Contacts of the helix formed by residues 58 - 71 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B LEU 3.7 5.9 + - - +
56B GLY 3.4 0.2 - - - -
57B LYS* 1.3 92.3 - - - +
59B PRO* 1.3 68.5 - - - +
60B HIS* 3.2 21.9 - - + -
61B LEU* 3.0 34.4 + - + +
62B ALA* 3.1 10.2 + - - +
491B THR* 6.2 1.8 - - - +
492B PRO 4.7 6.6 + - - +
494B TYR* 3.9 14.7 + - - +
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Residues in contact with PRO 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 3.7 33.4 - - + +
56B GLY 4.3 9.2 - - - +
57B LYS 3.5 9.0 - - - +
58B ASN* 1.3 86.9 - - - +
60B HIS* 1.3 55.6 + - - +
62B ALA* 3.2 1.0 + - + +
63B LEU* 2.8 38.9 + - + +
230B SER 4.1 7.6 - - - +
231B GLY* 5.5 2.2 - - - +
384B PHE* 3.9 15.3 - - + -
494B TYR* 3.5 35.2 - - + +
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Residues in contact with HIS 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ASN* 3.6 30.1 - - + -
59B PRO* 1.3 78.8 - - - +
61B LEU* 1.3 86.2 + - + +
64B SER* 2.7 33.8 + - - -
383B PRO* 3.7 17.7 - - + -
384B PHE* 3.4 26.4 - - + -
410B ASN* 3.4 5.1 + - - +
412B TRP* 3.5 32.7 + + + -
492B PRO* 5.6 3.9 - - + +
494B TYR* 3.3 25.0 - + + -
498B MET* 3.8 18.0 - - - +
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B ASN* 3.0 34.4 + - + +
60B HIS* 1.3 104.5 - - + +
62B ALA* 1.3 65.3 + - - +
64B SER* 3.2 4.9 + - - -
65B ARG* 3.1 42.5 + - - +
412B TRP* 3.4 31.9 - - + -
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B THR* 3.3 31.7 - - + +
55B LEU* 3.6 20.9 - - + +
58B ASN 3.1 5.6 + - - +
59B PRO 3.8 4.5 - - - +
61B LEU* 1.3 77.9 - - - +
63B LEU* 1.3 58.8 + - - +
65B ARG* 3.7 23.7 + - - +
66B MET* 3.2 28.6 + - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 3.9 28.5 - - + -
59B PRO* 2.8 17.6 + - + +
62B ALA* 1.3 74.3 - - - +
64B SER* 1.3 59.6 + - - +
66B MET* 3.8 27.5 - - + +
67B SER* 3.2 25.1 + - - -
74B LEU* 4.7 3.1 - - + +
76B ILE* 4.3 6.3 - - + -
85B VAL* 3.8 38.1 - - + +
87B SER* 4.7 1.9 + - - -
384B PHE* 3.7 27.8 - - + -
408B PHE* 4.5 10.3 - - + -
410B ASN* 3.9 15.2 + - - +
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Residues in contact with SER 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B HIS 2.7 21.6 + - - -
61B LEU* 3.2 6.7 + - - -
63B LEU* 1.3 76.0 - - - +
65B ARG* 1.3 64.5 + - - +
67B SER* 2.7 23.8 + - - -
68B GLN* 3.3 17.2 + - - +
410B ASN* 3.3 11.9 + - - +
412B TRP* 3.3 30.7 - - - -
413B GLN* 3.8 11.9 - - - +
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B THR 5.5 0.4 + - - -
61B LEU* 3.1 29.7 + - - +
62B ALA* 3.7 27.9 + - - +
64B SER* 1.3 75.8 - - - +
66B MET* 1.3 64.5 + - - +
68B GLN* 3.1 33.8 + - - +
69B GLN* 3.6 5.4 + - - +
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Residues in contact with MET 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PRO* 3.7 28.7 - - + -
51B HIS* 5.3 1.6 - - + -
54B THR* 3.6 31.4 - - + -
55B LEU* 5.0 3.6 - - + -
62B ALA 3.2 15.1 + - - +
63B LEU* 3.8 25.4 - - + +
64B SER 3.2 0.4 - - - -
65B ARG* 1.3 79.2 - - - +
67B SER* 1.3 62.4 + - - +
69B GLN* 3.0 7.0 + - - -
70B TYR* 3.0 45.4 + - + +
74B LEU* 3.9 12.6 - - + -
76B ILE* 3.8 22.4 - - + -
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B LEU 3.2 12.3 + - - -
64B SER* 2.7 22.9 + - - -
66B MET* 1.3 76.5 - - - +
68B GLN* 1.3 61.0 + - - +
71B GLY* 2.7 43.4 + - - +
72B ASP* 5.5 0.2 - - - -
74B LEU* 3.7 6.7 - - - +
87B SER* 3.4 28.3 - - - -
413B GLN* 3.8 16.2 + - - +
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B SER* 3.4 20.7 + - - +
65B ARG* 3.1 27.0 + - - +
67B SER* 1.3 78.1 + - - +
69B GLN* 1.3 56.9 + - - +
413B GLN* 6.2 1.3 - - - +
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ARG 3.6 4.5 + - - +
66B MET* 3.0 10.5 + - - +
68B GLN* 1.3 80.4 - - - +
70B TYR* 1.3 95.9 + - + +
71B GLY 3.7 0.4 - - - -
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Residues in contact with TYR 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PRO* 3.5 28.0 - - + +
42B GLY* 3.3 34.5 + - - -
43B PRO* 3.2 38.3 - - + +
66B MET* 3.0 31.1 + - + +
69B GLN* 1.3 114.7 + - + +
71B GLY* 1.3 61.0 + - - +
73B VAL 3.8 4.4 - - - +
74B LEU* 3.9 19.1 - - + -
399B PHE* 5.8 0.7 - - - -
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Residues in contact with GLY 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B SER* 2.7 41.0 + - - -
68B GLN 4.8 0.2 - - - -
69B GLN 3.7 0.8 - - - -
70B TYR* 1.3 73.9 - - - +
72B ASP* 1.3 68.0 + - - -
73B VAL 3.3 3.3 + - - -
74B LEU* 3.8 8.1 - - - +
87B SER* 4.2 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