASN* 4.2 10.3 + - - +
48D ARG 4.5 1.1 - - - +
49D HIS* 1.3 72.4 - - - +
51D ILE* 1.3 63.4 + - + +
89D ASP 4.5 0.3 - - - +
90D LEU* 4.4 0.3 - - - -
91D SER* 3.3 39.1 + - - -
92D ALA* 4.3 4.0 + - - +
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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