Contacts of the helix formed by residues 43 - 53 (chain D) in PDB entry 3L43
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 GLY 43 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D SER 3.3 1.0 - - - -
42D ALA* 1.3 78.6 - - - +
44D LYS* 1.3 63.9 + - - +
45D SER 3.7 1.6 - - - -
46D SER* 3.6 9.0 - - - -
47D VAL* 3.5 19.2 - - - +
174D VAL* 4.3 4.7 - - - -
205D THR* 4.1 1.8 - - - +
236D ASN* 3.7 4.7 + - - -
901D GDP 3.1 43.1 + - - -
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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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36D VAL* 3.6 39.1 - - + +
38D GLY* 3.6 25.6 - - - +
39D GLY 3.0 20.0 + - - -
40D GLN* 4.0 1.6 - - - +
42D ALA* 4.3 4.3 - - + -
43D GLY* 1.3 74.5 - - - +
45D SER* 1.4 66.5 + - - +
47D VAL* 3.2 20.3 + - - +
48D LEU* 3.7 7.1 + - - +
65D THR* 4.7 3.5 + - - -
136D ASP* 3.8 9.6 - - - +
137D LEU 3.3 21.8 - - - +
139D GLY* 3.3 21.9 - - - +
174D VAL* 4.2 16.2 - - + -
901D GDP 2.7 33.3 + - - +
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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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44D LYS* 1.4 71.6 - - - +
46D SER* 1.4 60.4 + - - +
48D LEU* 3.2 11.3 + - - -
49D GLU* 3.2 11.1 + - - +
57D LEU* 3.4 25.5 - - - +
59D ARG* 3.7 18.2 - - - -
65D THR* 3.7 2.3 + - - -
136D ASP* 2.8 26.7 + - - -
307D UNX 3.2 10.2 - - - -
901D GDP 2.8 26.5 + - - -
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Residues in contact with SER 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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43D GLY 3.6 6.3 - - - -
44D LYS 3.2 0.2 - - - -
45D SER* 1.4 71.9 - - - +
47D VAL* 1.4 59.8 - - - +
49D GLU* 3.4 8.0 + - - +
50D ASN* 3.1 34.9 + - - +
59D ARG* 3.5 13.4 + - - +
236D ASN* 3.6 30.2 - - - +
237D ARG* 4.8 3.2 + - - +
242D ILE* 5.2 1.4 - - - +
901D GDP 2.6 39.9 + - - -
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Residues in contact with VAL 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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36D VAL* 5.0 6.1 - - + -
43D GLY 3.5 15.0 - - - +
44D LYS* 3.2 12.9 + - - +
46D SER* 1.4 76.3 - - - +
48D LEU* 1.4 63.4 + - + +
50D ASN* 3.1 9.1 + - - +
51D PHE* 2.9 58.4 + - + -
134D LEU* 5.2 0.9 - - + -
172D LEU* 4.5 13.9 - - + -
174D VAL* 5.3 1.6 - - + -
203D VAL* 4.5 21.8 - - + -
205D THR* 5.1 0.4 - - + -
234D VAL* 4.8 11.7 - - + -
236D ASN* 4.9 2.5 - - - +
274D THR* 4.9 2.7 - - + -
277D LEU* 4.2 11.4 - - + -
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Residues in contact with LEU 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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36D VAL* 4.2 12.8 - - + -
44D LYS 4.2 7.6 - - - +
45D SER 3.2 11.1 + - - +
47D VAL* 1.4 78.0 - - + +
49D GLU* 1.3 55.6 + - - +
51D PHE* 3.4 5.1 + - - +
52D VAL* 3.0 34.3 + - - +
56D PHE* 4.0 3.6 - - + -
57D LEU* 3.9 8.5 - - + -
69D LEU* 3.8 20.6 - - + -
71D LEU* 3.8 21.5 - - + -
134D LEU* 3.7 41.1 - - + -
136D ASP* 3.6 33.7 - - + +
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Residues in contact with GLU 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 SER 3.2 7.8 + - - +
46D SER* 3.7 8.4 + - - +
47D VAL 3.3 0.2 - - - -
48D LEU* 1.3 78.2 - - - +
50D ASN* 1.4 56.8 + - - +
53D GLY* 2.9 24.9 + - - -
54D ARG 3.5 18.2 + - - +
55D ASP* 3.5 5.5 - - - +
56D PHE* 3.0 30.7 + - + -
57D LEU* 2.9 30.0 + - + +
59D ARG* 2.8 40.6 + - - -
98D ARG* 4.1 1.7 + - - -
237D ARG* 3.4 15.0 + - - -
248D ILE* 3.8 15.4 - - + +
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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 SER 3.1 17.9 + - - +
47D VAL* 3.1 7.8 + - - +
49D GLU* 1.4 73.2 - - - +
51D PHE* 1.3 65.2 + - - +
53D GLY* 3.7 8.1 + - - -
235D VAL 4.9 2.2 + - - -
236D ASN* 2.8 37.7 + - - +
237D ARG* 5.4 2.3 + - - -
248D ILE* 3.7 26.9 - - - +
251D ALA* 4.9 7.4 - - - +
252D MET* 3.4 40.1 - - + +
255D GLU* 5.0 0.2 + - - -
274D THR* 3.8 16.9 + - + -
278D GLN* 4.5 1.6 - - - +
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Residues in contact with PHE 51 (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 ILE* 5.9 0.2 - - + -
47D VAL* 2.9 39.3 + - + +
48D LEU* 3.6 7.9 - - - +
50D ASN* 1.3 78.1 - - - +
52D VAL* 1.4 60.5 + - - +
53D GLY* 4.7 0.2 - - - -
73D LEU* 3.9 16.8 - - + -
128D HIS 4.3 4.3 - - - +
129D VAL* 3.3 16.8 - - - +
132D LEU* 4.0 10.8 - - + -
134D LEU* 3.6 28.5 - - + -
274D THR* 3.7 23.8 - - + -
277D LEU* 3.8 8.5 - - + -
278D GLN* 3.5 52.4 + - + +
281D LEU* 3.5 33.0 - - + -
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Residues in contact with VAL 52 (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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48D LEU 3.0 18.8 + - - +
49D GLU 4.0 1.8 - - - +
51D PHE* 1.4 74.3 - - - +
53D GLY* 1.3 58.3 + - - +
54D ARG* 4.0 22.7 + - + +
56D PHE* 3.6 21.8 - - + -
71D LEU* 3.8 10.5 - - + -
73D LEU* 3.7 24.7 - - + -
79D GLU* 5.6 0.5 - - - +
94D PHE* 4.1 17.0 - - + -
124D VAL* 3.9 21.3 - - + -
126D SER* 4.3 8.4 + - - -
128D HIS* 5.0 6.3 + - - +
129D VAL* 3.7 17.6 - - - +
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Residues in contact with GLY 53 (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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49D GLU 2.9 9.3 + - - -
50D ASN 3.7 3.8 + - - -
51D PHE 3.5 2.0 - - - -
52D VAL* 1.3 76.6 - - - +
54D ARG* 1.3 76.9 + - - +
128D HIS* 6.0 3.8 - - - -
247D ASP* 4.7 6.2 - - - +
248D ILE* 3.6 27.6 - - - +
249D LYS 5.0 1.2 + - - -
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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