Contacts of the helix formed by residues 58 - 71 (chain D) in PDB entry 6DWN
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D LEU 3.6 7.8 + - - +
57D LYS* 1.3 102.2 - - - +
59D PRO* 1.3 68.5 - - - +
60D HIS* 3.2 14.3 - - + -
61D LEU* 3.1 40.1 + - + +
62D ALA* 3.2 9.5 + - - +
491D THR* 6.2 2.0 - - - +
492D PRO 4.8 6.0 - - - +
494D TYR* 3.9 13.9 + - - +
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Residues in contact with PRO 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 LEU* 3.7 34.3 - - + +
56D GLY 4.2 8.7 - - - +
57D LYS 3.6 8.3 - - - +
58D ASN* 1.3 86.9 - - - +
60D HIS* 1.3 55.5 + - - +
62D ALA* 3.3 0.5 + - - +
63D LEU* 2.9 37.6 + - + +
230D SER 4.4 6.5 - - - +
231D GLY* 5.8 1.8 - - - -
384D PHE* 4.0 15.0 - - + -
494D TYR* 3.6 38.1 - - + +
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Residues in contact with HIS 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ASN* 3.7 29.3 - - + -
59D PRO* 1.3 77.6 - - - +
61D LEU* 1.3 91.2 + - + +
64D SER* 2.9 28.4 + - - -
383D PRO* 3.9 16.6 - - + -
384D PHE* 3.4 26.9 - - + -
410D ASN* 3.5 6.3 + - - +
412D TRP* 3.5 34.9 + + + -
492D PRO* 5.6 3.5 - - - +
494D TYR* 3.3 20.6 - + + -
498D MET* 3.7 24.5 - - - +
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Residues in contact with LEU 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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58D ASN* 3.1 34.6 + - + +
60D HIS* 1.3 99.0 - - + +
62D ALA* 1.3 65.1 + - - +
64D SER* 3.2 13.1 + - - -
65D ARG* 3.4 30.5 + - - +
412D TRP* 3.3 39.7 - - + +
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Residues in contact with ALA 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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54D THR* 3.3 32.7 - - + +
55D LEU* 3.8 19.5 - - + +
58D ASN 3.2 4.4 + - - +
59D PRO 3.9 4.3 - - - +
61D LEU* 1.3 79.1 - - - +
63D LEU* 1.3 58.7 + - - +
65D ARG* 3.5 22.3 + - - +
66D MET* 3.1 28.6 + - - +
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Residues in contact with LEU 63 (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 LEU* 3.7 28.9 - - + -
59D PRO* 2.9 18.4 + - + +
62D ALA* 1.3 74.3 - - - +
64D SER* 1.3 60.8 + - - +
66D MET* 3.8 26.3 - - + +
67D SER* 3.1 26.3 + - - -
74D LEU* 4.8 3.8 - - + +
76D ILE* 4.4 5.8 - - + -
85D VAL* 4.0 37.4 - - + +
87D SER* 4.7 1.2 + - - -
384D PHE* 3.7 28.5 - - + -
408D PHE* 4.7 8.3 - - + -
410D ASN* 3.9 15.3 + - - +
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Residues in contact with SER 64 (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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60D HIS 2.9 20.9 + - - -
61D LEU 3.2 7.2 + - - -
63D LEU* 1.3 74.8 - - - +
65D ARG* 1.3 65.3 + - - +
67D SER* 2.8 20.6 + - - -
68D GLN* 3.2 19.7 + - - +
410D ASN* 3.5 10.6 + - - +
412D TRP* 3.2 29.6 - - - -
413D GLN* 3.6 13.3 - - - +
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Residues in contact with ARG 65 (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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61D LEU* 3.4 24.0 + - - +
62D ALA* 3.9 27.3 - - - +
64D SER* 1.3 78.4 - - - +
66D MET* 1.3 63.5 + - - +
68D GLN* 3.1 31.0 + - - +
69D GLN* 3.5 7.1 + - - +
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Residues in contact with MET 66 (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 PRO* 3.8 26.7 - - + -
51D HIS* 5.1 3.8 - - + -
54D THR* 3.4 34.8 - - + -
55D LEU* 5.1 2.9 - - + -
62D ALA 3.1 18.3 + - - +
63D LEU* 3.9 23.1 - - + +
64D SER 3.3 0.4 - - - -
65D ARG* 1.3 76.8 - - - +
67D SER* 1.3 62.4 + - - +
69D GLN* 3.1 7.6 + - - +
70D TYR* 3.0 44.6 + - + +
74D LEU* 4.0 10.5 - - + -
76D ILE* 3.9 24.7 - - + -
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Residues in contact with SER 67 (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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63D LEU 3.1 16.7 + - - -
64D SER* 2.8 22.5 + - - -
66D MET* 1.3 77.0 - - - +
68D GLN* 1.3 58.7 + - - +
71D GLY* 2.6 50.1 + - - +
72D ASP* 5.6 0.4 - - - -
74D LEU* 3.7 7.4 - - - +
87D SER* 3.5 20.4 - - - -
413D GLN* 3.8 16.5 + - - +
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Residues in contact with GLN 68 (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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64D SER* 3.2 19.6 - - - +
65D ARG* 3.1 24.3 + - - +
67D SER* 1.3 79.1 + - - +
69D GLN* 1.3 57.1 + - - +
71D GLY 4.7 0.2 - - - -
413D GLN* 5.9 3.6 - - - +
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Residues in contact with GLN 69 (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 PRO* 5.1 1.4 - - - +
65D ARG 3.5 6.2 + - - +
66D MET* 3.1 11.3 + - - +
67D SER 3.0 0.6 - - - -
68D GLN* 1.3 79.4 - - - +
70D TYR* 1.3 97.6 + - + +
71D GLY 3.7 0.4 - - - -
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Residues in contact with TYR 70 (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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41D PRO* 3.6 27.6 - - + +
42D GLY* 3.2 32.9 + - - -
43D PRO* 3.0 42.8 - - + +
66D MET* 3.0 24.3 + - + +
69D GLN* 1.3 116.3 + - + +
71D GLY* 1.3 61.5 + - - +
73D VAL 3.8 4.8 - - - +
74D LEU* 4.0 19.3 - - + -
399D PHE* 5.9 0.3 - - - -
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Residues in contact with GLY 71 (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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67D SER* 2.6 42.0 + - - +
68D GLN 4.7 0.2 - - - -
69D GLN 3.7 0.8 - - - -
70D TYR* 1.3 74.0 - - - +
72D ASP* 1.3 68.8 + - - -
73D VAL 3.3 3.6 + - - -
74D LEU* 3.9 6.8 - - - +
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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