Contacts of the helix formed by residues 58 - 71 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU 3.6 6.7 + - - +
56A GLY 3.4 0.4 - - - -
57A LYS* 1.3 89.5 - - - +
59A PRO* 1.3 66.6 - - - +
60A HIS* 3.2 23.0 - - + -
61A LEU* 3.0 32.0 + - + +
62A ALA* 3.1 9.5 + - - +
65A ARG* 5.5 0.2 + - - -
491A THR* 6.4 0.4 - - - +
492A PRO 4.7 6.8 - - - +
494A TYR* 3.8 14.0 + - - +
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Residues in contact with PRO 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.6 27.6 - - + +
56A GLY 4.1 10.8 - - - +
57A LYS 3.3 10.3 - - - +
58A ASN* 1.3 87.6 - - - +
60A HIS* 1.3 55.1 + - - +
62A ALA* 4.3 2.7 - - + +
63A LEU* 2.7 44.7 + - + +
230A SER 4.0 8.7 - - - +
231A GLY* 5.4 1.8 - - - -
384A PHE* 3.9 15.0 - - + -
408A PHE* 6.5 0.2 - - + -
494A TYR* 3.7 32.1 - - + +
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Residues in contact with HIS 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASN* 3.6 31.7 - - + -
59A PRO* 1.3 77.9 - - - +
61A LEU* 1.3 82.1 + - + +
64A SER* 2.6 36.7 + - - -
383A PRO* 3.7 16.8 - - + -
384A PHE* 3.4 26.0 - - + -
410A ASN* 3.4 3.0 + - - +
412A TRP* 3.5 34.5 + + + -
492A PRO* 5.7 2.6 - - + +
494A TYR* 3.4 17.4 - + - -
498A MET* 3.7 26.7 - - + +
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ASN* 3.0 31.7 + - + +
60A HIS* 1.3 96.1 - - + +
62A ALA* 1.3 66.0 + - - +
64A SER* 3.2 5.6 + - - -
65A ARG* 3.1 45.1 + - - +
412A TRP* 3.4 38.8 - - + -
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR* 3.3 31.9 - - + +
55A LEU* 3.7 22.4 - - + +
58A ASN 3.1 4.8 + - - +
59A PRO 3.1 5.5 + - - +
61A LEU* 1.3 76.6 - - - +
63A LEU* 1.3 60.2 + - - +
65A ARG* 3.5 22.3 + - - +
66A MET* 3.1 29.1 + - - +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.6 29.6 - - + -
59A PRO* 2.7 22.3 + - + +
62A ALA* 1.3 69.7 - - - +
64A SER* 1.3 58.6 + - - +
66A MET* 3.7 27.4 - - + +
67A SER* 3.1 25.6 + - - -
74A LEU* 4.7 3.6 - - + +
76A ILE* 4.1 13.5 - - + -
85A VAL* 3.8 34.6 - - + +
87A SER* 4.7 1.6 + - - -
384A PHE* 3.6 24.9 - - + -
408A PHE* 4.4 10.1 - - + -
410A ASN* 3.9 14.3 + - - +
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A HIS 2.6 23.4 + - - -
61A LEU 3.2 4.7 + - - -
63A LEU* 1.3 76.0 - - - +
65A ARG* 1.3 64.8 + - - +
67A SER* 2.7 23.6 + - - -
68A GLN* 3.3 16.8 + - - +
410A ASN* 3.2 13.2 + - - +
412A TRP* 3.4 27.9 - - - -
413A GLN* 3.7 12.4 - - - +
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Residues in contact with ARG 65 (chain A).
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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54A THR 5.4 0.8 + - - -
61A LEU* 3.1 33.8 + - - +
62A ALA* 3.5 30.3 + - - +
64A SER* 1.3 74.5 - - - +
66A MET* 1.3 64.4 + - - +
68A GLN* 3.1 34.7 + - - +
69A GLN* 3.7 5.0 + - - +
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Residues in contact with MET 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PRO* 3.8 22.9 - - + -
51A HIS* 5.1 2.9 - - + -
54A THR* 3.7 31.9 - - + -
55A LEU* 5.0 3.1 - - + -
62A ALA 3.1 17.2 + - - +
63A LEU* 3.8 25.6 - - + +
64A SER 3.2 0.2 - - - -
65A ARG* 1.3 77.0 - - - +
67A SER* 1.3 62.0 + - - +
69A GLN* 3.0 14.1 + - - -
70A TYR* 3.1 34.7 + - + +
74A LEU* 4.0 13.9 - - + -
76A ILE* 3.7 29.6 - - + -
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU 3.1 14.8 + - - -
64A SER* 2.7 23.7 + - - -
66A MET* 1.3 76.1 - - - +
68A GLN* 1.3 60.3 + - - +
71A GLY* 2.7 43.1 + - - +
72A ASP* 5.8 0.4 - - - -
74A LEU* 3.8 6.7 - - - +
87A SER* 3.6 24.7 - - - -
413A GLN* 3.8 16.8 + - - +
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Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 3.5 17.6 + - - +
65A ARG* 3.1 26.9 + - - +
67A SER* 1.3 78.6 + - - +
69A GLN* 1.3 57.8 + - - +
71A GLY 5.1 0.2 + - - -
413A GLN* 6.1 1.8 - - - +
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG 3.7 4.7 + - - +
66A MET* 3.0 10.0 + - - +
68A GLN* 1.3 81.2 - - - +
70A TYR* 1.3 100.9 + - + +
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Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PRO* 3.5 28.9 - - + +
42A GLY* 3.5 30.4 + - - -
43A PRO* 3.3 40.1 - - + +
66A MET* 3.1 28.5 + - + +
69A GLN* 1.3 117.4 + - + +
71A GLY* 1.3 60.9 + - - +
73A VAL 3.8 4.6 - - - +
74A LEU* 4.0 19.5 - - + -
399A PHE* 6.0 0.3 - - - -
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER* 2.7 40.7 + - - +
68A GLN 4.8 0.2 - - - -
69A GLN 3.7 1.0 - - - -
70A TYR* 1.3 74.1 - - - +
72A ASP* 1.3 67.0 + - - -
73A VAL 3.3 3.5 + - - -
74A LEU* 4.0 7.4 - - - +
87A SER* 4.5 0.3 + - - -
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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