Contacts of the helix formed by residues 69 - 82 (chain B) in PDB entry 1W8D
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 THR 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B GLY 3.4 5.4 + - - +
68B GLY* 1.3 82.6 - - - +
70B GLY* 1.3 68.7 + - - +
71B LEU 3.3 0.5 + - - -
72B GLY 3.2 5.9 + - - -
73B LYS* 2.9 19.0 + - - +
95B VAL* 4.4 18.8 - - + -
1330B NAP 3.0 46.6 + - - +
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Residues in contact with GLY 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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69B THR* 1.3 72.2 - - - +
71B LEU* 1.3 63.7 + - - -
73B LYS* 3.4 9.4 + - - +
74B GLY 3.1 23.4 + - - -
274B VAL* 3.7 13.0 - - - +
1330B NAP 3.5 7.4 - - - -
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Residues in contact with LEU 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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70B GLY* 1.3 73.7 - - - -
72B GLY* 1.3 57.6 + - - +
74B GLY* 3.4 1.7 + - - -
75B MSE 3.0 34.8 + - - +
144B ASN* 3.9 3.1 - - - +
195B ILE* 4.4 2.0 - - + -
240B PRO* 4.4 4.9 - - + -
243B ILE* 3.7 32.8 - - + +
244B LYS 6.2 0.2 - - - -
274B VAL* 4.3 14.2 - - + +
277B LEU* 3.6 30.1 - - + +
1330B NAP 2.9 80.7 + - + +
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Residues in contact with GLY 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.0 3.0 - - - +
66B GLY 3.6 6.1 - - - -
67B GLY* 3.6 10.4 - - - -
69B THR 3.2 3.4 + - - -
71B LEU* 1.3 75.5 - - - +
73B LYS* 1.3 58.0 - - - +
75B MSE 3.5 11.5 + - - +
76B THR* 2.8 33.3 + - - -
144B ASN* 3.5 26.5 - - - +
1330B NAP 4.3 0.4 + - - -
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Residues in contact with LYS 73 (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 GLY 3.3 11.0 + - - +
68B GLY 3.9 9.3 + - - +
69B THR* 2.9 16.2 + - - +
70B GLY* 3.5 15.7 - - - +
72B GLY* 1.3 72.6 - - - +
74B GLY* 1.3 53.5 + - - +
76B THR* 3.0 5.5 + - - -
77B THR* 2.7 45.2 + - - +
99B THR* 3.7 32.3 + - + -
102B GLN* 3.6 33.4 + - - +
103B ILE* 4.0 2.8 - - + +
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Residues in contact with GLY 74 (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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70B GLY 3.1 7.7 + - - -
73B LYS* 1.3 79.8 - - - +
75B MSE 1.3 61.9 + - - +
77B THR* 3.3 7.9 + - - -
78B LEU* 3.2 24.3 + - - +
274B VAL* 3.6 24.7 - - - -
275B GLU* 6.3 0.2 - - - -
278B ALA* 3.9 8.7 - - - +
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Residues in contact with MSE 75 (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 ILE* 4.7 2.7 - - + -
71B LEU* 3.0 26.9 + - + +
72B GLY* 3.6 6.7 - - - +
73B LYS 3.2 0.2 - - - -
74B GLY* 1.3 75.7 - - - +
76B THR* 1.3 61.7 + - - +
78B LEU* 4.1 0.9 - - - +
79B LEU* 3.1 33.2 + - + +
142B ILE* 3.9 31.6 - - + -
144B ASN* 3.2 41.1 - - + +
195B ILE* 3.9 17.0 - - + -
274B VAL 5.7 0.2 - - - +
277B LEU* 4.5 8.7 - - + -
278B ALA* 4.1 17.5 - - - +
281B ALA* 3.6 31.9 - - + -
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 3.2 24.0 - - - +
67B GLY 3.9 3.5 + - - +
72B GLY 2.8 23.2 + - - -
73B LYS 3.0 4.9 + - - -
75B MSE 1.3 74.7 - - - +
77B THR* 1.3 65.0 + - - +
79B LEU* 3.4 1.1 + - - -
80B SER* 2.8 26.0 + - - -
86B CYS* 3.8 12.9 - - + -
88B ILE* 3.3 28.9 - - + +
103B ILE* 3.9 12.1 - - + -
111B VAL* 3.8 20.4 - - + -
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Residues in contact with THR 77 (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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73B LYS* 2.7 27.5 + - - +
74B GLY* 3.5 10.8 - - - -
76B THR* 1.3 71.4 - - - +
78B LEU* 1.3 53.6 + - - +
80B SER* 3.1 4.0 + - - -
81B SER* 2.6 39.0 + - - -
102B GLN* 6.2 0.2 - - - +
103B ILE* 3.4 29.0 - - + +
106B GLN* 4.0 32.5 - - - +
107B THR* 3.9 2.5 - - + +
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Residues in contact with LEU 78 (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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49B LYS 5.1 0.4 - - - -
50B ALA* 3.7 37.7 - - + +
51B MSE 5.0 0.2 - - - +
74B GLY 3.2 12.9 + - - +
75B MSE 4.1 2.9 - - - +
77B THR* 1.3 77.7 - - - +
79B LEU* 1.3 66.3 + - + +
81B SER* 3.0 11.5 + - - +
82B LEU* 3.0 35.6 + - + +
275B GLU* 5.6 3.8 - - + +
278B ALA* 3.5 36.6 - - + +
279B ASN* 3.5 18.6 - - - +
282B ALA* 3.7 17.3 - - + -
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Residues in contact with LEU 79 (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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57B PHE* 3.7 41.5 - - + +
62B ALA* 3.7 26.5 - - + -
64B ILE* 4.7 4.7 - - + -
75B MSE 3.1 23.0 + - + +
78B LEU* 1.3 76.9 - - + +
80B SER* 1.3 60.9 + - - +
82B LEU* 3.3 5.7 + - + +
83B GLY 3.2 5.0 + - - -
84B ALA* 3.0 30.2 + - + +
86B CYS* 3.8 11.7 - - - -
140B ILE* 4.3 9.0 - - + -
142B ILE* 4.2 23.3 - - + -
282B ALA* 4.3 16.2 - - + -
285B CYS* 5.4 1.8 - - + -
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Residues in contact with SER 80 (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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76B THR 2.8 19.0 + - - -
77B THR 3.3 3.1 - - - -
79B LEU* 1.3 72.5 - - - +
81B SER* 1.3 55.2 + - - +
82B LEU 3.0 4.3 - - - -
83B GLY* 2.8 10.9 + - - -
84B ALA 3.9 11.0 + - - -
86B CYS* 3.8 4.6 - - - -
103B ILE* 3.8 12.3 - - - -
107B THR* 2.9 22.9 + - - -
109B ASN* 2.8 37.9 + - - +
110B LYS 4.9 0.2 + - - -
111B VAL* 3.6 20.0 - - - +
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Residues in contact with SER 81 (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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50B ALA* 4.8 3.8 - - - +
54B PRO* 5.9 0.3 - - - +
55B ASN* 5.2 3.8 + - - +
77B THR* 2.6 21.0 + - - -
78B LEU* 3.0 24.5 + - - +
80B SER* 1.3 70.8 - - - +
82B LEU* 1.3 66.2 + - - +
83B GLY 3.4 0.4 + - - -
106B GLN* 5.7 2.7 - - - -
107B THR* 3.4 21.0 - - - +
109B ASN* 4.9 1.6 + - - -
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Residues in contact with LEU 82 (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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50B ALA* 4.1 22.9 - - + -
51B MSE 5.8 0.2 - - - +
52B LEU* 3.9 32.8 - - + +
53B PRO 4.4 7.4 - - - +
54B PRO* 4.7 7.0 - - + -
55B ASN* 3.1 19.2 - - - +
56B SER* 4.1 2.5 - - - +
57B PHE* 3.1 54.3 + - + +
78B LEU* 3.0 35.7 + - + +
79B LEU 3.6 5.8 - - - +
80B SER 3.0 0.6 - - - -
81B SER* 1.3 84.9 - - - +
83B GLY* 1.3 58.0 + - - +
84B ALA 3.7 0.2 - - - -
282B ALA* 4.8 4.0 - - + -
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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