Contacts of the helix formed by residues 58 - 66 (chain A) 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 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A VAL 3.7 14.6 - - - +
55A ILE 3.1 11.0 + - - +
57A PRO* 1.3 82.1 - - + +
59A ALA* 1.3 64.5 + - - +
60A GLN 3.5 1.8 - - - -
61A GLU* 3.5 22.4 + - - +
62A TYR* 3.1 50.3 + - + +
72A VAL* 4.1 17.3 - - + -
114A ILE* 4.3 6.1 - - + -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE 3.2 10.1 + - - +
56A LEU* 3.4 16.1 + - + +
57A PRO 3.4 0.4 - - - -
58A VAL* 1.3 77.9 - - - +
60A GLN* 1.3 66.8 + - + +
62A TYR* 3.3 2.4 + - - +
63A ASP* 3.1 21.5 + - - +
110A ALA 4.2 18.6 - - - +
111A CYS* 4.2 10.9 - - + -
114A ILE* 4.6 9.1 - - - +
236A ALA* 5.8 0.7 - - - +
286A ARG* 5.8 1.6 - - - +
381A LYS* 4.0 15.4 - - + +
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Residues in contact with GLN 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A LEU 4.9 1.5 + - - +
57A PRO 5.0 2.6 + - - +
58A VAL 3.5 0.2 - - - -
59A ALA* 1.3 79.0 - - + +
61A GLU* 1.3 64.6 - - - +
63A ASP* 3.0 8.1 + - - +
64A GLU* 2.9 42.3 + - - +
375A ARG* 2.6 30.7 + - + +
376A GLU* 3.5 17.3 + - - +
377A PHE 3.8 8.9 + - - -
378A PRO* 4.4 7.8 - - + +
381A LYS* 4.8 10.1 - - + +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A PRO 5.1 2.3 + - - +
58A VAL* 3.5 29.6 + - - +
59A ALA 3.2 0.2 - - - -
60A GLN* 1.3 79.3 - - - +
62A TYR* 1.3 88.2 + - - +
64A GLU* 3.5 4.7 + - - +
65A LYS* 3.2 48.6 + - + +
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Residues in contact with TYR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A VAL* 3.1 48.2 + - + +
59A ALA 4.2 1.6 - - - +
61A GLU* 1.3 99.9 + - - +
63A ASP* 1.3 60.9 + - - +
65A LYS* 3.8 23.3 + - - +
66A GLU* 2.9 27.0 + - - -
67A GLU* 3.3 30.3 + - + +
68A VAL 4.1 4.0 - - - -
69A PRO* 3.4 36.3 - - + +
71A PRO* 4.3 15.5 - - + +
72A VAL* 5.4 1.3 - - + -
114A ILE* 5.2 2.5 - - + -
236A ALA* 4.0 21.0 + - + -
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Residues in contact with ASP 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ALA 3.1 13.2 + - - +
60A GLN* 3.0 8.9 + - - +
62A TYR* 1.3 78.8 - - - +
64A GLU* 1.3 69.9 + - - +
65A LYS 3.5 0.2 + - - -
66A GLU* 3.6 2.8 + - - +
235A ARG* 2.9 56.8 + - - +
236A ALA* 4.9 3.1 - - - +
375A ARG* 4.4 3.3 - - - +
381A LYS* 3.7 24.2 - - + +
384A ARG* 3.0 42.3 + - - -
385A ASP* 4.6 4.0 - - - +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLN* 2.9 33.8 + - - +
61A GLU* 3.5 5.6 + - - +
63A ASP* 1.3 83.4 - - - +
65A LYS* 1.3 59.1 - - + +
66A GLU* 5.2 0.4 - - - +
235A ARG* 4.3 6.3 + - - +
375A ARG* 2.9 58.7 + - - +
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Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLU* 3.2 42.0 + - + +
62A TYR* 4.2 21.9 + - - +
64A GLU* 1.3 79.4 - - + +
66A GLU* 1.3 72.0 + - - +
67A GLU* 3.2 41.8 + - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TYR 2.9 13.3 + - - -
63A ASP 3.6 1.9 + - - +
64A GLU 3.5 1.7 - - - +
65A LYS* 1.3 83.3 - - - +
67A GLU* 1.3 60.1 + - - +
227A LYS* 3.6 19.9 + - - +
228A ILE 4.5 2.2 - - - +
229A HIS* 3.8 12.3 - - + +
230A GLY* 2.9 24.1 + - - -
231A LYS* 3.1 34.4 + - - +
235A ARG* 3.2 43.4 - - + +
237A SER 5.7 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