Contacts of the helix formed by residues 69 - 79 (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 PRO 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A TYR* 3.4 42.4 - - + -
67A GLU 3.4 8.3 - - - +
68A VAL* 1.3 85.1 - - + +
70A TRP* 1.3 65.8 + - - +
71A PRO* 3.2 4.3 - - + -
72A VAL* 2.8 32.3 + - + +
73A ILE* 3.3 7.1 + - + +
114A ILE* 4.1 23.3 - - + -
117A ILE* 4.1 8.3 - - + -
236A ALA* 3.5 15.0 - - + +
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Residues in contact with TRP 70 (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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68A VAL* 3.1 19.9 + - + +
69A PRO* 1.3 70.9 - - - +
71A PRO* 1.3 71.1 - - + +
73A ILE* 2.8 52.4 + - + +
74A GLU* 3.0 45.7 + - + +
148A PRO* 3.6 30.2 + - - +
149A ALA* 4.9 3.1 - - - -
150A LEU* 4.2 9.9 - - + -
192A GLU* 3.7 42.6 - - + -
218A ARG* 5.1 6.1 - - - -
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Residues in contact with PRO 71 (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* 4.3 14.1 - - + +
68A VAL 5.1 0.2 - - - +
69A PRO* 3.2 8.5 - - + -
70A TRP* 1.3 94.5 - - + +
72A VAL* 1.3 62.0 + - + +
74A GLU* 3.3 20.4 + - - +
75A LYS* 3.2 37.6 + - - +
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Residues in contact with VAL 72 (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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50A PHE* 3.8 19.6 - - + -
54A VAL* 4.0 21.1 - - + +
55A ILE* 4.2 4.9 - - + -
58A VAL* 4.1 21.8 - - + -
62A TYR* 5.4 0.9 - - + -
69A PRO* 2.8 29.4 + - + +
71A PRO* 1.3 77.0 - - + +
73A ILE* 1.3 62.5 + - + +
75A LYS* 3.3 2.8 + - + +
76A LEU* 2.9 30.9 + - + +
114A ILE* 4.0 26.7 - - + -
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Residues in contact with ILE 73 (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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68A VAL* 3.8 18.6 - - + -
69A PRO 3.8 8.5 - - - +
70A TRP* 2.8 49.5 + - + +
72A VAL* 1.3 80.5 - - + +
74A GLU* 1.3 61.3 + - - +
76A LEU* 3.4 11.1 + - + +
77A HIS* 3.0 21.3 + - - +
82A LEU* 3.9 22.1 - - + +
117A ILE* 4.0 26.2 - - + -
148A PRO* 4.1 10.7 - - + +
150A LEU* 4.0 13.5 - - + -
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Residues in contact with GLU 74 (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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70A TRP* 3.0 42.8 + - + +
71A PRO* 3.3 21.8 - - - +
73A ILE* 1.3 75.0 - - - +
75A LYS* 1.3 55.7 + - + +
77A HIS* 3.1 4.0 + - - +
78A GLU* 2.5 52.0 + - + +
148A PRO* 3.7 22.2 - - + -
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Residues in contact with LYS 75 (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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50A PHE* 3.5 19.9 - - + -
54A VAL* 3.7 29.6 - - + -
71A PRO* 3.2 24.3 + - - +
72A VAL* 3.7 3.4 - - + +
74A GLU* 1.3 75.1 - - - +
76A LEU* 1.3 56.6 + - - +
78A GLU* 3.4 25.2 + - - +
79A VAL* 2.7 36.7 + - - +
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Residues in contact with LEU 76 (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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50A PHE* 3.4 32.0 - - + -
55A ILE* 5.8 2.9 - - + -
72A VAL* 2.9 18.2 + - + +
73A ILE* 3.6 14.1 - - + +
74A GLU 3.2 0.2 - - - -
75A LYS* 1.3 73.4 - - - +
77A HIS* 1.3 67.1 + - - +
79A VAL* 3.0 20.2 - - + +
80A GLY 3.0 4.2 + - - -
81A LEU* 3.1 34.0 + - + +
82A LEU* 3.9 17.3 - - + -
107A LEU* 4.4 15.9 - - + -
114A ILE* 5.9 2.0 - - + -
118A PRO* 3.7 38.4 - - + -
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Residues in contact with HIS 77 (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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73A ILE 3.0 10.9 + - - +
74A GLU 3.2 7.2 - - - +
76A LEU* 1.3 78.7 - - - +
78A GLU* 1.3 71.4 + - + +
80A GLY* 2.5 29.2 + - - -
82A LEU* 3.5 23.1 + - + +
144A LEU 5.4 0.8 + - - -
145A THR* 3.2 28.7 + - - -
146A GLU 3.7 6.0 + - - -
147A LYS* 3.5 25.8 + - - -
148A PRO* 3.7 29.6 - - + -
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Residues in contact with GLU 78 (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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74A GLU* 2.5 42.5 + - + +
75A LYS* 3.4 26.3 + - - +
77A HIS* 1.3 82.7 - - + +
79A VAL* 1.3 59.6 + - - +
80A GLY 3.5 0.3 + - - -
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Residues in contact with VAL 79 (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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46A LEU* 3.1 40.1 - - + +
50A PHE* 4.0 20.4 - - + -
75A LYS 2.7 17.5 + - - +
76A LEU* 3.0 22.4 - - + +
77A HIS 2.9 0.2 + - - -
78A GLU* 1.3 73.3 - - + +
80A GLY* 1.3 58.0 + - - +
81A LEU* 3.7 21.3 - - + +
93A MET* 5.8 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