Contacts of the helix formed by residues 58 - 71 (chain C) in PDB entry 6DWM
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 ASN 58 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C LEU 3.5 6.9 + - - +
56C GLY 3.4 0.4 - - - -
57C LYS* 1.3 110.2 + - - +
59C PRO* 1.3 67.8 - - - +
60C HIS* 3.2 19.9 - - + -
61C LEU* 3.1 38.5 + - + +
62C ALA* 3.3 8.7 + - - +
492C PRO 4.5 9.3 + - - -
494C TYR* 4.0 12.5 - - - +
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Residues in contact with PRO 59 (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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55C LEU* 3.7 34.3 - - + +
56C GLY 4.1 10.3 - - - +
57C LYS 3.5 8.5 - - - +
58C ASN* 1.3 86.1 - - - +
60C HIS* 1.3 64.3 + - - +
62C ALA* 3.1 2.0 + - + +
63C LEU* 2.9 30.6 + - + +
230C SER 4.2 7.2 - - - +
231C GLY* 5.5 3.4 - - - +
384C PHE* 4.1 13.9 - - + -
494C TYR* 3.7 34.5 - - + +
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Residues in contact with HIS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ASN* 3.8 31.3 - - + -
59C PRO* 1.3 78.9 - - - +
61C LEU* 1.3 89.5 + - + +
64C SER* 2.9 28.1 + - - -
383C PRO* 3.7 16.2 - - + -
384C PHE* 3.5 27.2 - - + -
410C ASN* 3.6 5.2 + - - +
412C TRP* 3.5 34.5 + + + -
492C PRO* 5.7 2.1 - - - +
494C TYR* 3.5 16.8 - + - -
498C MET* 3.6 27.0 - - - +
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Residues in contact with LEU 61 (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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58C ASN* 3.1 32.3 + - + +
60C HIS* 1.3 95.7 - - + +
62C ALA* 1.3 65.2 + - - +
64C SER* 3.2 13.1 + - - -
65C ARG* 3.2 39.0 + - - +
412C TRP* 3.3 39.7 - - + -
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Residues in contact with ALA 62 (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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54C THR* 3.4 32.5 - - + +
55C LEU* 4.0 20.9 - - + +
58C ASN 3.3 2.0 + - - +
59C PRO 3.1 7.5 + - - +
61C LEU* 1.3 81.2 - - - +
63C LEU* 1.3 57.0 + - - +
64C SER 3.3 0.2 + - - -
65C ARG* 3.4 17.9 + - - +
66C MET* 2.8 31.2 + - + +
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Residues in contact with LEU 63 (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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55C LEU* 3.9 26.9 - - + -
59C PRO* 2.9 17.5 + - + +
62C ALA* 1.3 72.0 - - - +
64C SER* 1.3 61.1 + - - +
66C MET* 3.7 25.4 - - - +
67C SER* 3.0 26.5 + - - -
74C LEU* 4.6 4.1 - - + +
76C ILE* 4.2 6.7 - - + -
85C VAL* 3.8 38.7 - - + +
87C SER* 4.7 1.7 + - - -
384C PHE* 3.6 30.5 - - + -
408C PHE* 4.8 7.6 - - + -
410C ASN* 3.8 15.4 + - - +
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Residues in contact with SER 64 (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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60C HIS 2.9 21.4 + - - -
61C LEU 3.2 6.8 + - - -
63C LEU* 1.3 74.8 - - - +
65C ARG* 1.3 64.9 + - - +
67C SER* 2.8 21.9 + - - -
68C GLN* 3.4 14.9 + - - +
410C ASN* 3.7 1.1 + - - +
412C TRP* 3.2 31.5 - - - -
413C GLN* 3.6 23.2 + - - +
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Residues in contact with ARG 65 (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 LEU* 3.2 28.3 + - - +
62C ALA* 3.9 25.3 - - - +
64C SER* 1.3 80.2 - - - +
66C MET* 1.3 62.3 + - - +
68C GLN* 3.3 33.6 + - - +
69C GLN* 3.9 4.9 + - - +
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Residues in contact with MET 66 (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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43C PRO* 3.9 29.2 - - + -
51C HIS* 5.2 2.5 - - + -
54C THR* 3.6 32.1 - - + -
55C LEU* 4.6 6.1 - - + -
62C ALA 2.8 23.9 + - - +
63C LEU* 3.9 24.0 - - + +
64C SER 3.2 0.2 - - - -
65C ARG* 1.3 78.6 - - - +
67C SER* 1.3 60.0 + - - +
69C GLN* 3.3 11.3 + - - +
70C TYR* 3.3 24.0 + - + +
74C LEU* 4.1 10.1 - - + -
76C ILE* 3.7 28.9 - - + -
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Residues in contact with SER 67 (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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63C LEU 3.0 16.0 + - - -
64C SER 2.8 19.4 + - - -
66C MET* 1.3 74.5 - - - +
68C GLN* 1.3 62.8 + - - +
71C GLY* 2.8 36.7 + - - +
72C ASP* 5.7 0.2 - - - -
74C LEU* 3.7 12.7 - - - +
87C SER* 3.5 23.8 - - - -
413C GLN* 3.8 19.6 + - - +
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Residues in contact with GLN 68 (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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64C SER 3.4 10.9 - - - +
65C ARG* 3.4 32.6 + - - +
66C MET 3.2 0.6 - - - -
67C SER* 1.3 78.8 + - - +
69C GLN* 1.3 57.3 + - - +
413C GLN* 6.1 2.0 - - - +
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Residues in contact with GLN 69 (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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65C ARG 3.9 3.8 + - - +
66C MET* 3.3 4.5 + - - +
67C SER 3.1 0.4 - - - -
68C GLN* 1.3 80.4 - - - +
70C TYR* 1.3 100.6 + - + +
71C GLY 3.7 0.2 - - - -
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Residues in contact with TYR 70 (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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41C PRO* 3.6 29.0 - - + +
42C GLY* 3.3 37.0 + - - -
43C PRO* 3.2 38.2 - - + +
66C MET* 3.3 23.5 + - + +
69C GLN* 1.3 115.4 + - + +
71C GLY* 1.3 59.9 + - - +
73C VAL 3.9 3.3 - - - +
74C LEU* 4.0 18.4 - - + -
399C PHE* 6.0 0.3 - - - -
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Residues in contact with GLY 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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67C SER* 2.8 34.7 + - - -
68C GLN 4.8 0.2 - - - -
69C GLN 3.7 0.8 - - - -
70C TYR* 1.3 79.9 - - - +
72C ASP* 1.3 69.1 + - - -
73C VAL 3.3 3.8 + - - -
74C LEU* 3.7 7.6 - - - +
87C SER* 4.3 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