Contacts of the helix formed by residues 58 - 68 (chain B) in PDB entry 1DWQ
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 SER 58 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B MET* 4.2 4.9 - - - -
54B PHE 2.8 14.9 + - - -
55B ASP 3.5 11.0 - - - -
56B GLU 3.1 0.6 - - - -
57B TYR* 1.3 73.2 - - - +
59B GLU* 1.3 64.4 + - - +
60B PRO* 3.4 1.8 - - - -
61B LEU* 2.8 19.8 + - - +
62B LEU* 3.1 22.3 + - - -
85B ASN* 3.0 28.0 + - - -
88B ILE* 3.6 20.7 - - - +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ARG* 2.9 41.5 + - - +
55B ASP 3.8 3.5 + - - -
56B GLU* 3.1 20.0 + - - +
58B SER* 1.3 75.6 - - - +
60B PRO* 1.3 73.0 - - + +
62B LEU* 3.0 10.5 + - - +
63B THR* 2.6 56.1 + - - +
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Residues in contact with PRO 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.8 12.4 - - + +
37B ASP 3.0 28.9 - - - +
38B MET* 3.9 6.3 - - + -
39B ALA* 3.7 7.9 - - - +
44B ASP* 4.5 2.0 - - - +
46B ARG* 3.5 13.2 - - - +
57B TYR 3.5 13.9 - - - +
58B SER 3.5 1.6 - - - -
59B GLU* 1.3 108.6 - - + +
61B LEU* 1.3 60.2 + - - +
63B THR* 3.7 2.1 + - - -
64B PHE* 3.2 23.2 + - - +
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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
----------------------------------------------------------
7B VAL* 3.9 16.4 - - + -
9B ILE* 3.7 25.6 - - + -
36B LEU* 3.8 7.2 - - + -
38B MET* 3.9 14.5 - - + +
58B SER* 2.8 14.8 + - - +
60B PRO* 1.3 78.1 - - - +
62B LEU* 1.3 64.2 + - - +
64B PHE* 3.4 3.2 + - + +
65B LEU* 3.0 37.9 + - + +
76B ILE* 4.2 13.0 - - + -
85B ASN* 3.8 28.0 - - + +
89B ALA* 3.6 28.9 - - + -
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Residues in contact with LEU 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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55B ASP 4.2 18.4 - - - +
58B SER* 3.1 16.8 + - - +
59B GLU* 3.0 9.2 + - - +
61B LEU* 1.3 75.1 - - + +
63B THR* 1.4 52.5 + - - +
65B LEU 3.5 0.2 + - - -
66B GLU* 2.8 34.0 + - - +
88B ILE* 4.3 5.2 - - + +
89B ALA* 3.6 36.6 - - + +
92B ARG* 3.7 36.1 - - - +
93B TYR* 3.2 29.9 + - + +
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Residues in contact with THR 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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59B GLU* 2.6 38.6 + - - +
60B PRO* 4.0 4.0 - - - -
62B LEU* 1.4 71.3 - - - +
64B PHE* 1.3 67.7 + - - +
66B GLU* 3.1 8.7 + - + +
67B LYS* 2.9 54.4 + - + +
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Residues in contact with PHE 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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5B HIS* 3.5 28.5 - + - -
7B VAL* 3.4 32.3 - - + -
32B LYS* 6.3 0.2 - - - -
34B THR* 3.7 25.8 - - + -
36B LEU* 4.0 15.7 - - + -
60B PRO 3.2 16.5 + - - +
61B LEU 3.6 3.6 - - - +
63B THR* 1.3 77.3 - - - +
65B LEU* 1.3 74.6 + - + +
67B LYS* 2.9 9.5 + - - +
68B LEU* 2.9 34.8 + - + -
74B VAL* 4.3 8.5 - - + -
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Residues in contact with LEU 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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61B LEU* 3.0 31.8 + - + +
62B LEU 3.8 0.2 - - - +
64B PHE* 1.3 84.7 - - + +
66B GLU* 1.3 64.0 + - - +
68B LEU* 3.1 10.6 + - + +
74B VAL* 3.9 28.0 - - + -
76B ILE* 4.1 7.2 - - + -
89B ALA* 3.6 26.0 - - + -
93B TYR* 3.6 39.3 - - + -
96B LYS* 3.0 41.4 + - + +
97B ILE* 4.4 4.3 - - + -
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Residues in contact with GLU 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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62B LEU 2.8 23.0 + - - +
63B THR* 3.2 11.0 - - - +
65B LEU* 1.3 72.1 - - - +
67B LYS* 1.3 67.8 + - + +
68B LEU 4.3 0.5 - - - +
93B TYR* 2.7 35.8 + - - +
96B LYS* 3.7 9.0 + - - -
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Residues in contact with LYS 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 THR* 2.9 42.1 + - + +
64B PHE* 2.9 6.7 + - - +
66B GLU* 1.3 83.7 - - + +
68B LEU* 1.3 65.4 + - - +
69B PRO* 3.2 8.3 - - - +
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Residues in contact with LEU 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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5B HIS* 4.5 5.4 - - + +
64B PHE* 2.9 36.5 + - + +
65B LEU* 3.1 13.3 + - + +
66B GLU 4.3 0.5 - - - +
67B LYS* 1.3 75.7 - - - +
69B PRO* 1.3 73.3 - - + +
70B GLN 3.4 1.2 + - - -
72B GLU* 3.3 55.6 - - + +
73B LYS* 4.2 0.4 - - - +
74B VAL* 3.8 26.0 - - + -
96B LYS* 3.1 34.2 + - + -
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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