Contacts of the helix formed by residues 96 - 111 (chain B) in PDB entry 1UKW
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 LYS 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94B GLY 3.6 14.8 - - - +
95B LEU* 1.3 75.7 - - - +
97B MET* 1.3 61.4 + - - +
98B LEU* 3.2 2.9 - - + +
99B ASP* 2.8 35.4 + - - +
100B GLU* 2.9 17.6 + - - +
337B ASP* 3.6 20.6 - - + +
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Residues in contact with MET 97 (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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96B LYS* 1.3 71.4 - - - +
98B LEU* 1.3 62.1 + - - +
100B GLU* 3.2 35.7 + - - +
101B VAL* 3.0 28.3 + - - +
271B LYS* 3.3 55.0 - - + +
272B THR* 4.6 1.3 - - + +
274B ILE* 3.8 12.3 - - + -
275B PRO* 3.9 15.0 - - + -
333B ALA* 3.5 27.6 - - + +
336B ALA* 4.4 5.4 - - + -
337B ASP* 2.9 22.7 + - - +
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Residues in contact with LEU 98 (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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32A ILE* 3.1 51.4 - - + -
36B LEU* 5.9 2.0 - - + -
40B GLN* 2.9 35.4 - - - +
96B LYS* 3.2 1.8 - - + -
97B MET* 1.3 75.0 - - - +
99B ASP* 1.3 64.1 + - - +
101B VAL* 3.3 4.6 + - - +
102B ILE* 3.0 33.0 + - + +
330B TYR* 4.0 32.8 - - + +
333B ALA* 3.8 10.3 - - + +
334B TRP* 5.5 1.8 - - - +
337B ASP* 2.9 17.8 + - - +
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Residues in contact with ASP 99 (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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40B GLN* 3.6 29.0 + - - +
43B LEU* 3.8 13.6 - - + +
95B LEU* 3.5 29.3 - - + +
96B LYS* 2.8 37.7 + - - +
98B LEU* 1.3 75.1 - - - +
100B GLU* 1.3 58.0 + - - +
102B ILE* 3.1 9.5 + - - +
103B VAL* 2.9 33.1 + - - +
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Residues in contact with GLU 100 (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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85B ILE* 3.6 36.3 - - + +
95B LEU* 4.9 5.2 - - + +
96B LYS 2.9 19.8 + - - +
97B MET* 3.2 39.2 + - - +
99B ASP* 1.3 74.4 - - - +
101B VAL* 1.3 54.5 + - - +
103B VAL* 3.8 4.7 - - - +
104B GLY* 2.6 36.2 + - - -
115B TYR* 4.4 4.6 + - - +
122B ASP* 4.3 15.3 - - - +
275B PRO* 3.5 22.3 - - + +
278B ALA* 5.0 0.2 - - - +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 3.0 15.8 + - + +
98B LEU 3.5 7.9 - - - +
100B GLU* 1.3 75.4 - - + +
102B ILE* 1.3 64.4 + - - +
105B GLU* 3.1 28.1 + - - +
274B ILE* 3.6 32.3 - - + +
275B PRO* 5.3 1.1 - - + -
278B ALA* 3.9 15.5 - - + +
326B ARG* 5.7 0.9 - - + -
329B THR* 3.8 18.6 - - + -
330B TYR* 3.2 34.3 - - + -
333B ALA* 3.7 10.5 - - + -
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Residues in contact with ILE 102 (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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36B LEU* 3.6 27.4 - - + -
40B GLN* 3.6 28.7 - - + +
43B LEU* 4.8 5.8 - - + -
44B GLN* 3.6 42.4 + - + +
98B LEU* 3.0 26.0 + - + +
99B ASP* 3.1 11.4 + - - +
101B VAL* 1.3 78.7 - - - +
103B VAL* 1.3 63.8 + - - +
105B GLU* 4.2 2.9 - - - +
106B GLU* 3.4 21.8 + - - +
330B TYR* 4.1 23.6 - - + +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.4 44.6 - - + -
47B ALA* 4.0 17.7 - - + -
81B LEU* 4.3 17.0 - - + +
95B LEU* 4.4 7.2 - - + -
99B ASP 2.9 11.4 + - - +
100B GLU* 3.8 4.7 - - - +
102B ILE* 1.3 73.9 - - - +
104B GLY* 1.3 67.9 + - - +
106B GLU* 2.9 6.9 + - - +
107B LEU* 2.9 44.4 + - + +
115B TYR* 5.6 1.1 - - + -
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Residues in contact with GLY 104 (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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100B GLU 2.6 22.0 + - - -
101B VAL 3.9 0.4 - - - -
103B VAL* 1.3 74.1 - - - +
105B GLU* 1.3 61.3 + - - +
107B LEU* 3.2 0.9 + - - +
108B ALA* 2.9 29.7 + - - +
115B TYR* 3.5 34.6 - - - -
278B ALA* 4.7 5.6 - - - -
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Residues in contact with GLU 105 (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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101B VAL* 3.1 19.4 + - + +
102B ILE* 4.2 3.4 - - - +
104B GLY* 1.3 73.8 - - - +
106B GLU* 1.3 64.6 + - - +
109B TYR* 3.1 24.4 + - - +
278B ALA* 3.6 16.9 + - + +
281B VAL* 3.4 16.8 - - + +
282B GLY* 3.5 23.4 - - - +
285B ARG* 2.8 30.3 + - - +
326B ARG* 2.9 45.7 + - - +
330B TYR* 4.5 5.0 + - - -
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Residues in contact with GLU 106 (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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44B GLN* 3.7 32.6 + - + +
47B ALA* 3.7 16.4 - - + -
48B ARG* 3.1 48.2 + - - +
51B ALA* 3.3 17.4 - - - +
102B ILE 3.4 15.1 + - - +
103B VAL 2.9 8.1 + - - +
105B GLU* 1.3 78.5 - - - +
107B LEU* 1.3 67.8 + - - +
109B TYR* 3.3 14.9 - - - +
285B ARG* 3.0 33.7 + - - -
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Residues in contact with LEU 107 (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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47B ALA* 4.0 23.1 - - + +
50B PHE* 4.5 11.0 - - + -
51B ALA* 4.2 4.0 - - + -
55B ILE* 4.3 23.9 - - + +
76B LEU* 4.4 15.0 - - + -
81B LEU* 4.9 4.9 - - + +
103B VAL* 2.9 38.7 + - + +
104B GLY 3.9 0.7 - - - +
106B GLU* 1.3 75.7 - - - +
108B ALA* 1.3 58.1 + - - +
110B ALA* 2.8 25.8 + - - +
111B CYS 3.3 8.0 + - - +
115B TYR* 3.6 33.7 - - + -
118B PRO* 4.3 15.5 - - + -
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Residues in contact with ALA 108 (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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104B GLY 2.9 18.5 + - - +
105B GLU 4.4 1.3 - - - +
107B LEU* 1.3 72.0 - - - +
109B TYR* 1.3 62.4 + - - +
111B CYS* 3.2 20.6 + - - -
112B MET* 3.4 17.1 + - - -
115B TYR* 3.5 14.9 - - + +
279B GLY* 3.5 34.8 - - - +
282B GLY 4.4 2.0 - - - -
283B VAL* 4.0 11.3 - - + +
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Residues in contact with TYR 109 (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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51B ALA* 5.5 2.5 - - + -
52B LYS* 6.6 0.4 - - + -
56B LEU* 4.5 12.1 - - + -
105B GLU 3.1 20.2 + - - +
106B GLU* 3.3 9.6 - - - +
107B LEU 2.9 1.0 + - - -
108B ALA* 1.3 76.7 - - - +
110B ALA* 1.3 62.7 + - + +
282B GLY 3.4 24.0 + - - +
285B ARG* 3.4 38.6 - - - +
286B ARG* 2.9 61.3 + - - +
289B ASP* 2.4 38.6 + - - +
290B GLU* 5.5 0.3 + - - -
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Residues in contact with ALA 110 (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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51B ALA* 3.6 28.0 - - + +
55B ILE* 3.4 24.5 - - + -
56B LEU* 3.6 16.4 - - + +
59B ALA* 4.0 12.1 - - - +
106B GLU 3.8 0.2 + - - -
107B LEU 2.8 7.4 + - - +
109B TYR* 1.3 81.1 - - + +
111B CYS* 1.3 63.8 - - - +
286B ARG* 3.0 20.1 + - - +
381B LYS* 4.8 1.6 + - - -
382B LEU* 5.9 0.3 - - - +
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Residues in contact with CYS 111 (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 ILE* 3.7 18.2 - - + +
59B ALA* 4.0 9.0 - - + -
107B LEU 3.3 3.7 + - - +
108B ALA* 3.2 6.9 + - - -
110B ALA* 1.3 83.6 - - - +
112B MET* 1.3 60.4 + - - +
113B GLY* 3.5 6.7 - - - -
114B ILE* 3.3 33.9 - - + +
115B TYR* 3.0 26.9 + - - +
236B ALA* 5.0 4.0 - - - -
381B LYS* 3.1 31.4 - - - +
382B LEU* 6.5 0.4 - - - -
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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