Contacts of the helix formed by residues 54 - 66 (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 VAL 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B PHE* 2.7 58.5 + - + +
53B GLU* 1.3 84.8 - - + +
55B ILE* 1.3 66.3 + - - +
57B PRO* 3.5 6.5 - - - +
58B VAL* 3.4 17.0 + - - +
72B VAL* 4.1 17.7 - - + -
75B LYS* 4.1 32.3 - - + -
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Residues in contact with ILE 55 (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 PHE* 3.3 25.1 + - + -
51B ALA* 3.1 16.4 + - - +
54B VAL* 1.3 74.9 - - - +
56B LEU* 1.3 69.8 + - - +
57B PRO 3.0 1.7 - - - -
58B VAL* 3.0 17.7 + - - +
59B ALA* 3.1 10.4 + - - +
72B VAL* 3.9 20.9 - - + -
76B LEU* 5.8 2.0 - - + -
107B LEU* 4.3 28.3 - - + +
110B ALA* 3.4 16.6 - - + -
111B CYS* 3.7 24.0 - - + +
114B ILE* 3.9 25.1 - - + -
115B TYR 5.6 0.9 - - - +
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Residues in contact with LEU 56 (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 2.6 19.5 + - - +
52B LYS* 3.6 23.6 - - + +
55B ILE* 1.3 73.4 - - - +
57B PRO* 1.3 67.7 - - + +
59B ALA* 3.7 11.5 + - - +
60B GLN* 5.1 5.7 + - - -
109B TYR* 4.5 13.0 - - + -
110B ALA* 3.6 18.8 - - + +
286B ARG* 3.7 40.1 + - - +
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Residues in contact with PRO 57 (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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52B LYS 3.3 13.7 - - - +
53B GLU* 3.5 17.0 - - - +
54B VAL 3.5 13.7 - - - +
55B ILE 3.3 4.3 - - - -
56B LEU* 1.3 99.5 - - + +
58B VAL* 1.3 64.2 + - + +
60B GLN* 4.9 6.1 + - - +
61B GLU* 5.3 1.9 + - - +
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Residues in contact with VAL 58 (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 VAL* 3.4 20.2 - - + +
55B ILE* 3.5 5.8 - - - +
57B PRO* 1.3 80.0 - - + +
59B ALA* 1.3 67.0 + - - +
60B GLN 3.3 2.9 - - - -
61B GLU* 3.0 34.8 + - - +
62B TYR* 3.1 37.5 + - + -
72B VAL* 4.1 18.2 - - + -
114B ILE* 4.5 4.0 - - + -
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Residues in contact with ALA 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 ILE 3.1 13.0 + - - +
56B LEU 3.9 9.4 - - - +
57B PRO 3.5 1.6 - - - -
58B VAL* 1.3 76.1 - - - +
60B GLN* 1.3 65.2 + - + +
62B TYR* 3.5 1.7 + - - +
63B ASP* 3.1 23.0 + - - +
110B ALA 4.0 19.7 - - - +
111B CYS* 4.0 13.8 - - + -
114B ILE* 4.5 11.0 - - - -
236B ALA* 5.7 0.9 - - - +
286B ARG* 5.9 1.6 - - - +
381B LYS* 3.9 13.6 - - + +
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Residues in contact with GLN 60 (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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56B LEU 5.1 5.5 + - - +
57B PRO 4.9 5.6 + - - +
58B VAL 3.3 0.4 - - - -
59B ALA* 1.3 77.9 - - + +
61B GLU* 1.3 64.6 + - - +
63B ASP* 3.5 5.4 + - - +
64B GLU* 3.2 42.5 + - - +
375B ARG 3.3 22.7 - - - +
376B GLU* 4.7 7.6 + - - +
377B PHE 5.8 3.6 - - - -
378B PRO* 5.6 13.1 - - + +
381B LYS* 5.0 7.6 - - + -
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Residues in contact with GLU 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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57B PRO 5.3 1.1 + - - +
58B VAL* 3.0 32.8 + - - +
60B GLN* 1.3 82.1 - - - +
62B TYR* 1.3 74.0 + - - +
64B GLU* 3.2 5.7 + - - +
65B LYS* 2.6 66.2 + - + +
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Residues in contact with TYR 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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58B VAL* 3.1 43.3 + - + +
59B ALA 4.3 2.0 - - - +
61B GLU* 1.3 93.8 + - + +
63B ASP* 1.3 58.1 + - - +
64B GLU 3.1 2.0 - - - -
65B LYS* 4.3 11.5 + - - +
66B GLU* 2.6 33.9 + - - +
67B GLU* 3.1 38.3 + - + +
68B VAL 4.0 4.5 - - - -
69B PRO* 3.4 39.4 - - + +
71B PRO* 4.1 17.0 - - - +
72B VAL* 5.0 1.1 - - + -
114B ILE* 4.9 2.5 - - + -
236B ALA* 3.8 18.7 + - + -
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Residues in contact with ASP 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 ALA 3.1 18.8 + - - +
60B GLN* 3.8 4.8 - - - +
62B TYR* 1.3 76.7 - - - +
64B GLU* 1.3 68.7 + - - +
66B GLU* 3.8 1.4 + - - +
235B ARG* 2.8 72.9 + - - +
236B ALA* 4.6 4.4 - - - +
375B ARG* 4.1 2.9 - - - -
381B LYS* 3.5 25.9 - - + +
384B ARG* 3.1 33.8 + - - -
385B ASP* 4.6 2.1 - - - +
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Residues in contact with GLU 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 GLN* 3.2 35.6 + - - +
61B GLU* 3.6 4.9 - - - +
62B TYR 3.1 0.4 - - - -
63B ASP* 1.3 88.1 - - - +
65B LYS* 1.3 61.7 + - + +
66B GLU* 4.8 1.7 - - - +
235B ARG* 4.5 5.2 + - - +
375B ARG* 2.8 43.2 + - - +
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Residues in contact with LYS 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 GLU* 2.6 54.9 + - + +
62B TYR* 4.3 15.6 + - - +
64B GLU* 1.3 78.4 - - + +
66B GLU* 1.3 73.1 + - - +
67B GLU* 3.4 41.7 + - + +
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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 TYR 2.6 19.4 + - - -
63B ASP 3.8 2.0 + - - +
64B GLU 3.3 3.2 - - - +
65B LYS* 1.3 78.1 - - - +
67B GLU* 1.3 58.3 + - - +
227B LYS* 3.7 17.8 + - - +
228B ILE 4.5 1.9 - - - +
229B HIS* 3.8 15.0 - - + +
230B GLY* 3.1 32.7 + - - -
231B LYS* 3.2 19.0 + - - +
235B ARG* 3.5 41.7 - - + +
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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