Contacts of the helix formed by residues 49 - 58 (chain D) in PDB entry 4LLL
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 THR 49 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47D GLY 3.2 12.3 + - - +
48D LEU* 1.3 77.5 - - - +
50D GLN* 1.3 68.8 + - - +
51D ASN* 3.8 4.5 + - - +
52D ASP* 3.2 29.2 + - - +
53D ILE* 3.1 19.8 + - - +
88D ARG* 3.5 44.4 - - + +
89D LYS 3.8 5.2 - - - -
90D ASN* 4.1 6.7 - - - +
91D ILE* 4.2 3.8 - - - -
5F A 5.0 2.5 + - - -
6F G 3.5 10.1 - - - -
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Residues in contact with GLN 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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49D THR* 1.3 70.0 - - - +
51D ASN* 1.3 59.5 + - - +
53D ILE* 2.9 17.6 + - - +
54D ALA* 2.7 27.3 + - - +
61D GLY 5.1 2.0 + - - -
64D VAL* 3.9 5.3 - - + +
65D SER* 4.0 13.3 - - - +
68D LEU* 3.6 21.5 - - + +
79D ARG* 3.0 19.9 + - - -
89D LYS* 3.9 8.1 + - + +
91D ILE* 3.7 11.7 - - + +
6F G 3.0 42.4 + - - +
7F T 2.9 38.8 + - - -
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Residues in contact with ASN 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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49D THR* 3.3 4.4 + - - +
50D GLN* 1.3 75.8 - - - +
52D ASP* 1.3 55.7 + - - +
54D ALA* 3.8 13.6 - - - +
55D LYS* 2.9 46.5 + - - +
61D GLY* 5.4 6.6 - - - -
5F A 3.5 31.4 + - + +
6F G 2.8 20.8 + - - +
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Residues in contact with ASP 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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39D TYR* 5.5 1.6 - - - -
46D ASP 5.0 2.3 - - - +
47D GLY 3.8 5.5 - - - +
48D LEU* 3.8 20.3 - - + +
49D THR* 3.2 38.4 + - - +
50D GLN 3.1 0.4 - - - -
51D ASN* 1.3 74.7 - - - +
53D ILE* 1.3 55.0 + - - +
55D LYS* 3.1 19.4 + - - +
56D ALA* 2.8 35.7 + - - +
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Residues in contact with ILE 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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36D THR* 4.2 10.3 - - + -
39D TYR* 4.7 13.5 - - + -
40D LEU* 3.9 26.0 - - + -
48D LEU* 4.6 8.3 - - + -
49D THR 3.4 8.7 - - - +
50D GLN 2.9 5.8 + - - +
52D ASP* 1.3 79.4 - - - +
54D ALA* 1.3 63.8 + - - +
56D ALA* 3.1 5.2 + - - +
57D LEU* 2.9 48.0 + - + +
64D VAL* 3.7 17.7 - - + -
68D LEU* 3.9 15.9 - - + -
91D ILE* 3.6 33.0 - - + -
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Residues in contact with ALA 54 (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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50D GLN 2.7 14.6 + - - +
51D ASN* 3.4 24.7 - - - +
53D ILE* 1.3 72.8 - - - +
55D LYS* 1.3 56.9 + - - +
57D LEU* 5.3 0.2 - - - -
58D GLN* 2.9 22.3 + - - -
59D ARG 2.9 25.9 + - - +
60D THR 3.7 13.7 - - - +
61D GLY* 4.6 3.4 - - - -
64D VAL* 3.6 18.4 - - + +
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Residues in contact with LYS 55 (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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51D ASN* 2.9 43.5 + - - +
52D ASP* 3.3 19.8 + - - +
54D ALA* 1.3 77.4 - - - +
56D ALA* 1.3 61.7 + - - +
58D GLN* 3.2 22.5 + - - +
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Residues in contact with ALA 56 (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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7C TYR* 4.4 17.5 + - - -
39D TYR* 3.3 44.4 - - + +
52D ASP 2.8 18.4 + - - +
53D ILE 3.1 1.8 + - - +
55D LYS* 1.3 73.8 - - - +
57D LEU* 1.3 62.9 + - - +
58D GLN* 3.1 5.8 + - - +
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Residues in contact with LEU 57 (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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7C TYR* 5.7 2.5 - - + -
10C ARG* 4.8 15.0 - - - +
11C MET* 3.2 22.8 - - + +
32D GLU 5.2 0.2 - - - +
35D HIS* 4.6 12.8 - - + +
36D THR* 3.6 37.7 - - + +
39D TYR* 4.6 24.0 - - + -
53D ILE* 2.9 24.8 + - + +
54D ALA* 4.6 1.3 - - - +
56D ALA* 1.3 77.1 - - + +
58D GLN* 1.3 71.6 + - - +
59D ARG* 3.5 14.9 + - + +
64D VAL* 5.3 5.6 - - + -
67D LEU* 5.3 1.8 - - + -
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Residues in contact with GLN 58 (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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7C TYR* 4.2 8.3 + - - -
11C MET* 3.2 32.2 - - - +
14C HIS* 3.7 9.5 - - - -
15C GLU* 5.1 13.1 + - - +
54D ALA 2.9 10.9 + - - -
55D LYS* 3.3 15.3 - - - +
56D ALA 3.1 7.0 - - - +
57D LEU* 1.3 80.6 - - - +
59D ARG* 1.3 74.3 + - - +
139D GLN* 4.9 16.0 - - - +
15E C 4.5 0.2 + - - -
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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