Contacts of the strand formed by residues 65 - 72 (chain B) in PDB entry 1UEX
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 LEU 65 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ILE* 3.1 9.9 - - - +
64B VAL* 1.3 96.7 - - + +
66B VAL* 1.3 70.8 + - - +
100B VAL* 4.6 13.2 - - + -
101B ALA 3.2 10.1 - - - +
102B GLU* 3.8 16.4 - - + -
109B ILE* 4.9 2.9 - - + -
111B TRP* 4.0 29.4 - - + -
117B LYS* 4.5 22.4 - - + -
118B SER* 3.3 14.6 + - - +
659C LEU* 4.6 11.9 - - + -
676C VAL* 3.6 33.7 + - + +
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Residues in contact with VAL 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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18B VAL* 4.3 5.2 - - + -
42B MET* 4.4 10.5 - - + -
53B ILE* 5.1 4.3 - - + -
57B ALA* 4.4 7.0 - - + -
63B ILE* 3.6 16.6 - - + -
65B LEU* 1.3 81.4 - - - +
67B TRP* 1.3 62.6 + - - +
68B ILE* 3.9 0.2 - - - +
100B VAL* 3.1 7.6 - - - +
101B ALA* 2.7 56.0 + - + +
103B SER* 5.0 6.3 - - - +
118B SER 2.9 10.3 - - - +
119B PHE* 4.0 6.5 - - - +
120B VAL* 3.7 31.9 - - + -
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Residues in contact with TRP 67 (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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23B LYS 3.0 21.4 + - - -
24B THR 3.8 2.9 - - - -
25B TRP* 3.2 38.0 - + + +
28B ALA* 4.1 6.5 - - + -
41B LEU* 3.6 18.5 - - + +
42B MET* 4.3 3.5 - - - +
66B VAL* 1.3 76.2 - - - +
68B ILE* 1.3 61.6 + - - +
98B CYS* 3.6 22.7 - - + -
99B PHE 3.1 26.5 - - - -
100B VAL* 3.3 21.3 - - + -
111B TRP* 4.0 14.4 - + + -
112B THR 3.2 23.3 - - - -
113B CYS* 3.6 11.0 - - - -
115B ARG 3.2 20.9 - - - -
117B LYS* 3.4 33.1 - - + +
118B SER 3.2 6.9 + - - -
119B PHE* 3.7 11.2 - - + +
120B VAL 4.0 10.7 + - - +
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Residues in contact with ILE 68 (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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83A TRP* 4.0 10.1 - - + -
25B TRP* 2.7 20.2 + - - -
41B LEU* 3.5 6.5 - - - -
42B MET* 3.2 36.1 - - + +
44B VAL* 5.2 1.3 - - + -
66B VAL 3.9 1.6 - - - +
67B TRP* 1.3 76.8 - - - +
69B GLY* 1.3 52.3 + - - +
70B LEU* 2.6 29.7 + - + +
99B PHE* 2.9 40.6 + - + +
100B VAL 4.8 0.2 - - - +
101B ALA* 3.7 20.2 - - + +
108B TRP* 3.9 34.1 - - + -
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Residues in contact with GLY 69 (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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82A GLN 4.7 0.2 - - - +
83A TRP* 2.9 22.7 - - - -
84A THR* 3.1 50.0 + - - +
25B TRP* 4.2 1.6 - - - -
41B LEU* 3.0 9.8 + - - -
42B MET 2.8 19.8 + - - -
68B ILE* 1.3 67.5 - - - +
70B LEU* 1.3 56.5 + - - -
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Residues in contact with LEU 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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78A GLN* 3.5 40.8 - - + +
80A SER* 3.7 22.7 - - - +
82A GLN 4.4 2.2 - - - +
83A TRP* 3.6 21.3 - - + -
89A VAL* 3.8 19.5 - - + -
25B TRP* 3.9 1.7 + - - -
68B ILE* 2.6 18.1 + - + +
69B GLY* 1.3 73.6 - - - +
71B SER* 1.3 64.5 + - - +
98B CYS* 3.8 0.2 - - - -
99B PHE* 3.2 37.5 + - + +
108B TRP* 3.7 30.7 - - + -
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Residues in contact with SER 71 (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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80A SER* 2.8 21.6 + - - -
82A GLN 5.5 0.2 + - - -
84A THR* 5.9 0.2 - - - +
25B TRP* 3.5 29.9 - - - -
69B GLY 4.3 0.4 - - - -
70B LEU* 1.3 78.5 - - - +
72B HIS* 1.3 71.0 + - - +
73B PHE* 5.2 4.2 - - - -
96B PRO* 5.1 4.7 - - - +
97B ILE 2.9 19.7 - - - -
98B CYS* 3.8 10.5 - - - -
99B PHE* 4.7 1.8 - - - -
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Residues in contact with HIS 72 (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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78A GLN* 3.5 27.7 + - - +
79A CYS* 4.0 15.3 + - - +
80A SER* 3.6 15.9 - - - -
81A PRO* 5.7 0.2 - - + -
71B SER* 1.3 85.4 + - - +
73B PHE* 1.3 81.3 + - - +
74B TRP* 4.0 14.3 - + - -
76B ILE* 5.0 8.3 - - + -
77B CYS* 3.8 15.6 - - - -
96B PRO* 3.3 2.0 - - - +
97B ILE* 2.7 64.2 + - + +
99B PHE* 4.6 5.2 - + - -
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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