Contacts of the helix formed by residues 70 - 81 (chain C) in PDB entry 3DLX
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 PRO 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C VAL* 3.8 17.0 - - + -
62C GLY* 3.4 20.0 - - - +
68C GLY 3.7 4.5 - - - +
69C ILE* 1.3 76.6 - - + +
71C GLU* 1.3 57.2 + - - +
73C LEU* 4.2 6.1 - - + -
74C ILE* 3.0 32.8 + - + +
209C LEU* 3.4 28.3 - - + +
210C VAL 4.0 16.8 - - - +
211C LYS* 3.6 5.6 - - + -
244C GLU* 2.8 25.9 - - + +
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Residues in contact with GLU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ILE* 2.9 27.8 + - + +
70C PRO* 1.3 73.0 - - - +
72C ASN* 1.3 61.7 + - - +
74C ILE* 3.6 6.2 + - - +
75C ASP* 3.2 27.0 + - - +
97C PHE* 3.5 20.8 - - + -
98C GLY 6.1 0.4 - - - +
101C LEU* 5.9 1.6 - - - +
211C LYS* 5.8 0.2 - - - -
244C GLU* 3.2 1.8 + - - -
274C LYS 3.7 3.7 - - - +
275C TYR* 3.6 29.7 - - + -
276C GLU* 2.9 35.2 + - - +
277C LYS* 3.2 25.5 + - - +
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Residues in contact with ASN 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C PRO* 4.2 17.7 - - + +
71C GLU* 1.3 76.7 - - - +
73C LEU* 1.3 59.5 + - + +
75C ASP* 3.4 7.8 + - - +
76C ALA* 3.1 24.4 + - - +
244C GLU* 2.9 25.4 + - + +
270C ILE* 6.0 1.3 - - + -
272C GLY* 3.4 10.2 - - - -
273C GLU* 3.3 25.1 + - - +
274C LYS* 2.8 34.9 + - - +
275C TYR* 3.0 19.0 - - - -
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Residues in contact with LEU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C PRO* 4.4 15.5 - - + +
49C ALA* 4.7 0.2 - - + -
50C VAL* 4.2 11.4 - - + -
70C PRO* 3.8 6.5 - - + +
72C ASN* 1.3 71.7 - - + +
74C ILE* 1.3 64.4 + - - +
75C ASP 3.2 0.2 - - - -
76C ALA* 3.3 3.6 + - - +
77C LEU* 3.1 28.2 + - - +
209C LEU* 4.2 19.1 - - + -
210C VAL 4.1 9.9 - - - +
242C VAL* 3.5 50.9 - - + +
244C GLU* 2.8 37.0 + - + +
270C ILE* 3.9 19.3 - - + -
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 4.2 15.0 - - + -
69C ILE* 4.0 20.0 - - + -
70C PRO* 3.0 35.3 + - + +
71C GLU* 3.9 6.1 - - - +
72C ASN 3.4 0.2 - - - -
73C LEU* 1.3 75.2 - - - +
75C ASP* 1.3 61.8 + - - +
77C LEU* 3.3 10.2 + - - +
78C LEU* 3.2 21.2 + - + +
98C GLY* 3.7 34.5 - - - +
99C LEU* 4.1 3.1 - - - +
101C LEU* 4.3 18.6 - - + -
102C LEU* 3.7 30.6 - - + +
209C LEU* 5.0 4.9 - - + -
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Residues in contact with ASP 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C GLU 3.2 15.2 + - - +
72C ASN* 3.4 12.8 - - - +
74C ILE* 1.3 74.7 - - - +
76C ALA* 1.3 64.8 + - - +
78C LEU* 3.2 24.4 + - - +
79C LYS* 3.2 51.5 + - - +
101C LEU* 5.7 3.4 - - + +
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Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C PRO* 3.8 8.5 - - + +
47C VAL* 3.8 27.8 - - + +
50C VAL* 3.4 26.5 - - + -
72C ASN 3.1 13.4 + - - +
73C LEU* 3.5 9.2 - - - +
74C ILE 3.3 0.2 - - - -
75C ASP* 1.3 75.0 - - - +
77C LEU* 1.3 63.6 + - - +
79C LYS* 2.9 16.2 + - - +
80C THR* 3.0 15.8 + - - +
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C VAL* 3.7 31.2 - - + +
53C ILE* 4.0 13.5 - - + -
59C VAL* 5.2 2.5 - - + -
61C VAL* 6.1 0.7 - - + -
73C LEU 3.1 17.3 + - - +
74C ILE* 3.3 8.0 + - - +
76C ALA* 1.3 76.6 - - - +
78C LEU* 1.3 53.1 + - - +
80C THR* 3.2 7.8 + - - +
81C GLY 2.8 29.5 + - - -
82C VAL* 4.1 15.3 - - + -
85C LEU* 4.4 16.4 - - + -
102C LEU* 3.8 26.0 - - + -
107C GLN* 2.9 12.9 + - - +
209C LEU* 3.5 26.0 - - + -
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C ILE 3.2 16.5 + - - +
75C ASP* 3.3 29.6 - - - +
76C ALA 3.2 0.2 - - - -
77C LEU* 1.3 76.6 - - - +
79C LYS* 1.3 61.7 + - + +
81C GLY* 3.7 9.0 + - - -
101C LEU* 3.5 50.5 - - + +
102C LEU* 3.7 11.4 - - + -
105C SER* 3.6 17.9 - - - +
107C GLN* 3.9 7.2 - - - +
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Residues in contact with LYS 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 4.1 23.3 - - + +
75C ASP* 3.2 35.7 + - - +
76C ALA* 2.9 8.7 + - - +
78C LEU* 1.3 77.3 - - + +
80C THR* 1.3 62.9 + - - +
81C GLY* 3.2 2.1 + - - -
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Residues in contact with THR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 3.7 28.3 - - + -
50C VAL* 4.3 11.7 + - + +
51C LYS* 4.2 22.4 - - + +
76C ALA 3.0 10.8 + - - +
77C LEU* 3.2 15.9 + - - +
79C LYS* 1.3 75.8 - - - +
81C GLY* 1.3 63.4 + - - +
82C VAL* 3.2 16.8 + - - +
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Residues in contact with GLY 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C LEU 2.8 12.9 + - - -
78C LEU 4.0 8.1 - - - -
79C LYS 3.2 2.2 - - - -
80C THR* 1.3 78.2 - - - +
82C VAL* 1.3 64.8 + - - +
83C LYS* 3.2 10.4 + - - +
107C GLN* 3.4 16.9 + - - +
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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