Contacts of the helix formed by residues 53 - 62 (chain D) in PDB entry 3LL8
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 LEU 53 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356C PHE* 4.7 0.4 - - + -
357C VAL* 3.9 48.0 - - + +
360C LYS* 4.4 10.3 - - + -
361C VAL* 4.4 12.8 - - + +
364C MET* 5.1 0.2 - - - -
51D ASN* 3.0 10.4 + - - +
52D PRO* 1.3 86.8 - - + +
54D VAL* 1.3 64.6 + - - +
55D GLN 3.3 2.7 - - - -
56D ARG* 3.1 18.2 + - + +
57D VAL* 3.0 25.3 + - + +
97D ILE* 4.2 11.7 - - + -
114D VAL* 4.7 3.6 - - + -
117D MET* 4.5 15.7 - - + -
118D MET* 3.9 28.3 - - + -
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Residues in contact with VAL 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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364C MET* 3.8 20.1 - - + +
39D VAL* 6.0 0.4 - - + -
42D PHE* 4.7 1.8 - - + -
43D MET* 4.0 22.4 - - + -
48D LEU* 3.1 46.4 - - + +
51D ASN* 3.4 24.6 + - + +
52D PRO 3.5 1.8 - - - -
53D LEU* 1.3 75.6 - - - +
55D GLN* 1.3 59.9 + - - +
57D VAL* 3.1 4.2 + - - +
58D ILE* 3.0 45.2 + - + +
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Residues in contact with GLN 55 (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 VAL* 3.9 33.6 - - + +
52D PRO 5.0 3.0 + - - +
53D LEU 3.3 0.8 - - - -
54D VAL* 1.3 76.6 - - - +
56D ARG* 1.3 69.8 + - + +
58D ILE* 4.1 11.3 - - - +
59D ASP* 3.0 28.1 + - + +
117D MET* 6.5 0.7 - - - -
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Residues in contact with ARG 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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52D PRO 5.5 0.2 + - - -
53D LEU* 3.1 21.3 + - + +
55D GLN* 1.3 80.9 + - + +
57D VAL* 1.3 63.9 + - - +
59D ASP* 2.9 40.2 + - - +
60D ILE* 3.0 37.1 + - - +
96D ARG 2.7 27.9 + - - -
97D ILE* 2.8 37.2 + - + +
99D ASP 3.7 2.4 + - - -
100D MET* 3.5 39.8 + - - +
102D LYS* 5.7 1.6 - - - +
114D VAL* 4.6 1.8 - - + -
117D MET* 3.9 36.6 - - - -
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Residues in contact with VAL 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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361C VAL* 3.7 35.2 - - + -
364C MET* 3.6 31.6 - - + -
365C LEU* 4.9 7.0 - - + -
53D LEU 3.0 19.3 + - - +
54D VAL 3.5 7.2 - - - +
56D ARG* 1.3 76.6 - - - +
58D ILE* 1.3 64.0 + - - +
60D ILE* 3.1 6.6 + - - +
61D PHE* 3.0 46.3 + - + -
93D PHE* 4.5 6.5 - - + -
97D ILE* 4.2 7.2 - - + -
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Residues in contact with ILE 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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364C MET* 4.1 10.3 - - + -
37D LEU 5.4 1.8 - - - +
39D VAL* 4.3 29.4 - - + +
42D PHE* 3.6 43.1 - - + -
54D VAL* 3.0 27.8 + - + +
55D GLN* 4.0 12.6 - - - +
57D VAL* 1.3 76.3 - - - +
59D ASP* 1.3 64.4 + - - +
61D PHE* 3.3 7.1 + - - +
62D ASP* 2.9 24.9 + - + +
67D GLY 4.8 9.0 - - - +
69D VAL* 3.9 18.4 - - + -
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Residues in contact with ASP 59 (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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55D GLN* 3.0 25.4 + - + +
56D ARG* 2.9 30.6 + - - +
58D ILE* 1.3 76.7 - - - +
60D ILE* 1.3 60.9 + - - +
62D ASP* 3.4 19.4 + - - +
65D GLY* 6.0 0.9 - - - -
100D MET 3.8 9.0 - - - +
102D LYS* 2.9 42.0 + - - -
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Residues in contact with ILE 60 (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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56D ARG* 3.0 21.3 + - - +
57D VAL 3.1 5.1 + - - +
59D ASP* 1.3 79.2 - - - +
61D PHE* 1.3 63.5 + - + +
62D ASP 3.3 0.7 + - - -
63D THR* 4.0 6.8 + - - -
93D PHE* 3.7 31.0 - - + +
96D ARG* 3.5 67.1 - - + +
97D ILE* 3.5 27.8 - - + +
102D LYS* 4.1 12.5 + - + +
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Residues in contact with PHE 61 (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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365C LEU* 3.8 26.7 - - + -
42D PHE* 5.7 4.5 - + - -
57D VAL* 3.0 32.0 + - + +
58D ILE* 3.8 8.1 - - - +
60D ILE* 1.3 75.1 - - + +
62D ASP* 1.3 51.9 + - - +
63D THR* 2.7 25.6 + - - -
69D VAL* 4.0 20.0 - - + -
73D GLU* 3.4 25.8 - - - +
74D PHE* 3.8 21.5 - + - -
77D GLY* 3.4 42.4 - - - -
78D VAL* 3.7 14.4 - - + -
81D PHE* 4.6 1.3 - + - -
93D PHE* 3.9 23.3 - + - -
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Residues in contact with ASP 62 (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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58D ILE* 2.9 21.1 + - + +
59D ASP* 3.6 15.5 - - - +
60D ILE 3.2 1.7 - - - -
61D PHE* 1.3 71.7 - - - +
63D THR* 1.3 62.9 + - - +
64D ASP* 3.0 9.7 - - - +
65D GLY* 3.1 16.1 + - - -
66D ASN* 3.1 2.4 + - - +
67D GLY* 2.7 30.9 + - - -
68D GLU 2.9 11.8 - - - +
69D VAL* 4.4 2.4 - - + +
73D GLU* 3.9 7.2 - - - -
102D LYS* 3.4 13.6 + - - -
509D CA 2.3 30.3 - - - -
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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