Contacts of the helix formed by residues 69 - 79 (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 PRO 69 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B TYR* 3.4 35.9 - - + -
67B GLU 3.5 8.7 - - - +
68B VAL* 1.3 84.3 - - + +
70B TRP* 1.3 64.7 + - - +
71B PRO* 3.2 4.0 - - + -
72B VAL* 2.9 39.0 + - + +
73B ILE* 3.3 5.8 + - + +
114B ILE* 4.0 20.6 - - + -
117B ILE* 3.9 12.1 - - + -
236B ALA* 3.7 13.7 - - + +
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Residues in contact with TRP 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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68B VAL* 2.9 21.9 + - + +
69B PRO* 1.3 71.7 - - - +
71B PRO* 1.3 64.6 - - + +
73B ILE* 3.0 31.9 + - + +
74B GLU* 2.9 62.6 + - - +
148B PRO* 3.2 30.6 + - - +
149B ALA* 5.3 0.4 - - - -
150B LEU* 4.1 14.8 - - + -
192B GLU* 3.6 44.2 - - + -
218B ARG* 6.2 0.4 - - - -
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Residues in contact with PRO 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B TYR* 4.1 14.6 - - - +
68B VAL 4.8 0.7 - - - +
69B PRO* 3.2 8.3 - - + -
70B TRP* 1.3 95.9 - - + +
72B VAL* 1.3 57.5 + - + +
74B GLU* 3.4 18.1 + - - +
75B LYS* 2.9 44.4 + - - +
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.6 11.2 - - + -
54B VAL* 4.1 9.9 - - + -
55B ILE* 3.9 27.6 - - + -
58B VAL* 4.1 23.1 - - + -
62B TYR* 5.0 1.1 - - + -
69B PRO* 2.9 33.9 + - + +
71B PRO* 1.3 79.2 - - + +
73B ILE* 1.3 55.2 + - + +
75B LYS* 3.0 8.4 + - - +
76B LEU* 2.7 38.6 + - + +
114B ILE* 4.2 12.8 - - + -
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Residues in contact with ILE 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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68B VAL* 3.7 17.9 - - + -
69B PRO* 3.6 9.2 - - + +
70B TRP* 3.0 44.8 + - + +
72B VAL* 1.3 75.8 - - + +
74B GLU* 1.3 64.4 + - - +
76B LEU* 3.0 16.7 + - + +
77B HIS* 2.9 22.3 + - - +
82B LEU* 3.8 16.0 - - + +
117B ILE* 4.0 27.1 - - + -
148B PRO* 4.4 9.0 - - + -
150B LEU* 3.6 25.1 - - + -
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Residues in contact with GLU 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 TRP* 2.9 43.4 + - + +
71B PRO* 3.4 22.5 - - - +
73B ILE* 1.3 77.0 - - - +
75B LYS* 1.3 60.6 + - - +
77B HIS* 3.3 3.3 + - - +
78B GLU* 2.9 39.2 + - - +
148B PRO* 3.8 21.3 - - + -
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Residues in contact with LYS 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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50B PHE* 3.4 23.7 - - + -
54B VAL* 4.1 28.0 - - + -
71B PRO* 2.9 38.7 + - - +
72B VAL* 3.3 8.1 - - - +
74B GLU* 1.3 76.0 - - - +
76B LEU* 1.3 63.1 + - - +
78B GLU* 3.4 15.9 + - - +
79B VAL* 3.0 18.7 + - - +
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Residues in contact with LEU 76 (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* 3.4 28.0 - - + -
55B ILE* 5.8 1.6 - - + -
72B VAL* 2.7 24.8 + - + +
73B ILE* 3.1 20.0 - - + +
75B LYS* 1.3 70.0 - - - +
77B HIS* 1.3 66.8 + - - +
79B VAL* 3.1 8.2 - - - +
81B LEU* 3.0 55.2 + - + +
82B LEU* 4.1 14.1 - - + -
107B LEU* 4.4 17.0 - - + -
114B ILE* 5.7 3.6 - - + +
118B PRO* 4.2 30.5 - - + -
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Residues in contact with HIS 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 ILE 2.9 11.2 + - - +
74B GLU 3.5 6.5 - - - +
76B LEU* 1.3 75.8 - - - +
78B GLU* 1.3 66.2 + - + +
80B GLY* 2.7 27.8 + - - -
82B LEU* 3.6 24.8 + - + +
144B LEU 5.0 1.4 + - - -
145B THR* 3.1 28.3 + - - -
146B GLU 3.4 13.1 + - - -
147B LYS* 3.4 26.9 + - - -
148B PRO* 3.9 23.8 - - + -
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Residues in contact with GLU 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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74B GLU* 2.9 29.6 + - - +
75B LYS* 3.7 17.3 + - - +
77B HIS* 1.3 87.8 - - + +
79B VAL* 1.3 57.7 - - - +
80B GLY* 3.1 4.0 + - - -
148B PRO* 6.0 0.4 - - + -
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Residues in contact with VAL 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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46B LEU* 3.2 43.6 - - + +
50B PHE* 3.7 23.6 - - + -
75B LYS 3.0 16.0 + - - +
76B LEU* 3.1 16.4 - - - +
78B GLU* 1.3 76.2 - - - +
80B GLY* 1.3 57.4 + - - +
81B LEU* 3.6 18.1 + - + +
93B MET* 5.9 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