Contacts of the strand formed by residues 73 - 86 (chain B) in PDB entry 5LTU
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 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B CYS* 4.4 13.0 - - - -
35B LEU* 3.7 23.3 - - + -
67B VAL* 3.4 33.3 + - + +
68B TYR* 3.4 25.9 + - - +
71B ALA* 3.4 19.5 - - + +
72B GLY* 1.3 81.8 - - - +
74B LYS* 1.3 61.5 + - - +
98B LEU* 5.0 3.4 - - + -
100B VAL* 4.3 20.9 - - + -
102B GLU 3.2 10.5 - - - +
103B ILE* 4.5 9.0 - - + -
104B LEU* 5.4 1.1 - - - -
117B ARG* 5.7 0.7 - - - -
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Residues in contact with LYS 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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67B VAL* 5.8 1.1 - - - -
68B TYR* 5.2 8.7 - - + -
73B VAL* 1.3 76.5 - - - +
75B GLY* 1.3 58.8 + - - +
98B LEU* 4.8 2.5 - - - -
100B VAL* 3.8 4.3 - - - +
101B THR* 2.9 26.0 + - - +
102B GLU* 3.0 24.6 + - + +
104B LEU* 5.5 3.6 - - + +
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Residues in contact with GLY 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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64B VAL* 5.8 2.9 - - - +
74B LYS* 1.3 76.8 - - - +
76B LYS* 1.3 61.8 + - - -
77B LEU 3.8 2.6 + - - -
98B LEU* 4.0 17.9 - - - +
99B THR 3.2 13.0 - - - -
101B THR* 3.4 12.3 + - - -
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Residues in contact with LYS 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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75B GLY* 1.3 71.8 - - - -
77B LEU* 1.3 74.0 + - - +
78B GLY* 3.4 2.6 + - - -
98B LEU* 3.5 1.5 - - - -
99B THR* 2.9 40.6 + - + +
101B THR* 4.6 6.4 - - + +
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Residues in contact with LEU 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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23B CYS* 4.0 13.5 - - - -
60B GLY* 3.8 32.5 - - - +
63B ALA* 4.7 2.5 - - + -
64B VAL* 4.0 22.0 - - + -
75B GLY 3.8 4.0 + - - -
76B LYS* 1.3 79.7 - - - +
78B GLY* 1.3 67.4 + - - +
96B TYR* 3.8 35.0 - - + -
97B VAL 4.0 4.0 - - - +
98B LEU* 4.3 6.2 - - + +
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Residues in contact with GLY 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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76B LYS 3.4 3.3 + - - -
77B LEU* 1.3 78.5 - - - +
79B ARG* 1.3 66.3 + - - +
96B TYR* 3.8 13.2 - - - -
97B VAL* 2.8 25.0 + - - -
98B LEU* 5.2 0.2 - - - -
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Residues in contact with ARG 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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31B GLU* 3.2 29.3 + - - -
78B GLY* 1.3 73.1 - - - -
80B LEU* 1.3 71.0 + - - +
81B LEU* 3.4 7.4 + - - +
96B TYR* 3.5 2.7 - - - -
97B VAL* 3.1 47.4 + - + +
143B LEU* 3.3 30.7 + - - +
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Residues in contact with LEU 80 (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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78B GLY 3.9 0.2 + - - -
79B ARG* 1.3 75.8 - - - +
81B LEU* 1.3 63.0 + - - +
82B GLY* 3.6 25.8 - - - +
83B ILE* 4.9 7.0 - - + -
94B TYR* 4.1 19.7 - - + -
95B VAL 3.6 22.7 - - - +
96B TYR* 3.8 35.6 - - + +
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Residues in contact with LEU 81 (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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24B LEU* 4.1 14.6 - - + -
79B ARG* 3.4 12.3 + - - +
80B LEU* 1.3 73.6 - - - +
82B GLY* 1.3 56.8 + - - +
84B PHE* 4.0 22.4 - - + -
95B VAL* 2.8 26.2 + - + +
97B VAL* 5.0 9.2 - - + -
139B TYR 3.3 27.8 - - - +
142B LYS* 4.5 6.3 - - + +
143B LEU* 3.9 36.3 - - + +
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Residues in contact with GLY 82 (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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80B LEU* 3.4 14.1 - - - +
81B LEU* 1.3 82.4 - - - +
83B ILE* 1.3 64.3 + - - -
84B PHE* 3.6 13.2 - - - -
93B THR 3.5 1.4 - - - +
94B TYR* 3.7 0.2 - - - -
95B VAL 3.0 25.0 + - - -
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Residues in contact with ILE 83 (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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80B LEU* 4.9 6.7 - - + -
82B GLY* 1.3 72.8 - - - -
84B PHE* 1.3 63.8 + - - +
85B GLU* 3.8 3.7 + - + +
92B ARG* 4.2 30.7 - - + -
93B THR 3.4 9.6 - - - +
94B TYR* 3.6 43.3 - - + +
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Residues in contact with PHE 84 (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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81B LEU* 4.0 24.9 - - + -
82B GLY* 3.6 21.5 - - - -
83B ILE* 1.3 73.5 - - - +
85B GLU* 1.3 62.6 + - - +
86B ASN* 3.7 2.4 + - - +
91B HIS 3.9 0.3 - - - +
92B ARG* 3.5 2.3 - - - -
93B THR* 2.8 41.8 + - - +
95B VAL* 3.5 30.3 - - + -
135B VAL* 5.3 5.4 - - + -
138B GLU* 4.1 27.4 - - + -
139B TYR* 3.6 36.6 - + + +
142B LYS* 4.2 13.5 - - + -
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Residues in contact with GLU 85 (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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17B PHE* 3.8 25.1 - - + -
83B ILE* 3.8 5.4 + - + +
84B PHE* 1.3 71.3 - - - +
86B ASN* 1.3 60.5 + - - +
87B GLN* 3.2 40.2 + - + +
91B HIS 3.5 4.9 - - - +
92B ARG* 2.9 41.8 + - + +
135B VAL* 5.8 2.4 - - - +
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Residues in contact with ASN 86 (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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17B PHE* 4.3 0.3 - - - -
84B PHE 3.7 2.5 + - - +
85B GLU* 1.3 71.4 - - - +
87B GLN* 1.3 60.1 + - - +
88B ASP* 3.1 22.9 + - - +
89B ARG* 3.2 25.5 + - - +
90B LYS* 2.9 7.4 + - - -
91B HIS* 2.8 53.7 + - + +
135B VAL* 4.1 32.3 - - + +
201B EDO 4.6 13.3 + - - -
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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